General information for g13034.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Integrin beta-PS.
Parent gene
- The parent gene g13034 is located on chr_1: 27634379..27636423 (+ 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 | g13034 | g13034.t1 | isoform | g13034.t1 | 27630806 | 27635156 |
| chr_1 | g13034 | g13034.t1 | exon | g13034.t1.exon1 | 27630806 | 27631277 |
| chr_1 | g13034 | g13034.t1 | cds | g13034.t1.CDS1 | 27630806 | 27631277 |
| chr_1 | g13034 | g13034.t1 | exon | g13034.t1.exon2 | 27631333 | 27631561 |
| chr_1 | g13034 | g13034.t1 | cds | g13034.t1.CDS2 | 27631333 | 27631561 |
| chr_1 | g13034 | g13034.t1 | exon | g13034.t1.exon3 | 27631676 | 27631760 |
| chr_1 | g13034 | g13034.t1 | cds | g13034.t1.CDS3 | 27631676 | 27631760 |
| chr_1 | g13034 | g13034.t1 | exon | g13034.t1.exon4 | 27633188 | 27633619 |
| chr_1 | g13034 | g13034.t1 | cds | g13034.t1.CDS4 | 27633188 | 27633619 |
| chr_1 | g13034 | g13034.t1 | exon | g13034.t1.exon5 | 27633676 | 27634609 |
| chr_1 | g13034 | g13034.t1 | cds | g13034.t1.CDS5 | 27633676 | 27634609 |
| chr_1 | g13034 | g13034.t1 | exon | g13034.t1.exon6 | 27634673 | 27634782 |
| chr_1 | g13034 | g13034.t1 | cds | g13034.t1.CDS6 | 27634673 | 27634782 |
| chr_1 | g13034 | g13034.t1 | exon | g13034.t1.exon7 | 27634842 | 27635030 |
| chr_1 | g13034 | g13034.t1 | cds | g13034.t1.CDS7 | 27634842 | 27635030 |
| chr_1 | g13034 | g13034.t1 | exon | g13034.t1.exon8 | 27635091 | 27635156 |
| chr_1 | g13034 | g13034.t1 | cds | g13034.t1.CDS8 | 27635091 | 27635156 |
| chr_1 | g13034 | g13034.t1 | TTS | g13034.t1 | 27635742 | 27635742 |
| chr_1 | g13034 | g13034.t1 | TSS | g13034.t1 | NA | NA |
Sequences
>g13034.t1 Gene=g13034 Length=2517
ATGTTATTTTCAATAGTGCTGATAAGCACATTAGTAGTTATAAATGCACAATTTGGCATT
GACAAAGCTGCACTTTATCAAAATCCTTGTACAAGTAAAACATCATGTAGTGCTTGCATT
CAAACACAAAAGTGTGCTTGGTGTATGCAGCCAGATTTTGGTGATCGTCCAAGATGTTTC
CAACCTGATTTGAAACCAGCAACCACATGTCCAGAAGAATTTGTTGTGAATCCAGACAAT
GAAGAAATTATGATTAGAAATTGGGCATTGAGCAGAGGAGGCCAAGTATTAACAGGTGGT
GGTGGAATAGCAAGCGGTGGAACTTATGAAGAAGAACATCAATCTTCAGGATCAATGTCA
GGTCATGGGTCATCAGCAAGTGGTGGTTCAGCGGCTGGAAGTGCATCAGGAAGTGGTCAT
GGAAGTGTTGTTCAAGTCAGTCCACAACATGTTAACTTAAAATTGAGAATTAATGAAAAA
CATAGCATGAAAGTCAGTTATGCTCAAGCTGAAGATTATCCAGTAGATCTTTACTATCTT
ATGGACTTGTCAAAATCTATGGAAGATGATAAAGAAAAATTGTCGCATTTGGGAAATTTA
TTGTCAGACACAATGAGAAATATCACTTCAAATTTCCGTCTTGGTTTTGGATCATTTGTT
GATAAAGTTCTTATGCCTTATGTCTCAACTGTGCCTAAAAAATTACAGACACCTTGCGAT
GGTTGTGAAGCTCCATATGGTTATAAAAATCACATGTCACTTAGTGTTGACACAAATAAA
TTTGCTGAAAATGTAAGAGATGCTCATGTCTCAGGAAATTTGGATGCACCAGAAGGTGGA
TTTGATGCAATCATGCAAGCAGTTGTATGTAAGGATCACATTGGTTGGCGCGATCGTGCT
CGTCGTTTGCTCGTCTTCTCAACTGATGCTGGCTTCCATTATGCAGGAGATGGGAAACTT
GGTGGTGTAATAACTCCAAATGATGGTGAATGCCACATGGCAAATAATATGTACACTCAT
TCTACTATTCAAGATTATCCCAGCATTTCACAAATCAATTTGAAAGTTAAAGAAAATGCA
ATCAACATTATTTTTGCTGTTACACAATCACAGCATGAAGTTTATAAGAAACTTTCAAGT
CATATTGAAGGTTCATCAAGCGCTGTCTTATCAGAAGATTCATCAAATGTTGTTGAACTA
GTTAGAGATGAATATAATAAAATCACATCATCAGTTGAAATGAAAGACACTGCATCAGGT
TCAGTAAAAGTTACATATTGGTCAAAATGTTTAGGCGATACAAGAATGCAAACAAGCAAA
TGTGATGGTCTTAAAGTTGGTGATGTTGTTGCATTTGAAACTGAAATTGTTGTGACCTCA
TGTCCAGCTGATCCAAAAGATCGTAAACAGACTTTCCAAATTTATCCAGTTGGTGTTGGT
GAAGCTTTAACTGTTGATCTCGAAATGCTTTGTCATTGTGATTGTGAATCAAGTGGACCA
ACTTTCGAAATGAACTCACCATTGTGTAAAGGAAGTGGAACTTTAGCTTGTGGTATTTGC
GAATGTCATGAAGGCTTCTTTGGTCGTAATTGCGAGTGTAATAACAAAGACCTCGGTGAA
TCAGGACTCGATGCCTTCAAATGTAGACCAGATAATACAACTGATGTTGAATGTAGTGGA
CGAGGAAATTGTATTTGTGGTCAATGTCATTGCAACATTCGTGACAATCCCGAAGAAATC
ATTTCTGGACAATTCTGTGAATGTGATAACTTTTCATGCGATCGACACAATTCAATTTTG
TGTTCTGGTCCTGATCATGGTGTTTGTGAGTGTGGAACTTGCAAATGTCATGATGGATGG
CAAGGATCAGCTTGTGAATGCAGTAGTTCAATTGATGAATGTAAAGCATCAAATGGAGAA
ATTTGTTCTGGTCATGGAAGTTGCGTTTGTGGTCGATGCGAGTGTGAAATTAAAGAAGAT
GTGAGATACTCAGGAAAATATTGTGAAAAATGCCCAACATGTCCAGGACGTTGCGATGAA
TTGAGAGCTTGTGTTGAATGTCAAATGTACAAGAAAGGACCATTGAAAGATGAAAAAGAT
TGTGCCAGCAATTGCACTTTGTTTGTGCCAATTTCAGTTGAACATGTTGAATATAATGAA
GACGAAGATGAACATCTTTGTACATTCTACGATGAAGATGAATGTCGCTATCGTTTTGTT
TATAATGAAACTGTTGAAAAGAATGGAACTGTTACATTACATGTTCGTGCACAAGAAAAT
CCAGAATGTCCACCAAAAGTCTTTTTACTTGGAATTGTTCTTGGTGTTATTGCTGCTATT
GTATTGATTGGTATGGCAATGTTGCTACTTTGGAAACTTCTTACAACTATTCATGATAGA
CGAGAATTTGCTAGATTCGAGAAAGAACGAATGATGGCCAAATGGGATACTGGTGAAAAT
CCAATTTATAAACAAGCAACATCAACTTTCAAAAATCCAACATATGCTGGAAAATAA
>g13034.t1 Gene=g13034 Length=838
MLFSIVLISTLVVINAQFGIDKAALYQNPCTSKTSCSACIQTQKCAWCMQPDFGDRPRCF
QPDLKPATTCPEEFVVNPDNEEIMIRNWALSRGGQVLTGGGGIASGGTYEEEHQSSGSMS
GHGSSASGGSAAGSASGSGHGSVVQVSPQHVNLKLRINEKHSMKVSYAQAEDYPVDLYYL
MDLSKSMEDDKEKLSHLGNLLSDTMRNITSNFRLGFGSFVDKVLMPYVSTVPKKLQTPCD
GCEAPYGYKNHMSLSVDTNKFAENVRDAHVSGNLDAPEGGFDAIMQAVVCKDHIGWRDRA
RRLLVFSTDAGFHYAGDGKLGGVITPNDGECHMANNMYTHSTIQDYPSISQINLKVKENA
INIIFAVTQSQHEVYKKLSSHIEGSSSAVLSEDSSNVVELVRDEYNKITSSVEMKDTASG
SVKVTYWSKCLGDTRMQTSKCDGLKVGDVVAFETEIVVTSCPADPKDRKQTFQIYPVGVG
EALTVDLEMLCHCDCESSGPTFEMNSPLCKGSGTLACGICECHEGFFGRNCECNNKDLGE
SGLDAFKCRPDNTTDVECSGRGNCICGQCHCNIRDNPEEIISGQFCECDNFSCDRHNSIL
CSGPDHGVCECGTCKCHDGWQGSACECSSSIDECKASNGEICSGHGSCVCGRCECEIKED
VRYSGKYCEKCPTCPGRCDELRACVECQMYKKGPLKDEKDCASNCTLFVPISVEHVEYNE
DEDEHLCTFYDEDECRYRFVYNETVEKNGTVTLHVRAQENPECPPKVFLLGIVLGVIAAI
VLIGMAMLLLWKLLTTIHDRREFARFEKERMMAKWDTGENPIYKQATSTFKNPTYAGK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 23 | g13034.t1 | Gene3D | G3DSA:2.60.40.1510 | ntegrin | 142 | 491 | 3.1E-151 |
| 28 | g13034.t1 | Gene3D | G3DSA:3.40.50.410 | - | 170 | 412 | 3.1E-151 |
| 27 | g13034.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 492 | 534 | 5.1E-9 |
| 26 | g13034.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 544 | 589 | 5.8E-14 |
| 25 | g13034.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 590 | 627 | 1.8E-13 |
| 24 | g13034.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 631 | 674 | 9.6E-12 |
| 30 | g13034.t1 | Gene3D | G3DSA:3.10.450.180 | - | 675 | 764 | 1.1E-17 |
| 29 | g13034.t1 | Gene3D | G3DSA:1.20.5.100 | - | 765 | 838 | 1.1E-34 |
| 46 | g13034.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 109 | 145 | - |
| 7 | g13034.t1 | PANTHER | PTHR10082 | INTEGRIN BETA SUBUNIT | 23 | 837 | 8.2E-271 |
| 39 | g13034.t1 | PIRSF | PIRSF002512 | Integrin_B | 1 | 96 | 7.9E-7 |
| 38 | g13034.t1 | PIRSF | PIRSF002512 | Integrin_B | 108 | 838 | 2.9E-285 |
| 10 | g13034.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 32 | 48 | 2.8E-44 |
| 12 | g13034.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 345 | 368 | 2.8E-44 |
| 14 | g13034.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 381 | 405 | 2.8E-44 |
| 8 | g13034.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 558 | 571 | 2.8E-44 |
| 11 | g13034.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 767 | 784 | 2.8E-44 |
| 9 | g13034.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 784 | 802 | 2.8E-44 |
| 13 | g13034.t1 | PRINTS | PR01186 | Integrin beta subunit signature | 819 | 829 | 2.8E-44 |
| 1 | g13034.t1 | Pfam | PF17205 | Integrin plexin domain | 28 | 70 | 2.9E-10 |
| 3 | g13034.t1 | Pfam | PF00362 | Integrin beta chain VWA domain | 170 | 412 | 1.2E-109 |
| 5 | g13034.t1 | Pfam | PF18372 | Integrin beta epidermal growth factor like domain 1 | 503 | 526 | 3.0E-8 |
| 2 | g13034.t1 | Pfam | PF07974 | EGF-like domain | 634 | 668 | 9.4E-6 |
| 6 | g13034.t1 | Pfam | PF07965 | Integrin beta tail domain | 678 | 765 | 1.8E-16 |
| 4 | g13034.t1 | Pfam | PF08725 | Integrin beta cytoplasmic domain | 792 | 835 | 1.0E-24 |
| 33 | g13034.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 16 | - |
| 34 | g13034.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 1 | - |
| 35 | g13034.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 2 | 12 | - |
| 37 | g13034.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 16 | - |
| 32 | g13034.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 17 | 766 | - |
| 36 | g13034.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 767 | 791 | - |
| 31 | g13034.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 792 | 838 | - |
| 44 | g13034.t1 | ProSitePatterns | PS00243 | Integrins beta chain cysteine-rich domain signature. | 558 | 571 | - |
| 45 | g13034.t1 | ProSitePatterns | PS00243 | Integrins beta chain cysteine-rich domain signature. | 642 | 655 | - |
| 42 | g13034.t1 | SMART | SM00187 | INB_2 | 35 | 493 | 9.6E-230 |
| 41 | g13034.t1 | SMART | SM01242 | Integrin_B_tail_2 | 678 | 768 | 8.4E-25 |
| 43 | g13034.t1 | SMART | SM01241 | Integrin_b_cyt_2 | 792 | 838 | 2.8E-31 |
| 15 | g13034.t1 | SUPERFAMILY | SSF103575 | Plexin repeat | 27 | 78 | 5.75E-9 |
| 20 | g13034.t1 | SUPERFAMILY | SSF53300 | vWA-like | 170 | 410 | 1.03E-77 |
| 17 | g13034.t1 | SUPERFAMILY | SSF69179 | Integrin domains | 404 | 497 | 3.14E-17 |
| 18 | g13034.t1 | SUPERFAMILY | SSF57196 | EGF/Laminin | 587 | 627 | 1.45E-9 |
| 19 | g13034.t1 | SUPERFAMILY | SSF57196 | EGF/Laminin | 632 | 675 | 1.76E-6 |
| 16 | g13034.t1 | SUPERFAMILY | SSF69687 | Integrin beta tail domain | 676 | 765 | 8.24E-16 |
| 22 | g13034.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 16 | - |
| 21 | g13034.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 23 | - |
| 40 | g13034.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 769 | 791 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K05719 (integrin beta 1)
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.
