General information for g13797.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Thrombospondin-3.
Parent gene
- The parent gene g13797 is located on chr_1: 32425556..32437702 (- strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_1 | g13797 | g13797.t1 | TTS | g13797.t1 | 32423221 | 32423221 |
| chr_1 | g13797 | g13797.t1 | isoform | g13797.t1 | 32423393 | 32437702 |
| chr_1 | g13797 | g13797.t1 | exon | g13797.t1.exon1 | 32423393 | 32423469 |
| chr_1 | g13797 | g13797.t1 | cds | g13797.t1.CDS1 | 32423393 | 32423469 |
| chr_1 | g13797 | g13797.t1 | exon | g13797.t1.exon2 | 32423528 | 32424635 |
| chr_1 | g13797 | g13797.t1 | cds | g13797.t1.CDS2 | 32423528 | 32424635 |
| chr_1 | g13797 | g13797.t1 | exon | g13797.t1.exon3 | 32424696 | 32424848 |
| chr_1 | g13797 | g13797.t1 | cds | g13797.t1.CDS3 | 32424696 | 32424848 |
| chr_1 | g13797 | g13797.t1 | exon | g13797.t1.exon4 | 32424907 | 32424986 |
| chr_1 | g13797 | g13797.t1 | cds | g13797.t1.CDS4 | 32424907 | 32424986 |
| chr_1 | g13797 | g13797.t1 | exon | g13797.t1.exon5 | 32425049 | 32425188 |
| chr_1 | g13797 | g13797.t1 | cds | g13797.t1.CDS5 | 32425049 | 32425188 |
| chr_1 | g13797 | g13797.t1 | exon | g13797.t1.exon6 | 32425253 | 32425556 |
| chr_1 | g13797 | g13797.t1 | cds | g13797.t1.CDS6 | 32425253 | 32425556 |
| chr_1 | g13797 | g13797.t1 | exon | g13797.t1.exon7 | 32426242 | 32426302 |
| chr_1 | g13797 | g13797.t1 | cds | g13797.t1.CDS7 | 32426242 | 32426302 |
| chr_1 | g13797 | g13797.t1 | exon | g13797.t1.exon8 | 32426357 | 32426457 |
| chr_1 | g13797 | g13797.t1 | cds | g13797.t1.CDS8 | 32426357 | 32426457 |
| chr_1 | g13797 | g13797.t1 | exon | g13797.t1.exon9 | 32429523 | 32429591 |
| chr_1 | g13797 | g13797.t1 | cds | g13797.t1.CDS9 | 32429523 | 32429591 |
| chr_1 | g13797 | g13797.t1 | exon | g13797.t1.exon10 | 32429662 | 32429717 |
| chr_1 | g13797 | g13797.t1 | cds | g13797.t1.CDS10 | 32429662 | 32429717 |
| chr_1 | g13797 | g13797.t1 | exon | g13797.t1.exon11 | 32433972 | 32434089 |
| chr_1 | g13797 | g13797.t1 | cds | g13797.t1.CDS11 | 32433972 | 32434089 |
| chr_1 | g13797 | g13797.t1 | exon | g13797.t1.exon12 | 32434209 | 32434391 |
| chr_1 | g13797 | g13797.t1 | cds | g13797.t1.CDS12 | 32434209 | 32434391 |
| chr_1 | g13797 | g13797.t1 | exon | g13797.t1.exon13 | 32434461 | 32434589 |
| chr_1 | g13797 | g13797.t1 | cds | g13797.t1.CDS13 | 32434461 | 32434589 |
| chr_1 | g13797 | g13797.t1 | exon | g13797.t1.exon14 | 32434646 | 32435085 |
| chr_1 | g13797 | g13797.t1 | cds | g13797.t1.CDS14 | 32434646 | 32435085 |
| chr_1 | g13797 | g13797.t1 | exon | g13797.t1.exon15 | 32435149 | 32435212 |
| chr_1 | g13797 | g13797.t1 | cds | g13797.t1.CDS15 | 32435149 | 32435212 |
| chr_1 | g13797 | g13797.t1 | exon | g13797.t1.exon16 | 32437627 | 32437702 |
| chr_1 | g13797 | g13797.t1 | cds | g13797.t1.CDS16 | 32437627 | 32437702 |
| chr_1 | g13797 | g13797.t1 | TSS | g13797.t1 | NA | NA |
Sequences
>g13797.t1 Gene=g13797 Length=3159
ATGAGAAACATTTTTGTGCTTCTCGTACTTGTCATCATCGTTATTAGTGATGGATTCTCG
ATGTCACTTGATCCAGTGGCTTCAACTGAACTAGAGCAATTTATTCGAGATGATTTTACA
GTATCCCTAAGGCATATAAGACCACGCAGGAAGTTTCGAATTACTCTCGAGGCACTTTTC
ATGATTGATTTTCCAACTGTTAAGAATAAGTTTACATTTTATCTTGATCGAAAATCAAAA
CGTATTGTGATTGATATTAATTCAAATTCAAAAATTTTCTCAAAACATTTGAACTTGCCA
TCACTCAATGAGACAACCACAATTAGATCAATCGCCTTTGCTTTCTCTGAGAACTTTATA
ACGCTTTACGTCGATTGCAATGATATTCTTAAAGAAGAAATGGAGTTCAATCTCTCACGT
TTATTTATGGACATGGACGAGCCATTAGTAAAGCTCTTTAGGGAGAGAAAATATCCACTT
TACTTAGATACATCTCCTGAAAGTGCTCTCGCTAGAGCAAGTTGTCAGAAAAGCTCAAAA
CGCAAATCGAATCATAAGATAGTAAAGAATTACAGTGAAGGCTCAGAGAAAAACAGAAAA
CGTGAAGTGAATAATTATTATCGATCTCGTGATGATATTCGCAATAGAGACGATTTTAAT
GCTCCACCGGGACGTGGTGACATTCCAATTATTCATGGTGATTGTGATGAAAATCTTTTA
AGAGGCATCAACGATTTGATTGCTTTAATAAAAAAACTACAACAAGATATTGCAAATCAA
CATGCTGAAATCAAGCGCCTCCAATCACTCATTGAAAATTGTGCTGGTTGTCAAGAAGCT
CCACCATTAATTCGATATGATACTTGCCAGTATGCCAATCCATGTTTCCCCGGTGTGACT
TGTCACGACACATCATCAGGTATGCGCTGTGGACGATGCCCAAGTGGATATGTTGGCGAT
GGAAGAACTTGCAAGCCCGGACAAACTTGCGATGATCGACCCTGCTTTCCTGGAGTCACA
TGCTCAGATACTGTAGGCGGCGCAGTCTGTGGTCCTTGTCCGTCTGGATATGAAGGAGAT
GGAAAAACGTGTCAAGAAAGACGTAGTGTGTGCGACGATCGTCCATGTGCTGCAGGTGTT
CAATGTCAAGAAACAAGAGAATATCCGTATTATCGCTGCGGTGCCTGTCCAGCGGGCTTC
ACGGGCAATGGAACAACATGTCATGACATTGATGAGTGTGATCTAGTTGAACCATGTGAC
CAAAGAGTTCGCTGTCAAAATCTTTCACCTGGATTTAGATGTGATCCATGTCCTTCTGGA
TATCATGGTCAGCACTCGCAAGGAATAATATTACAAACTGGAATTGATCACACTTTCCAA
CGACAACGTTGTGATGACATTGATGAATGTCGTGAAGGAGTTGCTCGATGTGGTGCAAAT
TCACAGTGTGTAAATACTGAGGGTTCTTATGAATGCACATGCACAAGAGGTTTTGTTCGT
AATGAGACATATGGCTGCTTGCAAGTACCTGGTATGTGTCCTGATGGAACAATTTGCGAT
AGAAATGCCGTATGTCAGCATGCCGGTGGAAATCGCTTCAGATGTAAATGCCGTATTGGA
TGGGCAGGCGATGGATTGTTTTGCGCTGCTGATAAAGACTTGGATGGTTGGCCTGATTAC
GATCTCGGTTGTTCGGACCAGCGTTGCAGAGCAGATAATTGTCCGACAATTCCTAACTCA
GGTCAAGAAGATGCAGATGGTGATGGTTTAGGAGATGCATGTGATCCTGATGCTGACAAC
GATGGAGTGCTGAATAGTCCCGATAATTGCCCATTAATTTATAACCCAGATCAAGCAGAC
ACTGATGCTGACGGAGCTGATAAACAAGGTGATGCTTGTGACAATTGTCCAACAGTTTCA
AATAGTGACCAGTCTGACATTGATAGAGACGGTCTTGGTGATGCTTGTGACCCAGACATG
GATAATGATGGAATTCCAAATGAAAGAGACAATTGTCCGAGAATAGCAAATAGCAATCAA
TTAGATTCAGATAATGATGGTAGAGGAGATGTTTGTGATAATTGTCCACAAGTTCCAAAT
CCCAGTCAACAAGATAGCGACAATGATTTAGTAGGAGATGCATGTGACTCTGACATTGAT
AGAGATAAAGACGGTGTACAAGATAGCAAAGATAATTGTCCTAAAATTCCCAATTCAGAC
CAATTAGATCATGATGGAGATGGAAAAGGTGATGCTTGTGACCCTGACATGGATAATGAT
AATGTTTTAAATGAGAGAGACAATTGTCCATTCTATTACAATCCTGACCAAATGGATTTA
AACAATGATGGCGTTGGTGACGTTTGTGAAGAAGATTTTGATCGTGACAGTGTGCCAAAT
TATCTTGATAATTGTCCAAATAATTCAATGATTCACTCAACTGATTTTAGACGTTATCAA
ACGGTTGTTCTTGATCCTGAAGGTGAATCACAAATTGATCCAAATTGGGTAATTTATAAT
AAAGGAGCTGAAATTGTTCAGACTCAAAATTCTGACCCAGGCTTAGCAGTAGGCTATCAT
TCATTCGGTGGCGTTGATTTTGAGGGAACATTCTTTGTTGACACAGAAATTGATGACGAT
TATGCTGGATTTATTTTCTCATACCAAGATAATCATAAATTCTACACTGTCATGTGGAAA
AAGAATCATCAAACTTATTGGCAAGCTACACCATTCAGAGCAAGTGCAGAACCTGGAATT
CAACTTAAACTCGTTAATAGCAAGACAGGGCCAGGTGAAATGTTAAGAAACAGTTTGTGG
CATACAGGCGATACAAAAGATCAAGTCAAATTGCTTTGGAAAGATCCAAGAAATGTTGGT
TGGAAAGAAAGAACTGCTTATCGTTGGCTTCTATTACATAGACCGAAAATTGGTCTCATT
CGTCTTAGAATATTTGATGGAGAGAATATGGTTGCTGATTCTGGTAATATTTATGATTCA
ACACTTAAAGGTGGTCGTCTTGGTGTGTTTTGTTTCTCGCAAGAAATGATTATCTGGTCT
GATTTAGTTTATCGTTGTAACGACAACGTACCTGAGACTATTTATCGAGAGCTTCCTCCA
CGCTTGCAAAAAGAAGTCAGCATTGATCATCGAGTATGA
>g13797.t1 Gene=g13797 Length=1052
MRNIFVLLVLVIIVISDGFSMSLDPVASTELEQFIRDDFTVSLRHIRPRRKFRITLEALF
MIDFPTVKNKFTFYLDRKSKRIVIDINSNSKIFSKHLNLPSLNETTTIRSIAFAFSENFI
TLYVDCNDILKEEMEFNLSRLFMDMDEPLVKLFRERKYPLYLDTSPESALARASCQKSSK
RKSNHKIVKNYSEGSEKNRKREVNNYYRSRDDIRNRDDFNAPPGRGDIPIIHGDCDENLL
RGINDLIALIKKLQQDIANQHAEIKRLQSLIENCAGCQEAPPLIRYDTCQYANPCFPGVT
CHDTSSGMRCGRCPSGYVGDGRTCKPGQTCDDRPCFPGVTCSDTVGGAVCGPCPSGYEGD
GKTCQERRSVCDDRPCAAGVQCQETREYPYYRCGACPAGFTGNGTTCHDIDECDLVEPCD
QRVRCQNLSPGFRCDPCPSGYHGQHSQGIILQTGIDHTFQRQRCDDIDECREGVARCGAN
SQCVNTEGSYECTCTRGFVRNETYGCLQVPGMCPDGTICDRNAVCQHAGGNRFRCKCRIG
WAGDGLFCAADKDLDGWPDYDLGCSDQRCRADNCPTIPNSGQEDADGDGLGDACDPDADN
DGVLNSPDNCPLIYNPDQADTDADGADKQGDACDNCPTVSNSDQSDIDRDGLGDACDPDM
DNDGIPNERDNCPRIANSNQLDSDNDGRGDVCDNCPQVPNPSQQDSDNDLVGDACDSDID
RDKDGVQDSKDNCPKIPNSDQLDHDGDGKGDACDPDMDNDNVLNERDNCPFYYNPDQMDL
NNDGVGDVCEEDFDRDSVPNYLDNCPNNSMIHSTDFRRYQTVVLDPEGESQIDPNWVIYN
KGAEIVQTQNSDPGLAVGYHSFGGVDFEGTFFVDTEIDDDYAGFIFSYQDNHKFYTVMWK
KNHQTYWQATPFRASAEPGIQLKLVNSKTGPGEMLRNSLWHTGDTKDQVKLLWKDPRNVG
WKERTAYRWLLLHRPKIGLIRLRIFDGENMVADSGNIYDSTLKGGRLGVFCFSQEMIIWS
DLVYRCNDNVPETIYRELPPRLQKEVSIDHRV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 38 | g13797.t1 | CDD | cd16081 | TSPcc_insect | 236 | 277 | 4.60176E-13 |
| 37 | g13797.t1 | CDD | cd00053 | EGF | 289 | 322 | 0.00139115 |
| 35 | g13797.t1 | CDD | cd00054 | EGF_CA | 409 | 445 | 5.02501E-6 |
| 36 | g13797.t1 | CDD | cd00054 | EGF_CA | 466 | 498 | 1.92013E-6 |
| 29 | g13797.t1 | Coils | Coil | Coil | 243 | 270 | - |
| 22 | g13797.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 286 | 329 | 4.0E-7 |
| 21 | g13797.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 330 | 367 | 7.6E-8 |
| 20 | g13797.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 368 | 414 | 1.5E-10 |
| 23 | g13797.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 415 | 469 | 2.5E-13 |
| 24 | g13797.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 470 | 514 | 2.1E-10 |
| 25 | g13797.t1 | Gene3D | G3DSA:4.10.1080.10 | - | 537 | 629 | 2.9E-21 |
| 27 | g13797.t1 | Gene3D | G3DSA:4.10.1080.10 | - | 630 | 692 | 1.3E-23 |
| 26 | g13797.t1 | Gene3D | G3DSA:4.10.1080.10 | - | 693 | 816 | 2.4E-44 |
| 28 | g13797.t1 | Gene3D | G3DSA:2.60.120.200 | - | 817 | 1040 | 1.2E-105 |
| 54 | g13797.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 720 | 748 | - |
| 11 | g13797.t1 | PANTHER | PTHR10199 | THROMBOSPONDIN | 116 | 373 | 0.0 |
| 12 | g13797.t1 | PANTHER | PTHR10199 | THROMBOSPONDIN | 363 | 1029 | 0.0 |
| 1 | g13797.t1 | Pfam | PF11598 | Cartilage oligomeric matrix protein | 234 | 278 | 9.0E-10 |
| 3 | g13797.t1 | Pfam | PF07645 | Calcium-binding EGF domain | 409 | 442 | 2.6E-6 |
| 2 | g13797.t1 | Pfam | PF07645 | Calcium-binding EGF domain | 466 | 502 | 1.3E-9 |
| 5 | g13797.t1 | Pfam | PF02412 | Thrombospondin type 3 repeat | 583 | 618 | 4.1E-11 |
| 9 | g13797.t1 | Pfam | PF02412 | Thrombospondin type 3 repeat | 646 | 680 | 8.1E-13 |
| 7 | g13797.t1 | Pfam | PF02412 | Thrombospondin type 3 repeat | 681 | 703 | 2.5E-4 |
| 4 | g13797.t1 | Pfam | PF02412 | Thrombospondin type 3 repeat | 704 | 741 | 2.4E-10 |
| 8 | g13797.t1 | Pfam | PF02412 | Thrombospondin type 3 repeat | 743 | 777 | 5.0E-10 |
| 6 | g13797.t1 | Pfam | PF02412 | Thrombospondin type 3 repeat | 779 | 812 | 8.0E-14 |
| 10 | g13797.t1 | Pfam | PF05735 | Thrombospondin C-terminal region | 831 | 1028 | 1.6E-98 |
| 31 | g13797.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 22 | - |
| 32 | g13797.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 33 | g13797.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 15 | - |
| 34 | g13797.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 22 | - |
| 30 | g13797.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 23 | 1052 | - |
| 52 | g13797.t1 | ProSitePatterns | PS01187 | Calcium-binding EGF-like domain signature. | 466 | 492 | - |
| 53 | g13797.t1 | ProSitePatterns | PS00010 | Aspartic acid and asparagine hydroxylation site. | 483 | 494 | - |
| 50 | g13797.t1 | ProSitePatterns | PS01186 | EGF-like domain signature 2. | 492 | 506 | - |
| 51 | g13797.t1 | ProSitePatterns | PS01186 | EGF-like domain signature 2. | 535 | 548 | - |
| 65 | g13797.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 285 | 325 | 9.188 |
| 68 | g13797.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 326 | 365 | 7.847 |
| 69 | g13797.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 367 | 408 | 7.317 |
| 66 | g13797.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 409 | 447 | 11.12 |
| 67 | g13797.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 466 | 507 | 11.098 |
| 64 | g13797.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 509 | 549 | 9.686 |
| 59 | g13797.t1 | ProSiteProfiles | PS51234 | Thrombospondin type-3 (TSP3) repeat profile. | 550 | 582 | 10.62 |
| 60 | g13797.t1 | ProSiteProfiles | PS51234 | Thrombospondin type-3 (TSP3) repeat profile. | 583 | 618 | 18.458 |
| 55 | g13797.t1 | ProSiteProfiles | PS51234 | Thrombospondin type-3 (TSP3) repeat profile. | 622 | 644 | 9.945 |
| 61 | g13797.t1 | ProSiteProfiles | PS51234 | Thrombospondin type-3 (TSP3) repeat profile. | 645 | 680 | 17.552 |
| 57 | g13797.t1 | ProSiteProfiles | PS51234 | Thrombospondin type-3 (TSP3) repeat profile. | 681 | 703 | 12.791 |
| 58 | g13797.t1 | ProSiteProfiles | PS51234 | Thrombospondin type-3 (TSP3) repeat profile. | 704 | 741 | 15.588 |
| 56 | g13797.t1 | ProSiteProfiles | PS51234 | Thrombospondin type-3 (TSP3) repeat profile. | 742 | 777 | 17.352 |
| 62 | g13797.t1 | ProSiteProfiles | PS51234 | Thrombospondin type-3 (TSP3) repeat profile. | 778 | 813 | 15.077 |
| 63 | g13797.t1 | ProSiteProfiles | PS51236 | Thrombospondin C-terminal domain profile. | 817 | 1031 | 107.285 |
| 40 | g13797.t1 | SMART | SM00179 | egfca_6 | 285 | 325 | 0.074 |
| 44 | g13797.t1 | SMART | SM00181 | egf_5 | 288 | 325 | 0.024 |
| 48 | g13797.t1 | SMART | SM00181 | egf_5 | 329 | 365 | 0.024 |
| 43 | g13797.t1 | SMART | SM00179 | egfca_6 | 330 | 365 | 0.015 |
| 47 | g13797.t1 | SMART | SM00181 | egf_5 | 370 | 408 | 1.8 |
| 41 | g13797.t1 | SMART | SM00179 | egfca_6 | 409 | 447 | 1.0E-6 |
| 45 | g13797.t1 | SMART | SM00181 | egf_5 | 412 | 465 | 0.046 |
| 42 | g13797.t1 | SMART | SM00179 | egfca_6 | 466 | 507 | 3.1E-8 |
| 49 | g13797.t1 | SMART | SM00181 | egf_5 | 469 | 507 | 1.9 |
| 46 | g13797.t1 | SMART | SM00181 | egf_5 | 512 | 549 | 0.077 |
| 17 | g13797.t1 | SUPERFAMILY | SSF57184 | Growth factor receptor domain | 376 | 513 | 1.0E-6 |
| 18 | g13797.t1 | SUPERFAMILY | SSF57196 | EGF/Laminin | 459 | 506 | 1.09E-7 |
| 15 | g13797.t1 | SUPERFAMILY | SSF103647 | TSP type-3 repeat | 548 | 627 | 1.7E-13 |
| 13 | g13797.t1 | SUPERFAMILY | SSF103647 | TSP type-3 repeat | 627 | 693 | 9.68E-15 |
| 14 | g13797.t1 | SUPERFAMILY | SSF103647 | TSP type-3 repeat | 691 | 811 | 3.14E-36 |
| 16 | g13797.t1 | SUPERFAMILY | SSF49899 | Concanavalin A-like lectins/glucanases | 814 | 1029 | 3.8E-109 |
| 19 | g13797.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 39 | g13797.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 5 | 27 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0007155 | cell adhesion | BP |
| GO:0005509 | calcium ion binding | MF |
| GO:0005576 | extracellular region | CC |
KEGG
Orthology
- This transcript has been annotated with K04659 (thrombospondin 2/3/4/5)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
