Gene loci information

Transcript annotation

  • This transcript has been annotated as Paxillin.

Parent gene

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.t1 isoform g7354.t1 23338245 23352881
chr_2 g7354 g7354.t1 exon g7354.t1.exon1 23338245 23338309
chr_2 g7354 g7354.t1 cds g7354.t1.CDS1 23338245 23338309
chr_2 g7354 g7354.t1 exon g7354.t1.exon2 23339264 23339329
chr_2 g7354 g7354.t1 cds g7354.t1.CDS2 23339264 23339329
chr_2 g7354 g7354.t1 exon g7354.t1.exon3 23339413 23339548
chr_2 g7354 g7354.t1 cds g7354.t1.CDS3 23339413 23339548
chr_2 g7354 g7354.t1 exon g7354.t1.exon4 23342261 23342409
chr_2 g7354 g7354.t1 cds g7354.t1.CDS4 23342261 23342409
chr_2 g7354 g7354.t1 exon g7354.t1.exon5 23342504 23342585
chr_2 g7354 g7354.t1 cds g7354.t1.CDS5 23342504 23342585
chr_2 g7354 g7354.t1 exon g7354.t1.exon6 23342877 23343040
chr_2 g7354 g7354.t1 cds g7354.t1.CDS6 23342877 23343040
chr_2 g7354 g7354.t1 exon g7354.t1.exon7 23343225 23343468
chr_2 g7354 g7354.t1 cds g7354.t1.CDS7 23343225 23343468
chr_2 g7354 g7354.t1 exon g7354.t1.exon8 23345420 23345535
chr_2 g7354 g7354.t1 cds g7354.t1.CDS8 23345420 23345535
chr_2 g7354 g7354.t1 exon g7354.t1.exon9 23346446 23346527
chr_2 g7354 g7354.t1 cds g7354.t1.CDS9 23346446 23346527
chr_2 g7354 g7354.t1 exon g7354.t1.exon10 23346594 23346718
chr_2 g7354 g7354.t1 cds g7354.t1.CDS10 23346594 23346718
chr_2 g7354 g7354.t1 exon g7354.t1.exon11 23346791 23346943
chr_2 g7354 g7354.t1 cds g7354.t1.CDS11 23346791 23346943
chr_2 g7354 g7354.t1 exon g7354.t1.exon12 23347041 23347145
chr_2 g7354 g7354.t1 cds g7354.t1.CDS12 23347041 23347145
chr_2 g7354 g7354.t1 exon g7354.t1.exon13 23352869 23352881
chr_2 g7354 g7354.t1 cds g7354.t1.CDS13 23352869 23352881
chr_2 g7354 g7354.t1 TSS g7354.t1 23353038 23353038
chr_2 g7354 g7354.t1 TTS g7354.t1 NA NA

Sequences

>g7354.t1 Gene=g7354 Length=1500
ATGGATGATTTAGATGCATTGCTTGCTGATCTTCAAAACACCGTAGTGCCAAGTGCAAAT
GGCACTACCTCATATAAGAATACCGATAGCAATACCTCTGGCTACGGATGTTTGAAAGTA
CGGCAACTGGGCAGTGAAAATGAGCATTATACACAACAGCAGAAAGTCATTTATAGCAAC
GCATCGGCAGCGAGCGGTAATAGCAATTTGAATGAATTGGATACTTTATTGAAGGACTTG
AGCAATGCTCGCTATGGTAGCGGAGCCAAAAATCAACAAAATAATGGGCTCTCGCAAGAC
ATCATCGATCAAATTCAACGACCATCAGTTGACACACTCTTGGATGAGCTAAATGTTCGT
TCAACTAGTCCCGTTTATGCTGTGCCACATGACGAGAAACCCAAAGCTGGTCGTCATGTT
ACAATCACTGTTAAACAAACAACAACTGAGCGTGTTGAAGGAGTTCCTAGTCAATCATTG
CAAGCACAAAACTCATTGAGTTATACAACATCGGCAACACCAGCTTTAACACATAATGCA
TCATCTGCAACGAAAGAATTAGATGACTTAATGGCCTCTTTATCGGATTTTAAGATCAAT
CCAAGTCATCAGCAGCAATCTGTTACGGATTACGCAAAACCAACAAAGGGAGTTTCACAT
TATCAAGTAGGTGAAGAGACGGTTGTTGAGACAACGTACGGCAGAGAGCCTCGTCGGGAT
CAATTAGAACTTATGCTTGGAAACTTACAAGCGGATATGTCACGTCAAGGAGTTAATACG
CAACAAAAAGGATTCTGCTCGGGTTGTGATAAGCCGATTGTTGGACAAGTCATTACTGCT
CTCGGAAAACAATGGCATCCAGAGCACTTTACTTGTAACCACTGCAATCAGGAGCTTGGC
ACTCGAAACTTCTTCGAGCGTGATGGAAATCCATATTGTGAACCAGATTACCATAATCTT
TTTAGTCCACGATGCGCTTACTGCAACGCAGCCATTCTTGATAAATGCGTTACAGCCCTC
GATAAGACTTGGCACACTGAACATTTCTTCTGTGCACAGTGTGGGCAACAATTTGGAGAT
GAAGGTTTTCATGAACGCGATGGCAAACCATATTGTCGTAAGGATTATTTTGATATGTTT
GCACCACGCTGTGCCGGATGCAATCAAGCGATCATGGAAAATTACATATCTGCATTGAAC
AGTCAATTTCATCCTGATTGCTTCGTTTGTAGAGACTGTCGACAACCATTCTACAGCGGT
TCATTCTTCGATCACGAGGGAATGCCATATTGTGAGACGCATTACCATGCAAAGCGTGGC
TCTTTATGTGCAGGATGCTCAAAACCGATTACGGGTCGTTGCATCACAGCCATGTTCCGC
AAATTTCATCCTGAGCATTTTGTTTGCGCTTTCTGTTTGAAACAATTGAATAAAGGTACC
TTTAAGGAACAAAATGACAAACCATACTGCCATCAATGCTTTGACAAGCTCTTTGGATAA

>g7354.t1 Gene=g7354 Length=499
MDDLDALLADLQNTVVPSANGTTSYKNTDSNTSGYGCLKVRQLGSENEHYTQQQKVIYSN
ASAASGNSNLNELDTLLKDLSNARYGSGAKNQQNNGLSQDIIDQIQRPSVDTLLDELNVR
STSPVYAVPHDEKPKAGRHVTITVKQTTTERVEGVPSQSLQAQNSLSYTTSATPALTHNA
SSATKELDDLMASLSDFKINPSHQQQSVTDYAKPTKGVSHYQVGEETVVETTYGREPRRD
QLELMLGNLQADMSRQGVNTQQKGFCSGCDKPIVGQVITALGKQWHPEHFTCNHCNQELG
TRNFFERDGNPYCEPDYHNLFSPRCAYCNAAILDKCVTALDKTWHTEHFFCAQCGQQFGD
EGFHERDGKPYCRKDYFDMFAPRCAGCNQAIMENYISALNSQFHPDCFVCRDCRQPFYSG
SFFDHEGMPYCETHYHAKRGSLCAGCSKPITGRCITAMFRKFHPEHFVCAFCLKQLNKGT
FKEQNDKPYCHQCFDKLFG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
25 g7354.t1 CDD cd09336 LIM1_Paxillin_like 266 318 4.47043E-34
22 g7354.t1 CDD cd09337 LIM2_Paxillin_like 325 376 2.01445E-33
23 g7354.t1 CDD cd09338 LIM3_Paxillin_like 384 436 6.01731E-30
24 g7354.t1 CDD cd09411 LIM4_Paxillin 443 494 1.14557E-32
21 g7354.t1 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 260 318 3.0E-25
19 g7354.t1 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 319 377 5.1E-23
20 g7354.t1 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 378 440 5.7E-27
18 g7354.t1 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 441 499 1.1E-19
5 g7354.t1 PANTHER PTHR24216:SF11 PAXILLIN 47 221 9.8E-141
9 g7354.t1 PANTHER PTHR24216 PAXILLIN-RELATED 47 221 9.8E-141
8 g7354.t1 PANTHER PTHR24216:SF11 PAXILLIN 240 415 9.8E-141
12 g7354.t1 PANTHER PTHR24216 PAXILLIN-RELATED 240 415 9.8E-141
7 g7354.t1 PANTHER PTHR24216:SF11 PAXILLIN 413 470 9.8E-141
11 g7354.t1 PANTHER PTHR24216 PAXILLIN-RELATED 413 470 9.8E-141
6 g7354.t1 PANTHER PTHR24216:SF11 PAXILLIN 471 498 9.8E-141
10 g7354.t1 PANTHER PTHR24216 PAXILLIN-RELATED 471 498 9.8E-141
2 g7354.t1 Pfam PF00412 LIM domain 266 320 1.8E-18
1 g7354.t1 Pfam PF00412 LIM domain 325 380 1.5E-16
3 g7354.t1 Pfam PF00412 LIM domain 384 438 6.3E-15
4 g7354.t1 Pfam PF00412 LIM domain 443 496 1.7E-12
28 g7354.t1 ProSitePatterns PS00478 LIM zinc-binding domain signature. 266 299 -
27 g7354.t1 ProSitePatterns PS00478 LIM zinc-binding domain signature. 384 417 -
26 g7354.t1 ProSitePatterns PS00478 LIM zinc-binding domain signature. 443 476 -
36 g7354.t1 ProSiteProfiles PS50023 LIM domain profile. 264 323 14.652
33 g7354.t1 ProSiteProfiles PS50023 LIM domain profile. 324 381 9.484
34 g7354.t1 ProSiteProfiles PS50023 LIM domain profile. 382 441 14.217
35 g7354.t1 ProSiteProfiles PS50023 LIM domain profile. 442 499 10.286
30 g7354.t1 SMART SM00132 lim_4 265 316 7.8E-23
32 g7354.t1 SMART SM00132 lim_4 324 375 1.9E-18
29 g7354.t1 SMART SM00132 lim_4 383 434 5.3E-18
31 g7354.t1 SMART SM00132 lim_4 442 493 9.7E-18
13 g7354.t1 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 262 290 2.98E-8
17 g7354.t1 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 292 354 2.98E-21
16 g7354.t1 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 351 413 1.56E-20
15 g7354.t1 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 410 472 5.5E-18
14 g7354.t1 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 469 499 3.25E-9

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

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.

Raw TPM values