General information for g15618.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cartilage oligomeric matrix protein.
Parent gene
- The parent gene g15618 is located on chr_4: 6117608..6121037 (- 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_4 | g15618 | g15618.t1 | isoform | g15618.t1 | 6116996 | 6121037 |
| chr_4 | g15618 | g15618.t1 | exon | g15618.t1.exon1 | 6116996 | 6117105 |
| chr_4 | g15618 | g15618.t1 | cds | g15618.t1.CDS1 | 6116996 | 6117105 |
| chr_4 | g15618 | g15618.t1 | exon | g15618.t1.exon2 | 6117201 | 6117963 |
| chr_4 | g15618 | g15618.t1 | cds | g15618.t1.CDS2 | 6117201 | 6117963 |
| chr_4 | g15618 | g15618.t1 | exon | g15618.t1.exon3 | 6118027 | 6118080 |
| chr_4 | g15618 | g15618.t1 | cds | g15618.t1.CDS3 | 6118027 | 6118080 |
| chr_4 | g15618 | g15618.t1 | exon | g15618.t1.exon4 | 6118137 | 6118178 |
| chr_4 | g15618 | g15618.t1 | cds | g15618.t1.CDS4 | 6118137 | 6118178 |
| chr_4 | g15618 | g15618.t1 | exon | g15618.t1.exon5 | 6118269 | 6118368 |
| chr_4 | g15618 | g15618.t1 | cds | g15618.t1.CDS5 | 6118269 | 6118368 |
| chr_4 | g15618 | g15618.t1 | exon | g15618.t1.exon6 | 6118572 | 6118626 |
| chr_4 | g15618 | g15618.t1 | cds | g15618.t1.CDS6 | 6118572 | 6118626 |
| chr_4 | g15618 | g15618.t1 | exon | g15618.t1.exon7 | 6118691 | 6118784 |
| chr_4 | g15618 | g15618.t1 | cds | g15618.t1.CDS7 | 6118691 | 6118784 |
| chr_4 | g15618 | g15618.t1 | exon | g15618.t1.exon8 | 6119068 | 6119105 |
| chr_4 | g15618 | g15618.t1 | cds | g15618.t1.CDS8 | 6119068 | 6119105 |
| chr_4 | g15618 | g15618.t1 | exon | g15618.t1.exon9 | 6119162 | 6119231 |
| chr_4 | g15618 | g15618.t1 | cds | g15618.t1.CDS9 | 6119162 | 6119231 |
| chr_4 | g15618 | g15618.t1 | exon | g15618.t1.exon10 | 6119355 | 6119422 |
| chr_4 | g15618 | g15618.t1 | cds | g15618.t1.CDS10 | 6119355 | 6119422 |
| chr_4 | g15618 | g15618.t1 | exon | g15618.t1.exon11 | 6119477 | 6119519 |
| chr_4 | g15618 | g15618.t1 | cds | g15618.t1.CDS11 | 6119477 | 6119519 |
| chr_4 | g15618 | g15618.t1 | exon | g15618.t1.exon12 | 6119576 | 6120317 |
| chr_4 | g15618 | g15618.t1 | cds | g15618.t1.CDS12 | 6119576 | 6120317 |
| chr_4 | g15618 | g15618.t1 | exon | g15618.t1.exon13 | 6120409 | 6120700 |
| chr_4 | g15618 | g15618.t1 | cds | g15618.t1.CDS13 | 6120409 | 6120700 |
| chr_4 | g15618 | g15618.t1 | exon | g15618.t1.exon14 | 6120804 | 6120863 |
| chr_4 | g15618 | g15618.t1 | cds | g15618.t1.CDS14 | 6120804 | 6120863 |
| chr_4 | g15618 | g15618.t1 | exon | g15618.t1.exon15 | 6120947 | 6121037 |
| chr_4 | g15618 | g15618.t1 | cds | g15618.t1.CDS15 | 6120947 | 6121037 |
| chr_4 | g15618 | g15618.t1 | TSS | g15618.t1 | 6121125 | 6121125 |
| chr_4 | g15618 | g15618.t1 | TTS | g15618.t1 | NA | NA |
Sequences
>g15618.t1 Gene=g15618 Length=2622
ATGAAAATCTTAATTTATAAATTTGTCTTTCTTTTGATAACAATAAATTTTATCAATTTA
TCAAGTAGTGATACTTCTATTAATGATGATGAAGAAAATTACGAAGAGAGCAGTGAGATA
ACGACTGACAATGACCCGCAAAATTGTAATGGCGAATTAAAATCTGGAATGGATGAATTA
TTAAAAATGATGACATCTGTAAAAAAAGAATTAACTTATCAAAATGCAGAAATTAAATAT
GTGCAATCATTGATTGAAAATTGTGCATCATGTAAAATTTCACCTGAAGTTGAAACTTGT
GCAATTGCTAATCCATGCTTTCCTGGTGTTGAATGTTTTGATACTGTAAATGGAATTTCA
TGTGGAAATTGTCCTAGAGGTTATAAAGGTGATGGGAAAGATTGTTATAGAATTGAAATG
TGCAGTGATCGTCCATGCTTTAGTGGAGTTTTGTGCACTGACACTGAAAATGGTGCACTT
TGTGGTTCATGTCCAATTAATTATGAAGGTGATGGAAGAGTTTGCACTTTGAGAAGAAAC
TTTTGTGAAAATAATCCTTGCAAAAATGGATTTCAATGTATTCAAATTGATGATCATCCA
TTCTATCAATGTATCGCATGTCCACTTGGTTTTACAAGTTATGATGGTTTTGATTGTGTT
GATATAAATGAATGTGAAACAATTCATCCATGTGATCCAATTGTAAGATGCACAAATCTT
TCACCTGGTTTTAGATGTGATGCATGCCCTATTGGTTATAAAGGTCACTTTTCTGAAGGT
TTCTTTATGGAATCAGTTGATAGTCTTCCATTTCAAAGACAAATATGTGAAGATATTGAT
GAATGTCTTGATGGAACTGCACAATGTGGTCAATTTGCTTTGTGTCATAATTTACTTGGT
TCTTATGAATGTCTTTGCCCTGTTGGATACAAAAAATCAAACACAACTGATGACTGCATT
ATTCAACCTGGTGCTTGTTTAGATGGAACTGTTTGTGATAAAAATGCACAATGTAGACAT
ATTGGTTATGGAAGATATTCATGTAAATGCAAAGTAGGTTACGCTGGCGATGGACAGTAT
TGTGGAAGTGATCGAGATCTTGATGGATGGCCTGATTATGATTTAGGTTGTGCAAGCACT
TTTTGTAGAAAAGACAATTGCGTTTTAGTACCAAATTCTGGACAAGAAGATACAGATGCT
GATGGAATTGGAGATGTTTGTGATTCAGATATTGACAATGATGTAATTTACAATCATAAT
GACAATTGTGTTTATGTTTATAATCCGAATCAATCGGATATTGATGGTGATAAAGTTGGT
GATAGTTGTGATAATTGTCCAAATATTTTTAATGGTGATCAATCAGATATTGACAATGAT
GGATTGGGTGATCGATGCGACCATGATATTGATGATGATGGAATTTTCAATGAAGTTGAC
AACTGCCCAAAAATAGCGAACAGTGATCAAAAAGATAGTGATATGGATCGAGTTGGAGAT
GTTTGTGACAATTGTCCATTAACACCAAATATGGATCAAAAAGATAGTGACGCTGACCTA
ATTGGTGATGCTTGTGATAACAATAAAGATCGTGACCAAGATGGAATTCAAGACAACAGA
GATAACTGCCCAGATACACCTAATGCTGAACAAGTTGATACAGATGAAGATGGTTTAGGA
GATGCTTGTGATGATGATATTGATAACGATGGAATTGAAAATGAAATTGATAATTGTCGA
TTTGTTCCAAATTATGACCAATTAGATACAGACAATAATGGAATTGGTGATGCTTGTGAA
AAAGATTTTGATGGCGATGGACATGAAAATCTTGTTGATAATTGTCCATATAATAATAAA
ATTTATACAACTGACTTTAGAACATTCCAACAAGTTCCACTTGATCCTGAAGGAGATTCA
CAAATTGATCCAAAATGGGTTATTTACAATAAAGGAGCTGAAATGGTTCAAACAATGAAT
TCTGACCCTGGAATGGCTATTGGATATGACTCATTTAGCAGCGTTGATTTTGAAGGAACA
CTTTTTGTTGATACTGATGTTGATGACGATTATATTGGTTTTATTTTCTCTTATCAATCA
AACCAGCGCTTTTATGCTGTTATGTGGAAAAGAAGTGCTCAAGAATATTGGCATAAAGAG
CCATTTGTTGCAAATGCTGAACCTGGAATTCAAATTAAATTAATCAATTCTGAAACAGGA
CCAGGAAAATTATTGAGAAATAGCTTATGGCATACTGGAAACACAACAAATCAAGTCAAA
TTACTCTGGAAAGATCCAAAAAATGTCGGCTGGAAAGAAAGAACTGCTTATAGATGGCAT
TTAATTCATAGACCAAAAATTGGTTTGATAAATATGAAAATTTTCAATGGTAAACGATTG
GTTGTTGATTCTGGAAATATTTATGATTCAACATTAAAAGGTGGAAGACTTGGAATGTAT
GTTTTCTCCCAGCAAATGATTATTTGGTCTAATTTGGTTTATAAATGCAATGAAAATGTT
CCTGCAAAACTTTATGCCAAACTTCCACCATCACTTCAACGTGAGTGCCAAGTTGAAAAA
ATGCTTCAACGCAATCAACGAATGGAACCAATTAAAACATAA
>g15618.t1 Gene=g15618 Length=873
MKILIYKFVFLLITINFINLSSSDTSINDDEENYEESSEITTDNDPQNCNGELKSGMDEL
LKMMTSVKKELTYQNAEIKYVQSLIENCASCKISPEVETCAIANPCFPGVECFDTVNGIS
CGNCPRGYKGDGKDCYRIEMCSDRPCFSGVLCTDTENGALCGSCPINYEGDGRVCTLRRN
FCENNPCKNGFQCIQIDDHPFYQCIACPLGFTSYDGFDCVDINECETIHPCDPIVRCTNL
SPGFRCDACPIGYKGHFSEGFFMESVDSLPFQRQICEDIDECLDGTAQCGQFALCHNLLG
SYECLCPVGYKKSNTTDDCIIQPGACLDGTVCDKNAQCRHIGYGRYSCKCKVGYAGDGQY
CGSDRDLDGWPDYDLGCASTFCRKDNCVLVPNSGQEDTDADGIGDVCDSDIDNDVIYNHN
DNCVYVYNPNQSDIDGDKVGDSCDNCPNIFNGDQSDIDNDGLGDRCDHDIDDDGIFNEVD
NCPKIANSDQKDSDMDRVGDVCDNCPLTPNMDQKDSDADLIGDACDNNKDRDQDGIQDNR
DNCPDTPNAEQVDTDEDGLGDACDDDIDNDGIENEIDNCRFVPNYDQLDTDNNGIGDACE
KDFDGDGHENLVDNCPYNNKIYTTDFRTFQQVPLDPEGDSQIDPKWVIYNKGAEMVQTMN
SDPGMAIGYDSFSSVDFEGTLFVDTDVDDDYIGFIFSYQSNQRFYAVMWKRSAQEYWHKE
PFVANAEPGIQIKLINSETGPGKLLRNSLWHTGNTTNQVKLLWKDPKNVGWKERTAYRWH
LIHRPKIGLINMKIFNGKRLVVDSGNIYDSTLKGGRLGMYVFSQQMIIWSNLVYKCNENV
PAKLYAKLPPSLQRECQVEKMLQRNQRMEPIKT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 35 | g15618.t1 | CDD | cd00054 | EGF_CA | 221 | 256 | 4.45409E-5 |
| 34 | g15618.t1 | CDD | cd00054 | EGF_CA | 278 | 310 | 3.18858E-5 |
| 22 | g15618.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 96 | 139 | 1.8E-8 |
| 21 | g15618.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 140 | 180 | 4.5E-5 |
| 20 | g15618.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 181 | 227 | 6.2E-8 |
| 25 | g15618.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 228 | 280 | 1.6E-13 |
| 24 | g15618.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 281 | 316 | 5.0E-10 |
| 23 | g15618.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 317 | 364 | 6.9E-7 |
| 27 | g15618.t1 | Gene3D | G3DSA:4.10.1080.10 | - | 432 | 502 | 1.8E-22 |
| 26 | g15618.t1 | Gene3D | G3DSA:4.10.1080.10 | - | 503 | 624 | 2.1E-43 |
| 28 | g15618.t1 | Gene3D | G3DSA:2.60.120.200 | - | 625 | 847 | 1.9E-102 |
| 51 | g15618.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 529 | 560 | - |
| 12 | g15618.t1 | PANTHER | PTHR10199 | THROMBOSPONDIN | 51 | 172 | 1.2E-284 |
| 11 | g15618.t1 | PANTHER | PTHR10199 | THROMBOSPONDIN | 178 | 838 | 1.2E-284 |
| 1 | g15618.t1 | Pfam | PF11598 | Cartilage oligomeric matrix protein | 49 | 92 | 4.4E-7 |
| 3 | g15618.t1 | Pfam | PF07645 | Calcium-binding EGF domain | 221 | 254 | 4.1E-5 |
| 2 | g15618.t1 | Pfam | PF07645 | Calcium-binding EGF domain | 278 | 319 | 1.1E-10 |
| 4 | g15618.t1 | Pfam | PF02412 | Thrombospondin type 3 repeat | 396 | 431 | 1.8E-10 |
| 7 | g15618.t1 | Pfam | PF02412 | Thrombospondin type 3 repeat | 432 | 454 | 0.011 |
| 9 | g15618.t1 | Pfam | PF02412 | Thrombospondin type 3 repeat | 456 | 490 | 6.9E-10 |
| 6 | g15618.t1 | Pfam | PF02412 | Thrombospondin type 3 repeat | 514 | 551 | 2.3E-10 |
| 8 | g15618.t1 | Pfam | PF02412 | Thrombospondin type 3 repeat | 553 | 587 | 2.4E-11 |
| 5 | g15618.t1 | Pfam | PF02412 | Thrombospondin type 3 repeat | 589 | 621 | 6.7E-15 |
| 10 | g15618.t1 | Pfam | PF05735 | Thrombospondin C-terminal region | 641 | 838 | 2.7E-95 |
| 30 | g15618.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 23 | - |
| 31 | g15618.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 7 | - |
| 32 | g15618.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 8 | 15 | - |
| 33 | g15618.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 23 | - |
| 29 | g15618.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 24 | 873 | - |
| 49 | g15618.t1 | ProSitePatterns | PS01187 | Calcium-binding EGF-like domain signature. | 278 | 304 | - |
| 50 | g15618.t1 | ProSitePatterns | PS00010 | Aspartic acid and asparagine hydroxylation site. | 295 | 306 | - |
| 48 | g15618.t1 | ProSitePatterns | PS01186 | EGF-like domain signature 2. | 348 | 361 | - |
| 62 | g15618.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 96 | 136 | 7.972 |
| 61 | g15618.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 178 | 220 | 7.312 |
| 63 | g15618.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 221 | 259 | 9.54 |
| 65 | g15618.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 278 | 316 | 12.16 |
| 64 | g15618.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 322 | 362 | 10.898 |
| 55 | g15618.t1 | ProSiteProfiles | PS51234 | Thrombospondin type-3 (TSP3) repeat profile. | 363 | 395 | 11.028 |
| 58 | g15618.t1 | ProSiteProfiles | PS51234 | Thrombospondin type-3 (TSP3) repeat profile. | 396 | 431 | 16.646 |
| 54 | g15618.t1 | ProSiteProfiles | PS51234 | Thrombospondin type-3 (TSP3) repeat profile. | 432 | 454 | 10.979 |
| 59 | g15618.t1 | ProSiteProfiles | PS51234 | Thrombospondin type-3 (TSP3) repeat profile. | 455 | 490 | 15.765 |
| 52 | g15618.t1 | ProSiteProfiles | PS51234 | Thrombospondin type-3 (TSP3) repeat profile. | 491 | 513 | 11.8 |
| 53 | g15618.t1 | ProSiteProfiles | PS51234 | Thrombospondin type-3 (TSP3) repeat profile. | 514 | 551 | 14.834 |
| 57 | g15618.t1 | ProSiteProfiles | PS51234 | Thrombospondin type-3 (TSP3) repeat profile. | 552 | 587 | 17.23 |
| 56 | g15618.t1 | ProSiteProfiles | PS51234 | Thrombospondin type-3 (TSP3) repeat profile. | 588 | 623 | 15.053 |
| 60 | g15618.t1 | ProSiteProfiles | PS51236 | Thrombospondin C-terminal domain profile. | 627 | 841 | 100.509 |
| 38 | g15618.t1 | SMART | SM00179 | egfca_6 | 96 | 136 | 0.2 |
| 45 | g15618.t1 | SMART | SM00181 | egf_5 | 99 | 136 | 0.94 |
| 41 | g15618.t1 | SMART | SM00179 | egfca_6 | 137 | 176 | 0.15 |
| 42 | g15618.t1 | SMART | SM00181 | egf_5 | 140 | 176 | 5.3 |
| 37 | g15618.t1 | SMART | SM00179 | egfca_6 | 178 | 220 | 0.19 |
| 44 | g15618.t1 | SMART | SM00181 | egf_5 | 181 | 220 | 0.011 |
| 39 | g15618.t1 | SMART | SM00179 | egfca_6 | 221 | 259 | 5.5E-4 |
| 47 | g15618.t1 | SMART | SM00181 | egf_5 | 224 | 277 | 1.2 |
| 36 | g15618.t1 | SMART | SM00179 | egfca_6 | 278 | 320 | 3.5E-10 |
| 46 | g15618.t1 | SMART | SM00181 | egf_5 | 281 | 320 | 0.0048 |
| 43 | g15618.t1 | SMART | SM00181 | egf_5 | 325 | 362 | 0.083 |
| 40 | g15618.t1 | SMART | SM00179 | egfca_6 | 326 | 362 | 1.5 |
| 17 | g15618.t1 | SUPERFAMILY | SSF57196 | EGF/Laminin | 271 | 319 | 6.19E-7 |
| 14 | g15618.t1 | SUPERFAMILY | SSF103647 | TSP type-3 repeat | 357 | 444 | 9.68E-12 |
| 13 | g15618.t1 | SUPERFAMILY | SSF103647 | TSP type-3 repeat | 420 | 503 | 4.45E-16 |
| 15 | g15618.t1 | SUPERFAMILY | SSF103647 | TSP type-3 repeat | 501 | 621 | 1.18E-34 |
| 16 | g15618.t1 | SUPERFAMILY | SSF49899 | Concanavalin A-like lectins/glucanases | 624 | 838 | 1.9E-102 |
| 19 | g15618.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
| 18 | g15618.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 28 | - |
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.
