General information for g13030.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vinculin.
Parent gene
- The parent gene g13030 is located on chr_1: 27595760..27604584 (- 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 | g13030 | g13030.t1 | isoform | g13030.t1 | 27592429 | 27604584 |
| chr_1 | g13030 | g13030.t1 | exon | g13030.t1.exon1 | 27592429 | 27592492 |
| chr_1 | g13030 | g13030.t1 | cds | g13030.t1.CDS1 | 27592429 | 27592492 |
| chr_1 | g13030 | g13030.t1 | exon | g13030.t1.exon2 | 27593369 | 27593463 |
| chr_1 | g13030 | g13030.t1 | cds | g13030.t1.CDS2 | 27593369 | 27593463 |
| chr_1 | g13030 | g13030.t1 | exon | g13030.t1.exon3 | 27593520 | 27594146 |
| chr_1 | g13030 | g13030.t1 | cds | g13030.t1.CDS3 | 27593520 | 27594146 |
| chr_1 | g13030 | g13030.t1 | exon | g13030.t1.exon4 | 27594569 | 27595359 |
| chr_1 | g13030 | g13030.t1 | cds | g13030.t1.CDS4 | 27594569 | 27595359 |
| chr_1 | g13030 | g13030.t1 | exon | g13030.t1.exon5 | 27595408 | 27595564 |
| chr_1 | g13030 | g13030.t1 | cds | g13030.t1.CDS5 | 27595408 | 27595564 |
| chr_1 | g13030 | g13030.t1 | exon | g13030.t1.exon6 | 27595621 | 27596715 |
| chr_1 | g13030 | g13030.t1 | cds | g13030.t1.CDS6 | 27595621 | 27596715 |
| chr_1 | g13030 | g13030.t1 | exon | g13030.t1.exon7 | 27604528 | 27604584 |
| chr_1 | g13030 | g13030.t1 | cds | g13030.t1.CDS7 | 27604528 | 27604584 |
| chr_1 | g13030 | g13030.t1 | TSS | g13030.t1 | 27604809 | 27604809 |
| chr_1 | g13030 | g13030.t1 | TTS | g13030.t1 | NA | NA |
Sequences
>g13030.t1 Gene=g13030 Length=2886
ATGCCAGTTTTTCACACAAAGACGATTGAATCAATTTTGGAACCAGTCGCAAATCAGGTT
TCACGACTGGTGATTCTTCACGAAGAAGCAGAAGATGGAAATGCTATGCCAGATTTGTCA
AGACCCGTCCATGGAGTCTCAATTGCTGTCACAAATCTTGTTAAAGTTGGCAGAGAAACA
ATCAATAGTTCTGATGATCAAATTCTTAAACAAGACATGCCTTCTGCATTAATGCGTGTT
GAAACTGCATCACAATTATTAGAAGAAGCTTCTTCACTTCTTCGTGCTGATCCATATTCA
GGACCTGCTCGTCGTAAGCTTATTGAAGGATCACGTGGCATTCTTCAAGGCACATCACAA
CTTTTATTATGTTTTGATGAATCAGAAGTACGAAAAATTGTTCGCGAATGTAAACGTGTC
CTTGACTATCTCGCTGTAAGTGAGGTCATTGACACAATGGAAGATTTGGTACAATTTCTT
AAAGATCTCAGTCCATGTCTAAGTAAAGTATCACGTGAAGTCAGCAATCGTGAAAAAGAA
TTGACTCATCAAGTTCATAGTGAAATTCTTGTCAGATGCCTCGAACAAGTGAAAATTCTC
GCGCCAATTCTTATTTGCAGCATGAAAGTTTACATTCATATCATGGAGCAAGGTGGAAAA
GGTTCAGAAGAAGCTGCCGAAAATCGTAATTATCTTGCAGCAAGAATGACAGATGAAATT
CAAGAAATTATTCGTGTATTGCAATTGACAACATATGATGAAGACACAAGTGAACTTGAC
AATCTTACAGTGCTTAAAAAGATCAACAATGCCATTCGCAATAAAATGGAAGCTGCCAAA
GATTGGCTTAAGAATCCATACGCACTTAAGGGTGGCATTGGTGAAAAAGCTCTTCGACAG
ATTATCGATAATGCCCATAAAGTTGCCGACCGTTGCTTGCCAAGCGATTCTTACCGAATT
CGTCGTAATGCTGATGATTTGACTGCCATGGCAAATGCCTTATGCGAATTACGTCAACAA
AGTAAAGGAACATCACCACAAGCTGAATCATTGGCTCGTGAAATGATTGACAAATTGGAT
GAATTAGATCAAAATATTTTACAAGCTGTTATTAATGTTGATAAAGCTGGTCTTCAACAA
ACTGCGCATACTGTTCAAGGACGTTTAGAACAAGCAATTCGTTGGTTAACAAATCCTGGG
GCTGATGACAAAGGCTTGGGTCAACGTGCTATTGCACTTATCATTGAAGAAGGAAAGAAA
GTTGCCGATGGCTTGCCAGGACATCAAAAGTCCGATATTCTCTATCTTTCGGGCTTGGCT
CACACACCCGAAGCTCAAGAAATTGCTCGCAAATTAAATGCAAAATTGCATGAGTTGAAG
AATTTGATTCAATCAGCCGTTGTTGGTCGTGTAGTTGAAGATTTTATCGATATTTCAACG
CCATTGAAACAATTTACTGAAGCTGTCAATGCACCAGAAGGAACACCGAATCGCGAACAA
AATTTCAACCAAAAGGCGGCAAATTTGCAAGCATTCAGTGACCGTGCATCAAAGACAAGT
CGAATGGTTGCTGCTGGTGGTTCAGGTGGAAACAAAAAACTCGCTGAAGTTCTTCTTGCA
TCAGCTGCACAAATTGATAGTCTTACACCACAACTTATTAGTGCTGGTCGTATTCGTATG
AATTATCCAGGATCAAAGGCTGCTGAAGAACATTATAATAATCTTAAGCAACAATATGCT
GACACTATTTTGAGAATGAGAACTCTCTGCGATCAAGCAACTGATCCAGCTGATTTCATC
AAAGCCAGTGAAGAACAAATGCAAAAACACACATTATTGTGCGAAGATGCAATTAGAAAT
CGAGTCCCACAAAAAATGGTTGACAACACAAGCAGCATTGCACGTTTGGCCAATCGTGTA
TTGTTAGTTGCCAAACAAGAAGCTGACAATTCTGAAGATCCACAATTTACCTCAGAATTG
CTTAATGCTTCCGATAAGCTTCAAAATTCAGTTCCGACAATGGTACAAAATGCTAAATCT
GTTGCAACTGACATTACGAATGGGGCTGCTGGTGCTAATTGGCGTGATGCGAATAAGAAT
TTGCTTCAAAATGTCCGAAATGTTCGTAATGCAATCACACAACAACCAGAAATCCCAGCA
CCACCAGATCTTTCAGCACTTCGACTTAATGCAGAATCGCATGTTCCGCCACCAAGACCA
CCATTGCCACGTGAAGAAATTCCACCAGTTCGTCCTCCACCACCTGAAACTGATGATGAA
GATGAAGGCGTTTTCAAGGCAATGCCAACATCTAATCAACCAATTTTGCTTGCCGCTCAT
GGACTTCATCAAGAAGTTCGTCAATGGTCATCAAAGGACAATGAAATTATTGCAGCTGCT
AAACGTATGGCTGTTTTAATGGCTCGCTTGTCAGAACTTGTTCATCAAGACTCGAAAGGA
AGCAAACGTGAATTGATTGCCACTGCCAAATTAATTGCCGAAGCATCAGAAGATGTAACA
CGTATTGCTAAGGCATTGGCTAGAGAATGTACTGACAAGAGAATTAGAACAAATTTGCTA
CAAGTTTGTGAAAGAATACCAACAATTGGAACACAACTTAAAATTTTGTCAACAGTCAAA
GCAACAATGTTGGGTGCTCAAGGAAGCGATGAAGACCGTGAAGCAACAGAAATGCTTGTT
GGAAATGCTCAAAATCTCATGCAAAGCGTGAAAGAGACAGTTCGTGCCGCAGAAGGTGCT
AGTATTAAGATAAGAAGCGATCAAACAAATCATCGTCTGAGATGGATTCGTAGACAACCC
TGGCATGAGAGAATCGATCTTTCTGACGGAACCCGAGATATAATTGAGTATAAGCAATCG
TACTAA
>g13030.t1 Gene=g13030 Length=961
MPVFHTKTIESILEPVANQVSRLVILHEEAEDGNAMPDLSRPVHGVSIAVTNLVKVGRET
INSSDDQILKQDMPSALMRVETASQLLEEASSLLRADPYSGPARRKLIEGSRGILQGTSQ
LLLCFDESEVRKIVRECKRVLDYLAVSEVIDTMEDLVQFLKDLSPCLSKVSREVSNREKE
LTHQVHSEILVRCLEQVKILAPILICSMKVYIHIMEQGGKGSEEAAENRNYLAARMTDEI
QEIIRVLQLTTYDEDTSELDNLTVLKKINNAIRNKMEAAKDWLKNPYALKGGIGEKALRQ
IIDNAHKVADRCLPSDSYRIRRNADDLTAMANALCELRQQSKGTSPQAESLAREMIDKLD
ELDQNILQAVINVDKAGLQQTAHTVQGRLEQAIRWLTNPGADDKGLGQRAIALIIEEGKK
VADGLPGHQKSDILYLSGLAHTPEAQEIARKLNAKLHELKNLIQSAVVGRVVEDFIDIST
PLKQFTEAVNAPEGTPNREQNFNQKAANLQAFSDRASKTSRMVAAGGSGGNKKLAEVLLA
SAAQIDSLTPQLISAGRIRMNYPGSKAAEEHYNNLKQQYADTILRMRTLCDQATDPADFI
KASEEQMQKHTLLCEDAIRNRVPQKMVDNTSSIARLANRVLLVAKQEADNSEDPQFTSEL
LNASDKLQNSVPTMVQNAKSVATDITNGAAGANWRDANKNLLQNVRNVRNAITQQPEIPA
PPDLSALRLNAESHVPPPRPPLPREEIPPVRPPPPETDDEDEGVFKAMPTSNQPILLAAH
GLHQEVRQWSSKDNEIIAAAKRMAVLMARLSELVHQDSKGSKRELIATAKLIAEASEDVT
RIAKALARECTDKRIRTNLLQVCERIPTIGTQLKILSTVKATMLGAQGSDEDREATEMLV
GNAQNLMQSVKETVRAAEGASIKIRSDQTNHRLRWIRRQPWHERIDLSDGTRDIIEYKQS
Y
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 25 | g13030.t1 | Coils | Coil | Coil | 600 | 620 | - |
| 22 | g13030.t1 | Gene3D | G3DSA:1.20.120.230 | - | 1 | 128 | 3.5E-54 |
| 24 | g13030.t1 | Gene3D | G3DSA:1.20.120.230 | - | 129 | 257 | 1.8E-55 |
| 20 | g13030.t1 | Gene3D | G3DSA:1.20.120.810 | - | 269 | 373 | 9.0E-28 |
| 19 | g13030.t1 | Gene3D | G3DSA:1.20.120.810 | - | 381 | 594 | 2.9E-66 |
| 23 | g13030.t1 | Gene3D | G3DSA:1.20.120.230 | - | 597 | 712 | 2.8E-45 |
| 21 | g13030.t1 | Gene3D | G3DSA:1.20.120.230 | - | 756 | 943 | 3.5E-78 |
| 28 | g13030.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 734 | 750 | - |
| 29 | g13030.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 734 | 761 | - |
| 3 | g13030.t1 | PANTHER | PTHR46180:SF1 | VINCULIN | 4 | 342 | 0.0 |
| 5 | g13030.t1 | PANTHER | PTHR46180 | VINCULIN | 4 | 342 | 0.0 |
| 2 | g13030.t1 | PANTHER | PTHR46180:SF1 | VINCULIN | 336 | 942 | 0.0 |
| 4 | g13030.t1 | PANTHER | PTHR46180 | VINCULIN | 336 | 942 | 0.0 |
| 9 | g13030.t1 | PRINTS | PR00806 | Vinculin signature | 733 | 743 | 4.3E-62 |
| 7 | g13030.t1 | PRINTS | PR00806 | Vinculin signature | 748 | 761 | 4.3E-62 |
| 8 | g13030.t1 | PRINTS | PR00806 | Vinculin signature | 794 | 811 | 4.3E-62 |
| 11 | g13030.t1 | PRINTS | PR00806 | Vinculin signature | 830 | 845 | 4.3E-62 |
| 10 | g13030.t1 | PRINTS | PR00806 | Vinculin signature | 845 | 860 | 4.3E-62 |
| 12 | g13030.t1 | PRINTS | PR00806 | Vinculin signature | 864 | 885 | 4.3E-62 |
| 6 | g13030.t1 | PRINTS | PR00806 | Vinculin signature | 899 | 918 | 4.3E-62 |
| 1 | g13030.t1 | Pfam | PF01044 | Vinculin family | 3 | 942 | 0.0 |
| 27 | g13030.t1 | ProSitePatterns | PS00664 | Vinculin repeated domain signature. | 276 | 286 | - |
| 26 | g13030.t1 | ProSitePatterns | PS00664 | Vinculin repeated domain signature. | 389 | 399 | - |
| 18 | g13030.t1 | SUPERFAMILY | SSF47220 | alpha-catenin/vinculin-like | 38 | 248 | 2.07E-55 |
| 16 | g13030.t1 | SUPERFAMILY | SSF47220 | alpha-catenin/vinculin-like | 252 | 370 | 6.28E-35 |
| 14 | g13030.t1 | SUPERFAMILY | SSF47220 | alpha-catenin/vinculin-like | 382 | 519 | 3.73E-41 |
| 13 | g13030.t1 | SUPERFAMILY | SSF47220 | alpha-catenin/vinculin-like | 525 | 595 | 4.24E-17 |
| 15 | g13030.t1 | SUPERFAMILY | SSF47220 | alpha-catenin/vinculin-like | 597 | 761 | 6.28E-43 |
| 17 | g13030.t1 | SUPERFAMILY | SSF47220 | alpha-catenin/vinculin-like | 759 | 937 | 5.02E-53 |
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:0051015 | actin filament binding | MF |
| GO:0003779 | actin binding | MF |
| GO:0007155 | cell adhesion | BP |
| GO:0015629 | actin cytoskeleton | CC |
| GO:0005198 | structural molecule activity | MF |
KEGG
Orthology
- This transcript has been annotated with K05700 (vinculin)
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.
