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.t9 TTS g7354.t9 23341880 23341880
chr_2 g7354 g7354.t9 isoform g7354.t9 23341882 23344589
chr_2 g7354 g7354.t9 exon g7354.t9.exon1 23341882 23342163
chr_2 g7354 g7354.t9 exon g7354.t9.exon2 23342261 23342401
chr_2 g7354 g7354.t9 cds g7354.t9.CDS1 23342373 23342401
chr_2 g7354 g7354.t9 exon g7354.t9.exon3 23342504 23342585
chr_2 g7354 g7354.t9 cds g7354.t9.CDS2 23342504 23342585
chr_2 g7354 g7354.t9 exon g7354.t9.exon4 23342877 23343040
chr_2 g7354 g7354.t9 cds g7354.t9.CDS3 23342877 23343040
chr_2 g7354 g7354.t9 exon g7354.t9.exon5 23343225 23343468
chr_2 g7354 g7354.t9 cds g7354.t9.CDS4 23343225 23343330
chr_2 g7354 g7354.t9 exon g7354.t9.exon6 23344566 23344589
chr_2 g7354 g7354.t9 TSS g7354.t9 23344589 23344589

Sequences

>g7354.t9 Gene=g7354 Length=937
AGTTATAATCGAACATTTGAGACGATCAATCCAAGTCATCAGCAGCAATCTGTTACGGAT
TACGCAAAACCAACAAAGGGAGTTTCACATTATCAAGTAGGTGAAGAGACGGTTGTTGAG
ACAACGTACGGCAGAGAGCCTCGTCGGGATCAATTAGAACTTATGCTTGGAAACTTACAA
GCGGATATGTCACGTCAAGGAGTTAATACGCAACAAAAAGGATTCTGCTCGGGTTGTGAT
AAGCCGATTGTTGGACAAGTCATTACTGCTCTCGGAAAACAATGGCATCCAGAGCACTTT
ACTTGTAACCACTGCAATCAGGAGCTTGGCACTCGAAACTTCTTCGAGCGTGATGGAAAT
CCATATTGTGAACCAGATTACCATAATCTTTTTAGTCCACGATGCGCTTACTGCAACGCA
GCCATTCTTGATAAATGCGTTACAGCCCTCGATAAGACTTGGCACACTGAACATTTCTTC
TGTGCACAGTGTGGGCAACAATTTGGAGATGAAGGAACGCGATGGCAAACCATATTGTCG
TAAGGATTATTTTGATATGTTTGCACCACGCTGTGCCGGATGCAATCAAGCGATCATGGA
AAATTACATATCTGCATTGAACAGTCAATTTCATCCTGATTGCTTCGTTTGTAGAGATTG
TAAGCAGGCAGTAACTGGAAAATCATTTTATGCTATGGAAGGCAAACCCGTCTGTCCAAA
ATGTGTCGGTGTCGATGAAGAAGATTGAGATGTTTAATGTTGTACAAAAAATCCAAATAA
AAAAATATTTTTGTGTCCTCACCCACACTCTCTTTTCCTCAAAACAAAAAAATAATATAC
AACGCTAAAATTACCATTATTGTTTATATTTTGTTAATTTTTTTGCATTCTCTAAGTCAA
GTTATAAAAATATGTTCAATAAAAAAATGAAAAGAAA

>g7354.t9 Gene=g7354 Length=126
MLGNLQADMSRQGVNTQQKGFCSGCDKPIVGQVITALGKQWHPEHFTCNHCNQELGTRNF
FERDGNPYCEPDYHNLFSPRCAYCNAAILDKCVTALDKTWHTEHFFCAQCGQQFGDEGTR
WQTILS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g7354.t9 CDD cd09336 LIM1_Paxillin_like 22 74 1.04842E-34
8 g7354.t9 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 16 74 2.5E-26
7 g7354.t9 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 75 122 4.9E-16
3 g7354.t9 PANTHER PTHR24216:SF11 PAXILLIN 1 118 1.6E-69
4 g7354.t9 PANTHER PTHR24216 PAXILLIN-RELATED 1 118 1.6E-69
1 g7354.t9 Pfam PF00412 LIM domain 22 76 1.6E-19
2 g7354.t9 Pfam PF00412 LIM domain 81 119 4.8E-10
11 g7354.t9 ProSitePatterns PS00478 LIM zinc-binding domain signature. 22 55 -
10 g7354.t9 ProSitePatterns PS00478 LIM zinc-binding domain signature. 81 114 -
14 g7354.t9 ProSiteProfiles PS50023 LIM domain profile. 20 79 14.652
15 g7354.t9 ProSiteProfiles PS50023 LIM domain profile. 80 126 7.366
13 g7354.t9 SMART SM00132 lim_4 21 72 7.8E-23
12 g7354.t9 SMART SM00132 lim_4 80 123 8.8E-4
6 g7354.t9 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 17 46 6.49E-9
5 g7354.t9 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 48 110 8.11E-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