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.t4 isoform g7354.t4 23338245 23346943
chr_2 g7354 g7354.t4 exon g7354.t4.exon1 23338245 23338309
chr_2 g7354 g7354.t4 cds g7354.t4.CDS1 23338245 23338309
chr_2 g7354 g7354.t4 exon g7354.t4.exon2 23338823 23338870
chr_2 g7354 g7354.t4 cds g7354.t4.CDS2 23338823 23338870
chr_2 g7354 g7354.t4 exon g7354.t4.exon3 23339264 23339329
chr_2 g7354 g7354.t4 cds g7354.t4.CDS3 23339264 23339329
chr_2 g7354 g7354.t4 exon g7354.t4.exon4 23339413 23339548
chr_2 g7354 g7354.t4 cds g7354.t4.CDS4 23339413 23339548
chr_2 g7354 g7354.t4 exon g7354.t4.exon5 23342261 23342409
chr_2 g7354 g7354.t4 cds g7354.t4.CDS5 23342261 23342409
chr_2 g7354 g7354.t4 exon g7354.t4.exon6 23342504 23342585
chr_2 g7354 g7354.t4 cds g7354.t4.CDS6 23342504 23342585
chr_2 g7354 g7354.t4 exon g7354.t4.exon7 23342877 23343040
chr_2 g7354 g7354.t4 cds g7354.t4.CDS7 23342877 23343040
chr_2 g7354 g7354.t4 exon g7354.t4.exon8 23343225 23343468
chr_2 g7354 g7354.t4 cds g7354.t4.CDS8 23343225 23343468
chr_2 g7354 g7354.t4 exon g7354.t4.exon9 23345420 23345535
chr_2 g7354 g7354.t4 cds g7354.t4.CDS9 23345420 23345443
chr_2 g7354 g7354.t4 exon g7354.t4.exon10 23346446 23346527
chr_2 g7354 g7354.t4 exon g7354.t4.exon11 23346594 23346718
chr_2 g7354 g7354.t4 exon g7354.t4.exon12 23346791 23346943
chr_2 g7354 g7354.t4 TSS g7354.t4 NA NA
chr_2 g7354 g7354.t4 TTS g7354.t4 NA NA

Sequences

>g7354.t4 Gene=g7354 Length=1430
TACGGCAACTGGGCAGTGAAAATGAGCATTATACACAACAGCAGAAAGTCATTTATAGCA
ACGCATCGGCAGCGAGCGGTAATAGCAATTTGAATGAATTGGATACTTTATTGAAGGACT
TGAGCAATGCTCGCTATGGTAGCGGAGCCAAAAATCAACAAAATAATGGGCTCTCGCAAG
ACATCATCGATCAAATTCAACGACCATCAGTTGACACACTCTTGGATGAGCTAAATGTTC
GTTCAACTAGTCCCGTTTATGCTGTGCCACATGACGAGAAACCCAAAGCTGGTCGTCATG
TTACAATCACTGTTAAACAAACAACAACTGAGCGTGTTGAAGGAGTTCCTAGTCAATCAT
TGCAAGCACAAAACTCATTGAGTTATACAACATCGGCAACACCAGCTTTAACACATAATG
CATCATCTGCAACGAAAGAATTAGATGACTTAATGGCCTCTTTATCGGATTTTAAGATCA
ATCCAAGTCATCAGCAGCAATCTGTTACGGATTACGCAAAACCAACAAAGGGAGTTTCAC
ATTATCAAGTAGGTGAAGAGACGGTTGTTGAGACAACGTACGGCAGAGAGCCTCGTCGGG
ATCAATTAGAACTTATGCTTGGAAACTTACAAGCGGATATGTCACGTCAAGGAGTTAATA
CGCAACAAAAAGGATTCTGCTCGGGTTGTGATAAGCCGATTGTTGGACAAGTCATTACTG
CTCTCGGAAAACAATGGCATCCAGAGCACTTTACTTGTAACCACTGCAATCAGGAGCTTG
GCACTCGAAACTTCTTCGAGCGTGATGGAAATCCATATTGTGAACCAGATTACCATAATC
TTTTTAGTCCACGATGCGCTTACTGCAACGCAGCCATTCTTGATAAATGCGTTACAGCCC
TCGATAAGACTTGGCACACTGAACATTTCTTCTGTGCACAGTGTGGGCAACAATTTGGAG
ATGAAGGTTTTCATGAACGCGATGGCAAACCATATTGTCGTAAGGATTATTTTGATATGT
TTGCACCACGCTGTGCCGGATGCAATCAAGCGATCATGGAAAATTACATATCTGCATTGA
ACAGTCAATTTCATCCTGATTGCTTCGTTTGTAGAGACTGTCGACAACCATTCTACAGCG
GTTCATTCTTCGATCACGAGGGAATGCCATATTGTGAGACGCATTACCATGCAAAGCGTG
GCTCTTTATGTGCAGGATGCTCAAAACCGATTACGGGTCGTTGCATCACAGCCATGTTCC
GCAAATTTCATCCTGAGCATTTTGTTTGCGCTTTCTGTTTGAAACAATTGAATAAAGAAT
ATTCGGACAATAGCTACAAGAGATGTAATGATGGCGTTGTCACGGGTACCTTTAAGGAAC
AAAATGACAAACCATACTGCCATCAATGCTTTGACAAGCTCTTTGGATAA

>g7354.t4 Gene=g7354 Length=325
MASLSDFKINPSHQQQSVTDYAKPTKGVSHYQVGEETVVETTYGREPRRDQLELMLGNLQ
ADMSRQGVNTQQKGFCSGCDKPIVGQVITALGKQWHPEHFTCNHCNQELGTRNFFERDGN
PYCEPDYHNLFSPRCAYCNAAILDKCVTALDKTWHTEHFFCAQCGQQFGDEGFHERDGKP
YCRKDYFDMFAPRCAGCNQAIMENYISALNSQFHPDCFVCRDCRQPFYSGSFFDHEGMPY
CETHYHAKRGSLCAGCSKPITGRCITAMFRKFHPEHFVCAFCLKQLNKEYSDNSYKRCND
GVVTGTFKEQNDKPYCHQCFDKLFG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
24 g7354.t4 CDD cd09336 LIM1_Paxillin_like 76 128 3.2345E-32
22 g7354.t4 CDD cd09337 LIM2_Paxillin_like 135 186 1.31269E-30
23 g7354.t4 CDD cd09338 LIM3_Paxillin_like 194 246 1.06092E-27
19 g7354.t4 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 70 128 1.6E-25
18 g7354.t4 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 129 187 2.2E-23
21 g7354.t4 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 188 250 4.8E-27
20 g7354.t4 Gene3D G3DSA:2.10.110.10 Cysteine Rich Protein 251 325 3.0E-15
32 g7354.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 21 -
5 g7354.t4 PANTHER PTHR24216:SF11 PAXILLIN 50 225 1.4E-127
9 g7354.t4 PANTHER PTHR24216 PAXILLIN-RELATED 50 225 1.4E-127
7 g7354.t4 PANTHER PTHR24216:SF11 PAXILLIN 219 282 1.4E-127
11 g7354.t4 PANTHER PTHR24216 PAXILLIN-RELATED 219 282 1.4E-127
6 g7354.t4 PANTHER PTHR24216:SF11 PAXILLIN 252 283 1.4E-127
10 g7354.t4 PANTHER PTHR24216 PAXILLIN-RELATED 252 283 1.4E-127
8 g7354.t4 PANTHER PTHR24216:SF11 PAXILLIN 281 324 1.4E-127
12 g7354.t4 PANTHER PTHR24216 PAXILLIN-RELATED 281 324 1.4E-127
4 g7354.t4 Pfam PF00412 LIM domain 76 130 9.8E-19
1 g7354.t4 Pfam PF00412 LIM domain 135 190 8.0E-17
2 g7354.t4 Pfam PF00412 LIM domain 194 248 3.4E-15
3 g7354.t4 Pfam PF00412 LIM domain 253 290 1.3E-8
26 g7354.t4 ProSitePatterns PS00478 LIM zinc-binding domain signature. 76 109 -
25 g7354.t4 ProSitePatterns PS00478 LIM zinc-binding domain signature. 194 227 -
27 g7354.t4 ProSitePatterns PS00478 LIM zinc-binding domain signature. 253 286 -
36 g7354.t4 ProSiteProfiles PS50023 LIM domain profile. 74 133 14.652
35 g7354.t4 ProSiteProfiles PS50023 LIM domain profile. 134 191 9.484
34 g7354.t4 ProSiteProfiles PS50023 LIM domain profile. 192 251 14.217
33 g7354.t4 ProSiteProfiles PS50023 LIM domain profile. 252 325 9.366
31 g7354.t4 SMART SM00132 lim_4 75 126 7.8E-23
30 g7354.t4 SMART SM00132 lim_4 134 185 1.9E-18
29 g7354.t4 SMART SM00132 lim_4 193 244 5.3E-18
28 g7354.t4 SMART SM00132 lim_4 252 319 8.3E-13
17 g7354.t4 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 72 100 2.79E-8
16 g7354.t4 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 102 164 2.72E-21
13 g7354.t4 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 161 223 1.21E-20
15 g7354.t4 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 220 282 8.07E-18
14 g7354.t4 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 296 325 7.15E-5

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