General information for g3376.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g3376 is located on chr_3: 24965665..24967852 (- 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_3 | g3376 | g3376.t4 | TTS | g3376.t4 | 24962028 | 24962028 |
| chr_3 | g3376 | g3376.t4 | isoform | g3376.t4 | 24962131 | 24964293 |
| chr_3 | g3376 | g3376.t4 | exon | g3376.t4.exon1 | 24962131 | 24962428 |
| chr_3 | g3376 | g3376.t4 | cds | g3376.t4.CDS1 | 24962131 | 24962428 |
| chr_3 | g3376 | g3376.t4 | exon | g3376.t4.exon2 | 24962494 | 24962569 |
| chr_3 | g3376 | g3376.t4 | cds | g3376.t4.CDS2 | 24962494 | 24962569 |
| chr_3 | g3376 | g3376.t4 | exon | g3376.t4.exon3 | 24962686 | 24964293 |
| chr_3 | g3376 | g3376.t4 | cds | g3376.t4.CDS3 | 24962686 | 24963736 |
| chr_3 | g3376 | g3376.t4 | TSS | g3376.t4 | NA | NA |
Sequences
>g3376.t4 Gene=g3376 Length=1982
TGTTAATGATGCAATCAATTATTTAATTAAAAAAAGTTGAAAATAAAATATCAAAAATTT
AAATTTTTTTTGTTTCAAAAGTTGCGTTCAAGAATTAATCCACACAAAAAAACATTGCAT
CAAAACATCATTTTTGTGGATTATAAGTGTGCGAAAGTAAAGTGTGTTTTCAGTCAAAAG
CAAGTTAAAGAAAAAGTTTTAATATTTATAGGATATTACTATAAATTAACTGTTTTTAAA
TGTGATTAACTAACCAACACAATTAGCTAAATTTGTCGTGAATTAATTCATGACAGTGTA
GCTTAATATTTATTGGATAATTTAAAGTTGAAGAATTAAGCACGTGGAGAATATAAAAAA
TACAGGTTGATTCCGATTATGAGATAATTAAGCTCGATCCAAATGTTATTTATGAAACAG
ATGATGATGAGGATTTATTGAAAGAAGAGGAATATGTTGAGAAACAAAGATCTGCTAAAA
ATTGTGAAAATGCGGCCGAATTTGTTTTCATCGACGAAATCAACAAAACAAAAAATGAGG
AAGAAGATAATAAACAAATGGTAGATGATATCATTGATAAAAAGTCAAGTGCAGAATCAA
ACGACTTGCCTAATGAGGTAATTATAGAGCAAAAACCTCGTAAAAAACTGAATTTAGCGG
AATATAAAATTGTGCGTGCTAATAGACCTGCACCAATTGTCGAAGAATGCGAAAAAGTTG
TGCTCGAATTATGTGAAAATATTCCTGAAACTCTTCCAATTATTGAATTGCCAACTGATC
CTCGAAGCATTAAAGCTCTTCTTTCTGCTCAAAATCAGCAGCCGCAACCTCAATCAATAT
CTCAACCTGAACCAATGCAAATTGATAAAGCTTTAAATATGAAAGAAGAAGAAAAAGTTC
CAAAAGAAGTAGATCCAGATTATGAAGAAATTGTTTTAATATCAATGGAATGCAATACAG
ATATATCAATTTCACCACAAGAGAATGATGAGCAATTGGAAACAAAAGCTCCAGCCAAAT
TTCTTACAAATATCGTCAATACTATTAAGAAAGACGAATACGCAAAAACTTTGCTTAGTT
CTTCAACGACTCTCTTTTCTAGTATTAATGCAGTAGTTCATGAAAAGTGTAATTCGTTGA
ATGAAGCAACTATTGAAAATAGCAGTAGTCGCAAGAACTCAGAACATGGTGAGAACAAAA
TTATAATGCATTTGCGAAAAGATCGGATACGACCTAAATGCTCAAGTTTTGCTATGCAAA
CAGAAAATTCTCCACTCTTTCCACCGCTTTTATTGTCACCTGATATTATTTTCAATCGTA
TCAAAAATGTAAGAAATTTCCGAAGAAAATCACGAACTCGTAGTAGAAGCCGATCAAGAA
GTAGAAGTTTTAGTCCAGAAAATGATTATTATAAACGTAGCAATTATAAATATTCACGTT
CATTACACTCTTCTACTGTGAATAGTAGCGAATTTGATTCATCAGAAAGTGACAGTTCTG
CCTATAGCTCATGTCGTTCATCAGATTACGATTCAATTAGAAAATTCGATAATAGAATAT
CAGGGCAAAGATATCGTAATCATAGATCATCTAATTATACTTACGAAGAGGATTTACGTC
GAAATTTTTTAAAATATGGAACGATAAAAAAGATTTCTATTCATGCAAAGCAAGATGTTA
ATGGTAATTTACGTTTTGGTTTCATTACATTTGCTGAAGCTTCAGCTGCCTATGATGTTC
TTGATAAATTTAAACTAGATTCGTCATTGTGTGATTATGACATTCGTTTTGGAGGGAGAA
GAAGGTTTTGCAAACAGTCTTATGCTGATTTGGATTCTTTGCCTAAAGAAGATGACATTG
ATGATGTATATAATAACAACAATATTAATATTAACAACACGATGAAATCCAAAAAAGCTG
CCGAATTAAGTTTTGAGGAACTTTTAAATATTGCCCGTCAAAAAATGTGCAGAAATAACT
AA
>g3376.t4 Gene=g3376 Length=474
MVDDIIDKKSSAESNDLPNEVIIEQKPRKKLNLAEYKIVRANRPAPIVEECEKVVLELCE
NIPETLPIIELPTDPRSIKALLSAQNQQPQPQSISQPEPMQIDKALNMKEEEKVPKEVDP
DYEEIVLISMECNTDISISPQENDEQLETKAPAKFLTNIVNTIKKDEYAKTLLSSSTTLF
SSINAVVHEKCNSLNEATIENSSSRKNSEHGENKIIMHLRKDRIRPKCSSFAMQTENSPL
FPPLLLSPDIIFNRIKNVRNFRRKSRTRSRSRSRSRSFSPENDYYKRSNYKYSRSLHSST
VNSSEFDSSESDSSAYSSCRSSDYDSIRKFDNRISGQRYRNHRSSNYTYEEDLRRNFLKY
GTIKKISIHAKQDVNGNLRFGFITFAEASAAYDVLDKFKLDSSLCDYDIRFGGRRRFCKQ
SYADLDSLPKEDDIDDVYNNNNININNTMKSKKAAELSFEELLNIARQKMCRNN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g3376.t4 | Gene3D | G3DSA:3.30.70.330 | - | 344 | 421 | 8.0e-07 |
| 2 | g3376.t4 | PANTHER | PTHR15528 | PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA COACTIVATOR 1 PGC-1 -RELATED | 259 | 471 | 0.0e+00 |
| 3 | g3376.t4 | PANTHER | PTHR15528:SF11 | FI18188P1 | 259 | 471 | 0.0e+00 |
| 1 | g3376.t4 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 347 | 397 | 1.1e-04 |
| 4 | g3376.t4 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 347 | 398 | 1.0e-07 |
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:0003712 | transcription coregulator activity | MF |
| GO:0008134 | transcription factor binding | MF |
| GO:0003676 | nucleic acid binding | MF |
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.
