General information for g7354.t39
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t39 | isoform | g7354.t39 | 23342942 | 23346943 |
| chr_2 | g7354 | g7354.t39 | exon | g7354.t39.exon1 | 23342942 | 23343040 |
| chr_2 | g7354 | g7354.t39 | cds | g7354.t39.CDS1 | 23342943 | 23343040 |
| chr_2 | g7354 | g7354.t39 | exon | g7354.t39.exon2 | 23343225 | 23343468 |
| chr_2 | g7354 | g7354.t39 | cds | g7354.t39.CDS2 | 23343225 | 23343468 |
| chr_2 | g7354 | g7354.t39 | exon | g7354.t39.exon3 | 23345420 | 23345535 |
| chr_2 | g7354 | g7354.t39 | cds | g7354.t39.CDS3 | 23345420 | 23345443 |
| chr_2 | g7354 | g7354.t39 | exon | g7354.t39.exon4 | 23346446 | 23346527 |
| chr_2 | g7354 | g7354.t39 | exon | g7354.t39.exon5 | 23346594 | 23346718 |
| chr_2 | g7354 | g7354.t39 | exon | g7354.t39.exon6 | 23346791 | 23346943 |
| chr_2 | g7354 | g7354.t39 | TSS | g7354.t39 | NA | NA |
| chr_2 | g7354 | g7354.t39 | TTS | g7354.t39 | NA | NA |
Sequences
>g7354.t39 Gene=g7354 Length=819
TACGGCAACTGGGCAGTGAAAATGAGCATTATACACAACAGCAGAAAGTCATTTATAGCA
ACGCATCGGCAGCGAGCGGTAATAGCAATTTGAATGAATTGGATACTTTATTGAAGGACT
TGAGCAATGCTCGCTATGGTAGCGGAGCCAAAAATCAACAAAATAATGGGCTCTCGCAAG
ACATCATCGATCAAATTCAACGACCATCAGTTGACACACTCTTGGATGAGCTAAATGTTC
GTTCAACTAGTCCCGTTTATGCTGTGCCACATGACGAGAAACCCAAAGCTGGTCGTCATG
TTACAATCACTGTTAAACAAACAACAACTGAGCGTGTTGAAGGAGTTCCTAGTCAATCAT
TGCAAGCACAAAACTCATTGAGTTATACAACATCGGCAACACCAGCTTTAACACATAATG
CATCATCTGCAACGAAAGAATTAGATGACTTAATGGCCTCTTTATCGGATTTTAAGATCA
ATCCAAGTCATCAGCAGCAATCTGTTACGGATTACGCAAAACCAACAAAGGGAGTTTCAC
ATTATCAAGTAGGTGAAGAGACGGTTGTTGAGACAACGTACGGCAGAGAGCCTCGTCGGG
ATCAATTAGAACTTATGCTTGGAAACTTACAAGCGGATATGTCACGTCAAGGAGTTAATA
CGCAACAAAAAGGATTCTGCTCGGGTTGTGATAAGCCGATTGTTGGACAAGTCATTACTG
CTCTCGGAAAACAATGGCATCCAGAGCACTTTACTTGTAACCACTGCAATCAGGAGCTTG
GCACTCGAAACTTCTTCGAGCGTGATGGAAATCCATATT
>g7354.t39 Gene=g7354 Length=122
MASLSDFKINPSHQQQSVTDYAKPTKGVSHYQVGEETVVETTYGREPRRDQLELMLGNLQ
ADMSRQGVNTQQKGFCSGCDKPIVGQVITALGKQWHPEHFTCNHCNQELGTRNFFERDGN
PY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g7354.t39 | CDD | cd09336 | LIM1_Paxillin_like | 76 | 122 | 2.91057E-33 |
| 5 | g7354.t39 | Gene3D | G3DSA:2.10.110.10 | Cysteine Rich Protein | 70 | 122 | 4.2E-20 |
| 9 | g7354.t39 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 23 | - |
| 2 | g7354.t39 | PANTHER | PTHR24216 | PAXILLIN-RELATED | 1 | 122 | 1.4E-38 |
| 3 | g7354.t39 | PANTHER | PTHR24216:SF27 | TRANSFORMING GROWTH FACTOR BETA-1-INDUCED TRANSCRIPT 1 PROTEIN | 1 | 122 | 1.4E-38 |
| 1 | g7354.t39 | Pfam | PF00412 | LIM domain | 76 | 122 | 9.3E-15 |
| 7 | g7354.t39 | ProSitePatterns | PS00478 | LIM zinc-binding domain signature. | 76 | 109 | - |
| 10 | g7354.t39 | ProSiteProfiles | PS50023 | LIM domain profile. | 74 | 122 | 11.939 |
| 8 | g7354.t39 | SMART | SM00132 | lim_4 | 75 | 122 | 8.1E-15 |
| 4 | g7354.t39 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 71 | 100 | 6.14E-9 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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