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.t14 TTS g7354.t14 23341880 23341880
chr_2 g7354 g7354.t14 isoform g7354.t14 23342071 23343370
chr_2 g7354 g7354.t14 exon g7354.t14.exon1 23342071 23342409
chr_2 g7354 g7354.t14 cds g7354.t14.CDS1 23342213 23342409
chr_2 g7354 g7354.t14 exon g7354.t14.exon2 23342504 23342585
chr_2 g7354 g7354.t14 cds g7354.t14.CDS2 23342504 23342585
chr_2 g7354 g7354.t14 exon g7354.t14.exon3 23342877 23343040
chr_2 g7354 g7354.t14 cds g7354.t14.CDS3 23342877 23343040
chr_2 g7354 g7354.t14 exon g7354.t14.exon4 23343225 23343370
chr_2 g7354 g7354.t14 cds g7354.t14.CDS4 23343225 23343330
chr_2 g7354 g7354.t14 TSS g7354.t14 NA NA

Sequences

>g7354.t14 Gene=g7354 Length=731
AACGTACGGCAGAGAGCCTCGTCGGGATCAATTAGAACTTATGCTTGGAAACTTACAAGC
GGATATGTCACGTCAAGGAGTTAATACGCAACAAAAAGGATTCTGCTCGGGTTGTGATAA
GCCGATTGTTGGACAAGTCATTACTGCTCTCGGAAAACAATGGCATCCAGAGCACTTTAC
TTGTAACCACTGCAATCAGGAGCTTGGCACTCGAAACTTCTTCGAGCGTGATGGAAATCC
ATATTGTGAACCAGATTACCATAATCTTTTTAGTCCACGATGCGCTTACTGCAACGCAGC
CATTCTTGATAAATGCGTTACAGCCCTCGATAAGACTTGGCACACTGAACATTTCTTCTG
TGCACAGTGTGGGCAACAATTTGGAGATGAAGGTTTTCATGAACGCGATGGCAAACCATA
TTGTCGTAAGGATTATTTTGATATGTTTGCACCACGCTGTGCCGGATGCAATCAAGCGAT
CATGGAAAATTACATATCTGCATTGAACAGTCAATTTCATCCTGATTGCTTCGTTTGTAG
AGTAAGTTTGTCATTATTTTATTACCAATACACACATACGAGCACGTAGCTACCACGATA
AGAAAAAAACATAACCACGTCGTTGTTTTTCTCAATAGGATTGTAAGCAGGCAGTAACTG
GAAAATCATTTTATGCTATGGAAGGCAAACCCGTCTGTCCAAAATGTGTCGGTGTCGATG
AAGAAGATTGA

>g7354.t14 Gene=g7354 Length=182
MLGNLQADMSRQGVNTQQKGFCSGCDKPIVGQVITALGKQWHPEHFTCNHCNQELGTRNF
FERDGNPYCEPDYHNLFSPRCAYCNAAILDKCVTALDKTWHTEHFFCAQCGQQFGDEGFH
ERDGKPYCRKDYFDMFAPRCAGCNQAIMENYISALNSQFHPDCFVCRVSLSLFYYQYTHT
ST

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g7354.t14 CDD cd09336 LIM1_Paxillin_like 22 74 1.18362E-33
12 g7354.t14 CDD cd09337 LIM2_Paxillin_like 81 132 5.55795E-32
9 g7354.t14 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 16 74 5.4E-26
11 g7354.t14 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 75 133 9.1E-24
10 g7354.t14 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 134 179 2.9E-14
4 g7354.t14 PANTHER PTHR24216:SF11 PAXILLIN 1 173 6.4E-109
5 g7354.t14 PANTHER PTHR24216 PAXILLIN-RELATED 1 173 6.4E-109
1 g7354.t14 Pfam PF00412 LIM domain 22 76 3.6E-19
2 g7354.t14 Pfam PF00412 LIM domain 81 136 2.9E-17
3 g7354.t14 Pfam PF00412 LIM domain 140 167 6.8E-7
15 g7354.t14 ProSitePatterns PS00478 LIM zinc-binding domain signature. 22 55 -
14 g7354.t14 ProSitePatterns PS00478 LIM zinc-binding domain signature. 81 114 -
21 g7354.t14 ProSiteProfiles PS50023 LIM domain profile. 20 79 14.652
20 g7354.t14 ProSiteProfiles PS50023 LIM domain profile. 80 138 11.88
19 g7354.t14 ProSiteProfiles PS50023 LIM domain profile. 139 182 6.039
17 g7354.t14 SMART SM00132 lim_4 21 72 7.8E-23
16 g7354.t14 SMART SM00132 lim_4 80 131 1.9E-18
18 g7354.t14 SMART SM00132 lim_4 139 179 0.01
7 g7354.t14 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 18 46 1.21E-8
8 g7354.t14 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 48 110 9.16E-22
6 g7354.t14 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 107 167 7.14E-21

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