Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t24 TTS g7354.t24 23341880 23341880
chr_2 g7354 g7354.t24 isoform g7354.t24 23342071 23344589
chr_2 g7354 g7354.t24 exon g7354.t24.exon1 23342071 23342163
chr_2 g7354 g7354.t24 exon g7354.t24.exon2 23342261 23342413
chr_2 g7354 g7354.t24 cds g7354.t24.CDS1 23342400 23342413
chr_2 g7354 g7354.t24 exon g7354.t24.exon3 23342504 23342585
chr_2 g7354 g7354.t24 cds g7354.t24.CDS2 23342504 23342585
chr_2 g7354 g7354.t24 exon g7354.t24.exon4 23342877 23343040
chr_2 g7354 g7354.t24 cds g7354.t24.CDS3 23342877 23343040
chr_2 g7354 g7354.t24 exon g7354.t24.exon5 23343225 23343468
chr_2 g7354 g7354.t24 cds g7354.t24.CDS4 23343225 23343330
chr_2 g7354 g7354.t24 exon g7354.t24.exon6 23344566 23344589
chr_2 g7354 g7354.t24 TSS g7354.t24 23344589 23344589

Sequences

>g7354.t24 Gene=g7354 Length=760
AGTTATAATCGAACATTTGAGACGATCAATCCAAGTCATCAGCAGCAATCTGTTACGGAT
TACGCAAAACCAACAAAGGGAGTTTCACATTATCAAGTAGGTGAAGAGACGGTTGTTGAG
ACAACGTACGGCAGAGAGCCTCGTCGGGATCAATTAGAACTTATGCTTGGAAACTTACAA
GCGGATATGTCACGTCAAGGAGTTAATACGCAACAAAAAGGATTCTGCTCGGGTTGTGAT
AAGCCGATTGTTGGACAAGTCATTACTGCTCTCGGAAAACAATGGCATCCAGAGCACTTT
ACTTGTAACCACTGCAATCAGGAGCTTGGCACTCGAAACTTCTTCGAGCGTGATGGAAAT
CCATATTGTGAACCAGATTACCATAATCTTTTTAGTCCACGATGCGCTTACTGCAACGCA
GCCATTCTTGATAAATGCGTTACAGCCCTCGATAAGACTTGGCACACTGAACATTTCTTC
TGTGCACAGTGTGGGCAACAATTTGGAGATGAAGTAAGGTTTTCATGAACGCGATGGCAA
ACCATATTGTCGTAAGGATTATTTTGATATGTTTGCACCACGCTGTGCCGGATGCAATCA
AGCGATCATGGAAAATTACATATCTGCATTGAACAGTCAATTTCATCCTGATTGCTTCGT
TTGTAGAGATTGTAAGCAGGCAGTAACTGGAAAATCATTTTATGCTATGGAAGGCAAACC
CGTCTGTCCAAAATGTGTCGGTGTCGATGAAGAAGATTGA

>g7354.t24 Gene=g7354 Length=121
MLGNLQADMSRQGVNTQQKGFCSGCDKPIVGQVITALGKQWHPEHFTCNHCNQELGTRNF
FERDGNPYCEPDYHNLFSPRCAYCNAAILDKCVTALDKTWHTEHFFCAQCGQQFGDEVRF
S

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g7354.t24 CDD cd09336 LIM1_Paxillin_like 22 74 1.95883E-34
7 g7354.t24 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 16 74 2.2E-26
8 g7354.t24 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 75 121 3.4E-16
3 g7354.t24 PANTHER PTHR24216:SF11 PAXILLIN 1 117 1.1E-68
4 g7354.t24 PANTHER PTHR24216 PAXILLIN-RELATED 1 117 1.1E-68
1 g7354.t24 Pfam PF00412 LIM domain 22 76 1.5E-19
2 g7354.t24 Pfam PF00412 LIM domain 81 117 8.3E-10
11 g7354.t24 ProSitePatterns PS00478 LIM zinc-binding domain signature. 22 55 -
10 g7354.t24 ProSitePatterns PS00478 LIM zinc-binding domain signature. 81 114 -
15 g7354.t24 ProSiteProfiles PS50023 LIM domain profile. 20 79 14.652
14 g7354.t24 ProSiteProfiles PS50023 LIM domain profile. 80 121 7.781
12 g7354.t24 SMART SM00132 lim_4 21 72 7.8E-23
13 g7354.t24 SMART SM00132 lim_4 80 120 0.0025
6 g7354.t24 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 17 46 5.99E-9
5 g7354.t24 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 48 110 6.95E-22

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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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