General information for g7354.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Paxillin.
Parent gene
- The parent gene g7354 is located on chr_2: 23350197..23352881 (- 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_2 | g7354 | g7354.t3 | TTS | g7354.t3 | 23341880 | 23341880 |
| chr_2 | g7354 | g7354.t3 | isoform | g7354.t3 | 23342071 | 23350260 |
| chr_2 | g7354 | g7354.t3 | exon | g7354.t3.exon1 | 23342071 | 23342163 |
| chr_2 | g7354 | g7354.t3 | cds | g7354.t3.CDS1 | 23342071 | 23342163 |
| chr_2 | g7354 | g7354.t3 | exon | g7354.t3.exon2 | 23342261 | 23342409 |
| chr_2 | g7354 | g7354.t3 | cds | g7354.t3.CDS2 | 23342261 | 23342409 |
| chr_2 | g7354 | g7354.t3 | exon | g7354.t3.exon3 | 23342504 | 23342585 |
| chr_2 | g7354 | g7354.t3 | cds | g7354.t3.CDS3 | 23342504 | 23342585 |
| chr_2 | g7354 | g7354.t3 | exon | g7354.t3.exon4 | 23342877 | 23343040 |
| chr_2 | g7354 | g7354.t3 | cds | g7354.t3.CDS4 | 23342877 | 23343040 |
| chr_2 | g7354 | g7354.t3 | exon | g7354.t3.exon5 | 23343225 | 23343468 |
| chr_2 | g7354 | g7354.t3 | cds | g7354.t3.CDS5 | 23343225 | 23343468 |
| chr_2 | g7354 | g7354.t3 | exon | g7354.t3.exon6 | 23345420 | 23345535 |
| chr_2 | g7354 | g7354.t3 | cds | g7354.t3.CDS6 | 23345420 | 23345535 |
| chr_2 | g7354 | g7354.t3 | exon | g7354.t3.exon7 | 23346446 | 23346527 |
| chr_2 | g7354 | g7354.t3 | cds | g7354.t3.CDS7 | 23346446 | 23346527 |
| chr_2 | g7354 | g7354.t3 | exon | g7354.t3.exon8 | 23346594 | 23346718 |
| chr_2 | g7354 | g7354.t3 | cds | g7354.t3.CDS8 | 23346594 | 23346718 |
| chr_2 | g7354 | g7354.t3 | exon | g7354.t3.exon9 | 23346791 | 23346943 |
| chr_2 | g7354 | g7354.t3 | cds | g7354.t3.CDS9 | 23346791 | 23346943 |
| chr_2 | g7354 | g7354.t3 | exon | g7354.t3.exon10 | 23347041 | 23347145 |
| chr_2 | g7354 | g7354.t3 | cds | g7354.t3.CDS10 | 23347041 | 23347145 |
| chr_2 | g7354 | g7354.t3 | exon | g7354.t3.exon11 | 23350197 | 23350260 |
| chr_2 | g7354 | g7354.t3 | cds | g7354.t3.CDS11 | 23350197 | 23350260 |
| chr_2 | g7354 | g7354.t3 | TSS | g7354.t3 | 23350448 | 23350448 |
Sequences
>g7354.t3 Gene=g7354 Length=1377
ATGAATGGAACAACATTAATTGATGAAAATGTGCAGCCAGTATCAAAGTTTGAAGTTTAT
TTGAATGCATTGCTTGCTGATCTTCAAAACACCGTAGTGCCAAGTGCAAATGGCACTACC
TCATATAAGAATACCGATAGCAATACCTCTGGCTACGGATGTTTGAAAGTACGGCAACTG
GGCAGTGAAAATGAGCATTATACACAACAGCAGAAAGTCATTTATAGCAACGCATCGGCA
GCGAGCGGTAATAGCAATTTGAATGAATTGGATACTTTATTGAAGGACTTGAGCAATGCT
CGCTATGGTAGCGGAGCCAAAAATCAACAAAATAATGGGCTCTCGCAAGACATCATCGAT
CAAATTCAACGACCATCAGTTGACACACTCTTGGATGAGCTAAATGTTCGTTCAACTAGT
CCCGTTTATGCTGTGCCACATGACGAGAAACCCAAAGCTGGTCGTCATGTTACAATCACT
GTTAAACAAACAACAACTGAGCGTGTTGAAGGAGTTCCTAGTCAATCATTGCAAGCACAA
AACTCATTGAGTTATACAACATCGGCAACACCAGCTTTAACACATAATGCATCATCTGCA
ACGAAAGAATTAGATGACTTAATGGCCTCTTTATCGGATTTTAAGATCAATCCAAGTCAT
CAGCAGCAATCTGTTACGGATTACGCAAAACCAACAAAGGGAGTTTCACATTATCAAGTA
GGTGAAGAGACGGTTGTTGAGACAACGTACGGCAGAGAGCCTCGTCGGGATCAATTAGAA
CTTATGCTTGGAAACTTACAAGCGGATATGTCACGTCAAGGAGTTAATACGCAACAAAAA
GGATTCTGCTCGGGTTGTGATAAGCCGATTGTTGGACAAGTCATTACTGCTCTCGGAAAA
CAATGGCATCCAGAGCACTTTACTTGTAACCACTGCAATCAGGAGCTTGGCACTCGAAAC
TTCTTCGAGCGTGATGGAAATCCATATTGTGAACCAGATTACCATAATCTTTTTAGTCCA
CGATGCGCTTACTGCAACGCAGCCATTCTTGATAAATGCGTTACAGCCCTCGATAAGACT
TGGCACACTGAACATTTCTTCTGTGCACAGTGTGGGCAACAATTTGGAGATGAAGGTTTT
CATGAACGCGATGGCAAACCATATTGTCGTAAGGATTATTTTGATATGTTTGCACCACGC
TGTGCCGGATGCAATCAAGCGATCATGGAAAATTACATATCTGCATTGAACAGTCAATTT
CATCCTGATTGCTTCGTTTGTAGAGATTGTAAGCAGGCAGTAACTGGAAAATCATTTTAT
GCTATGGAAGGCAAACCCGTCTGTCCAAAATGTGTCGGTGTCGATGAAGAAGATTGA
>g7354.t3 Gene=g7354 Length=458
MNGTTLIDENVQPVSKFEVYLNALLADLQNTVVPSANGTTSYKNTDSNTSGYGCLKVRQL
GSENEHYTQQQKVIYSNASAASGNSNLNELDTLLKDLSNARYGSGAKNQQNNGLSQDIID
QIQRPSVDTLLDELNVRSTSPVYAVPHDEKPKAGRHVTITVKQTTTERVEGVPSQSLQAQ
NSLSYTTSATPALTHNASSATKELDDLMASLSDFKINPSHQQQSVTDYAKPTKGVSHYQV
GEETVVETTYGREPRRDQLELMLGNLQADMSRQGVNTQQKGFCSGCDKPIVGQVITALGK
QWHPEHFTCNHCNQELGTRNFFERDGNPYCEPDYHNLFSPRCAYCNAAILDKCVTALDKT
WHTEHFFCAQCGQQFGDEGFHERDGKPYCRKDYFDMFAPRCAGCNQAIMENYISALNSQF
HPDCFVCRDCKQAVTGKSFYAMEGKPVCPKCVGVDEED
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g7354.t3 | CDD | cd09336 | LIM1_Paxillin_like | 283 | 335 | 5.88601E-36 |
| 14 | g7354.t3 | CDD | cd09337 | LIM2_Paxillin_like | 342 | 393 | 9.63794E-36 |
| 15 | g7354.t3 | CDD | cd09338 | LIM3_Paxillin_like | 401 | 448 | 2.37369E-20 |
| 12 | g7354.t3 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 277 | 335 | 2.9E-25 |
| 13 | g7354.t3 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 336 | 394 | 4.8E-23 |
| 11 | g7354.t3 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 395 | 457 | 9.4E-22 |
| 4 | g7354.t3 | PANTHER | PTHR24216:SF11 | PAXILLIN | 2 | 239 | 1.1E-119 |
| 6 | g7354.t3 | PANTHER | PTHR24216 | PAXILLIN-RELATED | 2 | 239 | 1.1E-119 |
| 5 | g7354.t3 | PANTHER | PTHR24216:SF11 | PAXILLIN | 257 | 440 | 1.1E-119 |
| 7 | g7354.t3 | PANTHER | PTHR24216 | PAXILLIN-RELATED | 257 | 440 | 1.1E-119 |
| 2 | g7354.t3 | Pfam | PF00412 | LIM domain | 283 | 337 | 1.6E-18 |
| 3 | g7354.t3 | Pfam | PF00412 | LIM domain | 342 | 397 | 1.3E-16 |
| 1 | g7354.t3 | Pfam | PF00412 | LIM domain | 401 | 451 | 2.1E-13 |
| 17 | g7354.t3 | ProSitePatterns | PS00478 | LIM zinc-binding domain signature. | 283 | 316 | - |
| 18 | g7354.t3 | ProSitePatterns | PS00478 | LIM zinc-binding domain signature. | 401 | 434 | - |
| 24 | g7354.t3 | ProSiteProfiles | PS50023 | LIM domain profile. | 281 | 340 | 14.652 |
| 23 | g7354.t3 | ProSiteProfiles | PS50023 | LIM domain profile. | 341 | 398 | 9.484 |
| 22 | g7354.t3 | ProSiteProfiles | PS50023 | LIM domain profile. | 399 | 458 | 12.543 |
| 20 | g7354.t3 | SMART | SM00132 | lim_4 | 282 | 333 | 7.8E-23 |
| 19 | g7354.t3 | SMART | SM00132 | lim_4 | 341 | 392 | 1.9E-18 |
| 21 | g7354.t3 | SMART | SM00132 | lim_4 | 400 | 451 | 1.3E-15 |
| 8 | g7354.t3 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 279 | 307 | 4.96E-8 |
| 10 | g7354.t3 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 309 | 371 | 5.02E-21 |
| 9 | g7354.t3 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 368 | 431 | 2.91E-20 |
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:0007160 | cell-matrix adhesion | BP |
| GO:0005856 | cytoskeleton | CC |
KEGG
Orthology
- This transcript has been annotated with K05760 (paxillin)
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. There were no conditions that were differentially expressed