General information for g7354.t30
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Paxillin.
Parent gene
- The parent gene g7354 is located on chr_2: 23350197..23352881 (- strand)
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.t30 | TTS | g7354.t30 | 23341880 | 23341880 |
| chr_2 | g7354 | g7354.t30 | isoform | g7354.t30 | 23342071 | 23344589 |
| chr_2 | g7354 | g7354.t30 | exon | g7354.t30.exon1 | 23342071 | 23342163 |
| chr_2 | g7354 | g7354.t30 | cds | g7354.t30.CDS1 | 23342071 | 23342163 |
| chr_2 | g7354 | g7354.t30 | exon | g7354.t30.exon2 | 23342261 | 23342409 |
| chr_2 | g7354 | g7354.t30 | cds | g7354.t30.CDS2 | 23342261 | 23342409 |
| chr_2 | g7354 | g7354.t30 | exon | g7354.t30.exon3 | 23342504 | 23342585 |
| chr_2 | g7354 | g7354.t30 | cds | g7354.t30.CDS3 | 23342504 | 23342585 |
| chr_2 | g7354 | g7354.t30 | exon | g7354.t30.exon4 | 23342877 | 23343040 |
| chr_2 | g7354 | g7354.t30 | cds | g7354.t30.CDS4 | 23342877 | 23343040 |
| chr_2 | g7354 | g7354.t30 | exon | g7354.t30.exon5 | 23343225 | 23343468 |
| chr_2 | g7354 | g7354.t30 | cds | g7354.t30.CDS5 | 23343225 | 23343306 |
| chr_2 | g7354 | g7354.t30 | exon | g7354.t30.exon6 | 23344475 | 23344589 |
| chr_2 | g7354 | g7354.t30 | TSS | g7354.t30 | 23344589 | 23344589 |
Sequences
>g7354.t30 Gene=g7354 Length=847
AGTTATAATCGAACATTTGAGACGGTAAGACAAGGAAGACCGATCAAAAAAAGTTTAATT
TATTAGCAAGAGAGAGGAGGAAAAAAATAGTTTAAAAAAGTTCACACCTCACAAGATCAA
TCCAAGTCATCAGCAGCAATCTGTTACGGATTACGCAAAACCAACAAAGGGAGTTTCACA
TTATCAAGTAGGTGAAGAGACGGTTGTTGAGACAACGTACGGCAGAGAGCCTCGTCGGGA
TCAATTAGAACTTATGCTTGGAAACTTACAAGCGGATATGTCACGTCAAGGAGTTAATAC
GCAACAAAAAGGATTCTGCTCGGGTTGTGATAAGCCGATTGTTGGACAAGTCATTACTGC
TCTCGGAAAACAATGGCATCCAGAGCACTTTACTTGTAACCACTGCAATCAGGAGCTTGG
CACTCGAAACTTCTTCGAGCGTGATGGAAATCCATATTGTGAACCAGATTACCATAATCT
TTTTAGTCCACGATGCGCTTACTGCAACGCAGCCATTCTTGATAAATGCGTTACAGCCCT
CGATAAGACTTGGCACACTGAACATTTCTTCTGTGCACAGTGTGGGCAACAATTTGGAGA
TGAAGGTTTTCATGAACGCGATGGCAAACCATATTGTCGTAAGGATTATTTTGATATGTT
TGCACCACGCTGTGCCGGATGCAATCAAGCGATCATGGAAAATTACATATCTGCATTGAA
CAGTCAATTTCATCCTGATTGCTTCGTTTGTAGAGATTGTAAGCAGGCAGTAACTGGAAA
ATCATTTTATGCTATGGAAGGCAAACCCGTCTGTCCAAAATGTGTCGGTGTCGATGAAGA
AGATTGA
>g7354.t30 Gene=g7354 Length=189
MSRQGVNTQQKGFCSGCDKPIVGQVITALGKQWHPEHFTCNHCNQELGTRNFFERDGNPY
CEPDYHNLFSPRCAYCNAAILDKCVTALDKTWHTEHFFCAQCGQQFGDEGFHERDGKPYC
RKDYFDMFAPRCAGCNQAIMENYISALNSQFHPDCFVCRDCKQAVTGKSFYAMEGKPVCP
KCVGVDEED
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g7354.t30 | CDD | cd09336 | LIM1_Paxillin_like | 14 | 66 | 2.24114E-32 |
| 13 | g7354.t30 | CDD | cd09337 | LIM2_Paxillin_like | 73 | 124 | 1.14075E-30 |
| 10 | g7354.t30 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 8 | 67 | 5.1E-26 |
| 12 | g7354.t30 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 68 | 125 | 1.0E-23 |
| 11 | g7354.t30 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 126 | 188 | 3.1E-22 |
| 4 | g7354.t30 | PANTHER | PTHR24216:SF11 | PAXILLIN | 3 | 171 | 4.6E-102 |
| 5 | g7354.t30 | PANTHER | PTHR24216 | PAXILLIN-RELATED | 3 | 171 | 4.6E-102 |
| 3 | g7354.t30 | Pfam | PF00412 | LIM domain | 14 | 68 | 3.8E-19 |
| 2 | g7354.t30 | Pfam | PF00412 | LIM domain | 73 | 128 | 3.1E-17 |
| 1 | g7354.t30 | Pfam | PF00412 | LIM domain | 132 | 182 | 4.7E-14 |
| 15 | g7354.t30 | ProSitePatterns | PS00478 | LIM zinc-binding domain signature. | 14 | 47 | - |
| 16 | g7354.t30 | ProSitePatterns | PS00478 | LIM zinc-binding domain signature. | 73 | 106 | - |
| 17 | g7354.t30 | ProSitePatterns | PS00478 | LIM zinc-binding domain signature. | 132 | 165 | - |
| 23 | g7354.t30 | ProSiteProfiles | PS50023 | LIM domain profile. | 12 | 71 | 14.652 |
| 21 | g7354.t30 | ProSiteProfiles | PS50023 | LIM domain profile. | 72 | 129 | 9.484 |
| 22 | g7354.t30 | ProSiteProfiles | PS50023 | LIM domain profile. | 130 | 189 | 12.543 |
| 18 | g7354.t30 | SMART | SM00132 | lim_4 | 13 | 64 | 7.8E-23 |
| 20 | g7354.t30 | SMART | SM00132 | lim_4 | 72 | 123 | 1.9E-18 |
| 19 | g7354.t30 | SMART | SM00132 | lim_4 | 131 | 182 | 1.3E-15 |
| 7 | g7354.t30 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 10 | 38 | 1.5E-8 |
| 6 | g7354.t30 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 40 | 102 | 9.16E-22 |
| 8 | g7354.t30 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 99 | 162 | 4.08E-21 |
| 9 | g7354.t30 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 157 | 182 | 8.2E-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
- This transcript has been annotated with K05760 (paxillin)
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.
