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.t16 TTS g7354.t16 23341880 23341880
chr_2 g7354 g7354.t16 isoform g7354.t16 23342071 23343468
chr_2 g7354 g7354.t16 exon g7354.t16.exon1 23342071 23342163
chr_2 g7354 g7354.t16 exon g7354.t16.exon2 23342261 23342409
chr_2 g7354 g7354.t16 cds g7354.t16.CDS1 23342296 23342409
chr_2 g7354 g7354.t16 exon g7354.t16.exon3 23342504 23342572
chr_2 g7354 g7354.t16 cds g7354.t16.CDS2 23342504 23342572
chr_2 g7354 g7354.t16 exon g7354.t16.exon4 23342877 23343040
chr_2 g7354 g7354.t16 cds g7354.t16.CDS3 23342877 23343040
chr_2 g7354 g7354.t16 exon g7354.t16.exon5 23343225 23343468
chr_2 g7354 g7354.t16 cds g7354.t16.CDS4 23343225 23343330
chr_2 g7354 g7354.t16 TSS g7354.t16 NA NA

Sequences

>g7354.t16 Gene=g7354 Length=719
ATCAATCCAAGTCATCAGCAGCAATCTGTTACGGATTACGCAAAACCAACAAAGGGAGTT
TCACATTATCAAGTAGGTGAAGAGACGGTTGTTGAGACAACGTACGGCAGAGAGCCTCGT
CGGGATCAATTAGAACTTATGCTTGGAAACTTACAAGCGGATATGTCACGTCAAGGAGTT
AATACGCAACAAAAAGGATTCTGCTCGGGTTGTGATAAGCCGATTGTTGGACAAGTCATT
ACTGCTCTCGGAAAACAATGGCATCCAGAGCACTTTACTTGTAACCACTGCAATCAGGAG
CTTGGCACTCGAAACTTCTTCGAGCGTGATGGAAATCCATATTGTGAACCAGATTACCAT
AATCTTTTTAGTCCACGATGCGCTTACTGCAACGCAGCCATTCTTGATCCCTCGATAAGA
CTTGGCACACTGAACATTTCTTCTGTGCACAGTGTGGGCAACAATTTGGAGATGAAGGTT
TTCATGAACGCGATGGCAAACCATATTGTCGTAAGGATTATTTTGATATGTTTGCACCAC
GCTGTGCCGGATGCAATCAAGCGATCATGGAAAATTACATATCTGCATTGAACAGTCAAT
TTCATCCTGATTGCTTCGTTTGTAGAGATTGTAAGCAGGCAGTAACTGGAAAATCATTTT
ATGCTATGGAAGGCAAACCCGTCTGTCCAAAATGTGTCGGTGTCGATGAAGAAGATTGA

>g7354.t16 Gene=g7354 Length=150
MLGNLQADMSRQGVNTQQKGFCSGCDKPIVGQVITALGKQWHPEHFTCNHCNQELGTRNF
FERDGNPYCEPDYHNLFSPRCAYCNAAILDPSIRLGTLNISSVHSVGNNLEMKVFMNAMA
NHIVVRIILICLHHAVPDAIKRSWKITYLH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g7354.t16 CDD cd09336 LIM1_Paxillin_like 22 74 4.03457E-38
6 g7354.t16 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 2 104 4.9E-27
2 g7354.t16 PANTHER PTHR24216:SF11 PAXILLIN 1 90 1.7E-49
3 g7354.t16 PANTHER PTHR24216 PAXILLIN-RELATED 1 90 1.7E-49
1 g7354.t16 Pfam PF00412 LIM domain 22 76 2.4E-19
8 g7354.t16 ProSitePatterns PS00478 LIM zinc-binding domain signature. 22 55 -
10 g7354.t16 ProSiteProfiles PS50023 LIM domain profile. 20 79 14.652
9 g7354.t16 SMART SM00132 lim_4 21 72 7.8E-23
5 g7354.t16 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 17 46 9.76E-9
4 g7354.t16 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 48 95 3.66E-15

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