General information for g7354.t34
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.t34 | TTS | g7354.t34 | 23341880 | 23341880 |
| chr_2 | g7354 | g7354.t34 | isoform | g7354.t34 | 23342071 | 23344589 |
| chr_2 | g7354 | g7354.t34 | exon | g7354.t34.exon1 | 23342071 | 23342163 |
| chr_2 | g7354 | g7354.t34 | cds | g7354.t34.CDS1 | 23342071 | 23342163 |
| chr_2 | g7354 | g7354.t34 | exon | g7354.t34.exon2 | 23342261 | 23342412 |
| chr_2 | g7354 | g7354.t34 | cds | g7354.t34.CDS2 | 23342261 | 23342412 |
| chr_2 | g7354 | g7354.t34 | exon | g7354.t34.exon3 | 23342504 | 23342585 |
| chr_2 | g7354 | g7354.t34 | cds | g7354.t34.CDS3 | 23342504 | 23342585 |
| chr_2 | g7354 | g7354.t34 | exon | g7354.t34.exon4 | 23342877 | 23343040 |
| chr_2 | g7354 | g7354.t34 | cds | g7354.t34.CDS4 | 23342877 | 23343040 |
| chr_2 | g7354 | g7354.t34 | exon | g7354.t34.exon5 | 23343225 | 23343468 |
| chr_2 | g7354 | g7354.t34 | cds | g7354.t34.CDS5 | 23343225 | 23343330 |
| chr_2 | g7354 | g7354.t34 | exon | g7354.t34.exon6 | 23344566 | 23344589 |
| chr_2 | g7354 | g7354.t34 | TSS | g7354.t34 | 23344589 | 23344589 |
Sequences
>g7354.t34 Gene=g7354 Length=759
AGTTATAATCGAACATTTGAGACGATCAATCCAAGTCATCAGCAGCAATCTGTTACGGAT
TACGCAAAACCAACAAAGGGAGTTTCACATTATCAAGTAGGTGAAGAGACGGTTGTTGAG
ACAACGTACGGCAGAGAGCCTCGTCGGGATCAATTAGAACTTATGCTTGGAAACTTACAA
GCGGATATGTCACGTCAAGGAGTTAATACGCAACAAAAAGGATTCTGCTCGGGTTGTGAT
AAGCCGATTGTTGGACAAGTCATTACTGCTCTCGGAAAACAATGGCATCCAGAGCACTTT
ACTTGTAACCACTGCAATCAGGAGCTTGGCACTCGAAACTTCTTCGAGCGTGATGGAAAT
CCATATTGTGAACCAGATTACCATAATCTTTTTAGTCCACGATGCGCTTACTGCAACGCA
GCCATTCTTGATAAATGCGTTACAGCCCTCGATAAGACTTGGCACACTGAACATTTCTTC
TGTGCACAGTGTGGGCAACAATTTGGAGATGAAGAAGGTTTTCATGAACGCGATGGCAAA
CCATATTGTCGTAAGGATTATTTTGATATGTTTGCACCACGCTGTGCCGGATGCAATCAA
GCGATCATGGAAAATTACATATCTGCATTGAACAGTCAATTTCATCCTGATTGCTTCGTT
TGTAGAGATTGTAAGCAGGCAGTAACTGGAAAATCATTTTATGCTATGGAAGGCAAACCC
GTCTGTCCAAAATGTGTCGGTGTCGATGAAGAAGATTGA
>g7354.t34 Gene=g7354 Length=198
MLGNLQADMSRQGVNTQQKGFCSGCDKPIVGQVITALGKQWHPEHFTCNHCNQELGTRNF
FERDGNPYCEPDYHNLFSPRCAYCNAAILDKCVTALDKTWHTEHFFCAQCGQQFGDEEGF
HERDGKPYCRKDYFDMFAPRCAGCNQAIMENYISALNSQFHPDCFVCRDCKQAVTGKSFY
AMEGKPVCPKCVGVDEED
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g7354.t34 | CDD | cd09336 | LIM1_Paxillin_like | 22 | 74 | 8.66866E-33 |
| 11 | g7354.t34 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 16 | 75 | 5.9E-26 |
| 10 | g7354.t34 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 76 | 133 | 1.3E-22 |
| 12 | g7354.t34 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 134 | 197 | 2.0E-22 |
| 4 | g7354.t34 | PANTHER | PTHR24216:SF11 | PAXILLIN | 1 | 180 | 1.6E-106 |
| 5 | g7354.t34 | PANTHER | PTHR24216 | PAXILLIN-RELATED | 1 | 180 | 1.6E-106 |
| 2 | g7354.t34 | Pfam | PF00412 | LIM domain | 22 | 76 | 4.2E-19 |
| 1 | g7354.t34 | Pfam | PF00412 | LIM domain | 81 | 137 | 4.8E-17 |
| 3 | g7354.t34 | Pfam | PF00412 | LIM domain | 141 | 191 | 5.1E-14 |
| 16 | g7354.t34 | ProSitePatterns | PS00478 | LIM zinc-binding domain signature. | 22 | 55 | - |
| 15 | g7354.t34 | ProSitePatterns | PS00478 | LIM zinc-binding domain signature. | 81 | 114 | - |
| 14 | g7354.t34 | ProSitePatterns | PS00478 | LIM zinc-binding domain signature. | 141 | 174 | - |
| 22 | g7354.t34 | ProSiteProfiles | PS50023 | LIM domain profile. | 20 | 79 | 14.652 |
| 21 | g7354.t34 | ProSiteProfiles | PS50023 | LIM domain profile. | 80 | 138 | 9.435 |
| 20 | g7354.t34 | ProSiteProfiles | PS50023 | LIM domain profile. | 139 | 198 | 12.543 |
| 19 | g7354.t34 | SMART | SM00132 | lim_4 | 21 | 72 | 7.8E-23 |
| 17 | g7354.t34 | SMART | SM00132 | lim_4 | 80 | 132 | 3.3E-18 |
| 18 | g7354.t34 | SMART | SM00132 | lim_4 | 140 | 191 | 1.3E-15 |
| 6 | g7354.t34 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 18 | 46 | 1.43E-8 |
| 8 | g7354.t34 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 48 | 110 | 1.28E-21 |
| 9 | g7354.t34 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 107 | 171 | 2.5E-19 |
| 7 | g7354.t34 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 166 | 191 | 9.6E-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. There were no conditions that were differentially expressed