General information for g10957.t8
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t8 | TSS | g10957.t8 | 13011717 | 13011717 |
| chr_1 | g10957 | g10957.t8 | isoform | g10957.t8 | 13011883 | 13017711 |
| chr_1 | g10957 | g10957.t8 | exon | g10957.t8.exon1 | 13011883 | 13012002 |
| chr_1 | g10957 | g10957.t8 | cds | g10957.t8.CDS1 | 13011890 | 13012002 |
| chr_1 | g10957 | g10957.t8 | exon | g10957.t8.exon2 | 13012187 | 13012446 |
| chr_1 | g10957 | g10957.t8 | cds | g10957.t8.CDS2 | 13012187 | 13012446 |
| chr_1 | g10957 | g10957.t8 | exon | g10957.t8.exon3 | 13012723 | 13012809 |
| chr_1 | g10957 | g10957.t8 | cds | g10957.t8.CDS3 | 13012723 | 13012809 |
| chr_1 | g10957 | g10957.t8 | exon | g10957.t8.exon4 | 13017145 | 13017323 |
| chr_1 | g10957 | g10957.t8 | cds | g10957.t8.CDS4 | 13017145 | 13017323 |
| chr_1 | g10957 | g10957.t8 | exon | g10957.t8.exon5 | 13017396 | 13017711 |
| chr_1 | g10957 | g10957.t8 | cds | g10957.t8.CDS5 | 13017396 | 13017710 |
| chr_1 | g10957 | g10957.t8 | TTS | g10957.t8 | NA | NA |
Sequences
>g10957.t8 Gene=g10957 Length=962
CCTAAAAATGATGAATCTTCGATATAATTACGATTATATTCCTTCGACATTTCAATATTA
TGGCGCCTATCGTAAAAATTTAAATCGCTATTATGGTGGTTGTGGAGTGGACTATTTCAA
TGACTTAACGGCATTGAATAATAATAACGCTCATACAATCAATCAGAATCAGATCAATAG
CATGCATTTAAAGGACAATAATGTAAAGGATGTAGGATCGGATATGGAGCAAGATCAACC
AGATGCAGACTATATAAAGATGTTTGTTGGACAAGTGCCACGGGAAATGGATGAAGCGCA
ATTGCGAGAAATGTTTGAAGTTTATGGCCGTGTACATACGATTAATGTTTTGCGAGATAA
AGCTACAGGCATGAGTAAAGGATGCTGTTTTGTGACGTTTTATAAACGAAAAGCTGCATT
ATTGGCGCAAGATGCTCTTCATAATATTAAAATTTTAGATGGGGTAAAGCGAAAACTATT
TGTTGGCATGCTTAATAAAAAATACAATGAGAATGATGTGAGACAATTATTTACGGGACA
CGGGACAATTGAAGAGTGTACAGTTTTGCGAGATCCGAATGGACAGAGCAAAGGATGTGC
TTTTGTGACATTTTCAAGCAAACAAGCAGCTATTGGTGCTATTAAGGCACTTCATCAAAG
TCAGACTATGGAAGGATGTTCCGCACCACTTGTTGTGAAATTTGCCGACACTCAAAAAGA
GAAAGATGCCAAAAGGATTCATACGATGCAAACAAATCTGTGGAGTTTTGCTGCGGCCAT
TAATAATCCTTTGGCTCAGAGTCCAATATCAATTACTTCGCCTGTAACTGCTAGTTCGGC
AGTAAATACTAGTCCTTATTTGGCTACTGATGCTGCAACTGCTGCATCTCTTCCAGCTGC
AACTTCTTTACAATTATTACAACAAATTCAGGCTATTGGTTTGCAGCAACAATTATTGCA
TG
>g10957.t8 Gene=g10957 Length=318
MMNLRYNYDYIPSTFQYYGAYRKNLNRYYGGCGVDYFNDLTALNNNNAHTINQNQINSMH
LKDNNVKDVGSDMEQDQPDADYIKMFVGQVPREMDEAQLREMFEVYGRVHTINVLRDKAT
GMSKGCCFVTFYKRKAALLAQDALHNIKILDGVKRKLFVGMLNKKYNENDVRQLFTGHGT
IEECTVLRDPNGQSKGCAFVTFSSKQAAIGAIKALHQSQTMEGCSAPLVVKFADTQKEKD
AKRIHTMQTNLWSFAAAINNPLAQSPISITSPVTASSAVNTSPYLATDAATAASLPAATS
LQLLQQIQAIGLQQQLLH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g10957.t8 | CDD | cd12636 | RRM2_Bruno_like | 154 | 234 | 0.000 |
| 11 | g10957.t8 | Gene3D | G3DSA:3.30.70.330 | - | 69 | 154 | 0.000 |
| 12 | g10957.t8 | Gene3D | G3DSA:3.30.70.330 | - | 155 | 243 | 0.000 |
| 3 | g10957.t8 | PANTHER | PTHR24012 | RNA BINDING PROTEIN | 62 | 153 | 0.000 |
| 5 | g10957.t8 | PANTHER | PTHR24012:SF686 | CUGBP ELAV-LIKE FAMILY MEMBER 1 | 62 | 153 | 0.000 |
| 4 | g10957.t8 | PANTHER | PTHR24012 | RNA BINDING PROTEIN | 155 | 258 | 0.000 |
| 6 | g10957.t8 | PANTHER | PTHR24012:SF686 | CUGBP ELAV-LIKE FAMILY MEMBER 1 | 155 | 258 | 0.000 |
| 2 | g10957.t8 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 86 | 149 | 0.000 |
| 1 | g10957.t8 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 157 | 221 | 0.000 |
| 14 | g10957.t8 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 83 | 164 | 14.880 |
| 13 | g10957.t8 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 155 | 235 | 15.716 |
| 10 | g10957.t8 | SMART | SM00360 | rrm1_1 | 84 | 154 | 0.000 |
| 9 | g10957.t8 | SMART | SM00360 | rrm1_1 | 156 | 231 | 0.000 |
| 8 | g10957.t8 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 71 | 151 | 0.000 |
| 7 | g10957.t8 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 154 | 244 | 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. There were no conditions that were differentially expressed