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.t7 TTS g7354.t7 23341880 23341880
chr_2 g7354 g7354.t7 isoform g7354.t7 23341882 23343466
chr_2 g7354 g7354.t7 exon g7354.t7.exon1 23341882 23342151
chr_2 g7354 g7354.t7 cds g7354.t7.CDS1 23342071 23342151
chr_2 g7354 g7354.t7 exon g7354.t7.exon2 23342261 23342409
chr_2 g7354 g7354.t7 cds g7354.t7.CDS2 23342261 23342409
chr_2 g7354 g7354.t7 exon g7354.t7.exon3 23342504 23342585
chr_2 g7354 g7354.t7 cds g7354.t7.CDS3 23342504 23342585
chr_2 g7354 g7354.t7 exon g7354.t7.exon4 23342877 23343040
chr_2 g7354 g7354.t7 cds g7354.t7.CDS4 23342877 23343040
chr_2 g7354 g7354.t7 exon g7354.t7.exon5 23343225 23343466
chr_2 g7354 g7354.t7 cds g7354.t7.CDS5 23343225 23343330
chr_2 g7354 g7354.t7 TSS g7354.t7 NA NA

Sequences

>g7354.t7 Gene=g7354 Length=907
CAATCCAAGTCATCAGCAGCAATCTGTTACGGATTACGCAAAACCAACAAAGGGAGTTTC
ACATTATCAAGTAGGTGAAGAGACGGTTGTTGAGACAACGTACGGCAGAGAGCCTCGTCG
GGATCAATTAGAACTTATGCTTGGAAACTTACAAGCGGATATGTCACGTCAAGGAGTTAA
TACGCAACAAAAAGGATTCTGCTCGGGTTGTGATAAGCCGATTGTTGGACAAGTCATTAC
TGCTCTCGGAAAACAATGGCATCCAGAGCACTTTACTTGTAACCACTGCAATCAGGAGCT
TGGCACTCGAAACTTCTTCGAGCGTGATGGAAATCCATATTGTGAACCAGATTACCATAA
TCTTTTTAGTCCACGATGCGCTTACTGCAACGCAGCCATTCTTGATAAATGCGTTACAGC
CCTCGATAAGACTTGGCACACTGAACATTTCTTCTGTGCACAGTGTGGGCAACAATTTGG
AGATGAAGGTTTTCATGAACGCGATGGCAAACCATATTGTCGTAAGGATTATTTTGATAT
GTTTGCACCACGCTGTGCCGGATGCAATCAAGCGATCATGGAAAATTACATATCTGCATT
GAACAGTCAATTTCATCCTGATTGCTTCGTTTGTAGAGCAGTAACTGGAAAATCATTTTA
TGCTATGGAAGGCAAACCCGTCTGTCCAAAATGTGTCGGTGTCGATGAAGAAGATTGAGA
TGTTTAATGTTGTACAAAAAATCCAAATAAAAAAATATTTTTGTGTCCTCACCCACACTC
TCTTTTCCTCAAAACAAAAAAATAATATACAACGCTAAAATTACCATTATTGTTTATATT
TTGTTAATTTTTTTGCATTCTCTAAGTCAAGTTATAAAAATATGTTCAATAAAAAAATGA
AAAGAAA

>g7354.t7 Gene=g7354 Length=193
MLGNLQADMSRQGVNTQQKGFCSGCDKPIVGQVITALGKQWHPEHFTCNHCNQELGTRNF
FERDGNPYCEPDYHNLFSPRCAYCNAAILDKCVTALDKTWHTEHFFCAQCGQQFGDEGFH
ERDGKPYCRKDYFDMFAPRCAGCNQAIMENYISALNSQFHPDCFVCRAVTGKSFYAMEGK
PVCPKCVGVDEED

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g7354.t7 CDD cd09336 LIM1_Paxillin_like 22 74 4.76008E-33
12 g7354.t7 CDD cd09337 LIM2_Paxillin_like 81 132 2.07985E-31
11 g7354.t7 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 16 75 5.8E-26
10 g7354.t7 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 76 133 1.1E-23
9 g7354.t7 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 134 192 1.9E-17
4 g7354.t7 PANTHER PTHR24216:SF11 PAXILLIN 1 178 3.3E-108
5 g7354.t7 PANTHER PTHR24216 PAXILLIN-RELATED 1 178 3.3E-108
1 g7354.t7 Pfam PF00412 LIM domain 22 76 4.0E-19
2 g7354.t7 Pfam PF00412 LIM domain 81 136 3.3E-17
3 g7354.t7 Pfam PF00412 LIM domain 140 186 4.9E-9
15 g7354.t7 ProSitePatterns PS00478 LIM zinc-binding domain signature. 22 55 -
14 g7354.t7 ProSitePatterns PS00478 LIM zinc-binding domain signature. 81 114 -
21 g7354.t7 ProSiteProfiles PS50023 LIM domain profile. 20 79 14.652
19 g7354.t7 ProSiteProfiles PS50023 LIM domain profile. 80 138 11.88
20 g7354.t7 ProSiteProfiles PS50023 LIM domain profile. 139 193 6.663
17 g7354.t7 SMART SM00132 lim_4 21 72 7.8E-23
16 g7354.t7 SMART SM00132 lim_4 80 131 1.9E-18
18 g7354.t7 SMART SM00132 lim_4 139 186 1.5E-9
7 g7354.t7 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 18 46 1.36E-8
8 g7354.t7 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 48 110 1.06E-21
6 g7354.t7 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 107 167 1.2E-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

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