General information for g10957.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative CUGBP Elav-like family member 1.
Parent gene
- The parent gene g10957 is located on chr_1: 13020051..13021608 (+ 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_1 | g10957 | g10957.t2 | isoform | g10957.t2 | 13016854 | 13020051 |
| chr_1 | g10957 | g10957.t2 | exon | g10957.t2.exon1 | 13016854 | 13017004 |
| chr_1 | g10957 | g10957.t2 | cds | g10957.t2.CDS1 | 13016854 | 13017004 |
| chr_1 | g10957 | g10957.t2 | TSS | g10957.t2 | 13016863 | 13016863 |
| chr_1 | g10957 | g10957.t2 | exon | g10957.t2.exon2 | 13017145 | 13017323 |
| chr_1 | g10957 | g10957.t2 | cds | g10957.t2.CDS2 | 13017145 | 13017323 |
| chr_1 | g10957 | g10957.t2 | exon | g10957.t2.exon3 | 13017396 | 13017711 |
| chr_1 | g10957 | g10957.t2 | cds | g10957.t2.CDS3 | 13017396 | 13017711 |
| chr_1 | g10957 | g10957.t2 | exon | g10957.t2.exon4 | 13019346 | 13019564 |
| chr_1 | g10957 | g10957.t2 | cds | g10957.t2.CDS4 | 13019346 | 13019564 |
| chr_1 | g10957 | g10957.t2 | exon | g10957.t2.exon5 | 13019624 | 13020051 |
| chr_1 | g10957 | g10957.t2 | cds | g10957.t2.CDS5 | 13019624 | 13020051 |
| chr_1 | g10957 | g10957.t2 | TTS | g10957.t2 | 13020747 | 13020747 |
Sequences
>g10957.t2 Gene=g10957 Length=1293
ATGAAAAGCAGAACAAAACAGTCAACAACTACATCAGTTGTTTCAACATCTACCAAATCG
TCAATATGCGACAGTCAGGGAAAACTTTATCCTTCAATCAGCGCCGCTTACTGGTTACCG
GCATCAAATCCTACTCCATATTTGTTACCAGAGCGAAAACTATTTGTTGGCATGCTTAAT
AAAAAATACAATGAGAATGATGTGAGACAATTATTTACGGGACACGGGACAATTGAAGAG
TGTACAGTTTTGCGAGATCCGAATGGACAGAGCAAAGGATGTGCTTTTGTGACATTTTCA
AGCAAACAAGCAGCTATTGGTGCTATTAAGGCACTTCATCAAAGTCAGACTATGGAAGGA
TGTTCCGCACCACTTGTTGTGAAATTTGCCGACACTCAAAAAGAGAAAGATGCCAAAAGG
ATTCATACGATGCAAACAAATCTGTGGAGTTTTGCTGCGGCCATTAATAATCCTTTGGCT
CAGAGTCCAATATCAATTACTTCGCCTGTAACTGCTAGTTCGGCAGTAAATACTAGTCCT
TATTTGGCTACTGATGCTGCAACTGCTGCATCTCTTCCAGCTGCAACTTCTTTACAATTA
TTACAACAAATTCAGGCTATTGGTTTGCAGCAACAATTATTGCATGGACTTAGTGCTCAG
GCTGAAACTCCACAACCAGCAACAGTACCATCAGCAACTGCAAATCTTTCGTCACTAGCA
TCTCCTGCATCAGCAGCGGGACTGTTGGCTCCAATTACTGTTCAAAATCTTCTAACATTA
GCTGCAATGTCACAACAACCGTTGGCAAGTGCCACTGCTAATCAACCTTCGCCTTTGCAC
AATGCACCAGCACCAACAAGTTTATGGTCAAGTACTGCAACTGCTGATGGACTAGCGTCA
CAATTAGCAGCAACAGCTCCATCAGCAATGTCGCAATTTACTTCACCATTTAGTGCAACA
CATTTAACTAATCCTACGATGGCAGCGGCAGTCGCCAATGCGGCTGGAAAACAAGTCGAA
GGTCCTGAAGGCTGTAACTTATTCATTTATCACCTGCCGCAAGAATTTACTGATACCGAT
TTGGCATCAACTTTCATGCCATTTGGTCATGTAGTGTCCGCAAAGGTGTTCATTGATAAG
CAAACCAATTTAAGTAAATGCTTTGGATTCGTGTCATTTGATAATGTTACATCAGCTCAA
ACAGCAATTCAATCTATGCACGGCTTCCAAATTGGTACAAAGCGTTTAAAAGTGCAACTG
AAACGATCCAAAGATGCCTCAAAGCCATATTAA
>g10957.t2 Gene=g10957 Length=430
MKSRTKQSTTTSVVSTSTKSSICDSQGKLYPSISAAYWLPASNPTPYLLPERKLFVGMLN
KKYNENDVRQLFTGHGTIEECTVLRDPNGQSKGCAFVTFSSKQAAIGAIKALHQSQTMEG
CSAPLVVKFADTQKEKDAKRIHTMQTNLWSFAAAINNPLAQSPISITSPVTASSAVNTSP
YLATDAATAASLPAATSLQLLQQIQAIGLQQQLLHGLSAQAETPQPATVPSATANLSSLA
SPASAAGLLAPITVQNLLTLAAMSQQPLASATANQPSPLHNAPAPTSLWSSTATADGLAS
QLAATAPSAMSQFTSPFSATHLTNPTMAAAVANAAGKQVEGPEGCNLFIYHLPQEFTDTD
LASTFMPFGHVVSAKVFIDKQTNLSKCFGFVSFDNVTSAQTAIQSMHGFQIGTKRLKVQL
KRSKDASKPY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g10957.t2 | CDD | cd12636 | RRM2_Bruno_like | 51 | 131 | 0.000 |
| 9 | g10957.t2 | Gene3D | G3DSA:3.30.70.330 | - | 49 | 140 | 0.000 |
| 8 | g10957.t2 | Gene3D | G3DSA:3.30.70.330 | - | 308 | 422 | 0.000 |
| 3 | g10957.t2 | PANTHER | PTHR24012 | RNA BINDING PROTEIN | 51 | 417 | 0.000 |
| 4 | g10957.t2 | PANTHER | PTHR24012:SF716 | CUGBP ELAV-LIKE FAMILY MEMBER 6 | 51 | 417 | 0.000 |
| 2 | g10957.t2 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 54 | 118 | 0.000 |
| 1 | g10957.t2 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 347 | 417 | 0.000 |
| 10 | g10957.t2 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 52 | 132 | 15.716 |
| 11 | g10957.t2 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 345 | 423 | 16.517 |
| 7 | g10957.t2 | SMART | SM00360 | rrm1_1 | 53 | 128 | 0.000 |
| 6 | g10957.t2 | SMART | SM00360 | rrm1_1 | 346 | 419 | 0.000 |
| 5 | g10957.t2 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 51 | 426 | 0.000 |
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: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.
