General information for g10957.t9
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.t9 | isoform | g10957.t9 | 13016854 | 13021608 |
| chr_1 | g10957 | g10957.t9 | exon | g10957.t9.exon1 | 13016854 | 13017323 |
| chr_1 | g10957 | g10957.t9 | TSS | g10957.t9 | 13016863 | 13016863 |
| chr_1 | g10957 | g10957.t9 | cds | g10957.t9.CDS1 | 13017165 | 13017323 |
| chr_1 | g10957 | g10957.t9 | exon | g10957.t9.exon2 | 13017396 | 13017711 |
| chr_1 | g10957 | g10957.t9 | cds | g10957.t9.CDS2 | 13017396 | 13017711 |
| chr_1 | g10957 | g10957.t9 | exon | g10957.t9.exon3 | 13019346 | 13019558 |
| chr_1 | g10957 | g10957.t9 | cds | g10957.t9.CDS3 | 13019346 | 13019558 |
| chr_1 | g10957 | g10957.t9 | exon | g10957.t9.exon4 | 13019624 | 13021608 |
| chr_1 | g10957 | g10957.t9 | cds | g10957.t9.CDS4 | 13019624 | 13020051 |
| chr_1 | g10957 | g10957.t9 | TTS | g10957.t9 | NA | NA |
Sequences
>g10957.t9 Gene=g10957 Length=2984
ATGAAAAGCAGAACAAAACAGTCAACAACTACATCAGTTGTTTCAACATCTACCAAATCG
TCAATATGCGACAGTCAGGGAAAACTTTATCCTTCAATCAGCGCCGCTTACTGGTTACCG
GCATCAAATCCTACTCCATATTTGTTACCAGGTAACTTTTCTTTAAAAAACACAAACTTC
AATACACATGGCAAAATATTTTTCTCATTATGAACTCTCATATATTAATGAAATGTACCT
GTAATTAATTCTTCTTCCACCTACTTGTATAAATTTCTTCGAATTCAATAGAGCGAAAAC
TATTTGTTGGCATGCTTAATAAAAAATACAATGAGAATGATGTGAGACAATTATTTACGG
GACACGGGACAATTGAAGAGTGTACAGTTTTGCGAGATCCGAATGGACAGAGCAAAGGAT
GTGCTTTTGTGACATTTTCAAGCAAACAAGCAGCTATTGGTGCTATTAAGGCACTTCATC
AAAGTCAGACTATGGAAGGATGTTCCGCACCACTTGTTGTGAAATTTGCCGACACTCAAA
AAGAGAAAGATGCCAAAAGGATTCATACGATGCAAACAAATCTGTGGAGTTTTGCTGCGG
CCATTAATAATCCTTTGGCTCAGAGTCCAATATCAATTACTTCGCCTGTAACTGCTAGTT
CGGCAGTAAATACTAGTCCTTATTTGGCTACTGATGCTGCAACTGCTGCATCTCTTCCAG
CTGCAACTTCTTTACAATTATTACAACAAATTCAGGCTATTGGTTTGCAGCAACAATTAT
TGCATGGACTTAGTGCTCAGGCTGAAACTCCACAACCAGCAACAGTACCATCAGCAACTG
CAAATCTTTCGTCACTAGCATCTCCTGCATCAGCAGCGGGACTGTTGGCTCCAATTACTG
TTCAAAATCTTCTAACATTAGCTGCAATGTCACAACAACCGTTGGCAAGTGCCACTGCTA
ATCAACCTTCGCCTTTGCACAATGCACCAGCACCAACAAGGTCAAGTACTGCAACTGCTG
ATGGACTAGCGTCACAATTAGCAGCAACAGCTCCATCAGCAATGTCGCAATTTACTTCAC
CATTTAGTGCAACACATTTAACTAATCCTACGATGGCAGCGGCAGTCGCCAATGCGGCTG
GAAAACAAGTCGAAGGTCCTGAAGGCTGTAACTTATTCATTTATCACCTGCCGCAAGAAT
TTACTGATACCGATTTGGCATCAACTTTCATGCCATTTGGTCATGTAGTGTCCGCAAAGG
TGTTCATTGATAAGCAAACCAATTTAAGTAAATGCTTTGGATTCGTGTCATTTGATAATG
TTACATCAGCTCAAACAGCAATTCAATCTATGCACGGCTTCCAAATTGGTACAAAGCGTT
TAAAAGTGCAACTGAAACGATCCAAAGATGCCTCAAAGCCATATTAAAAAAAGAAAGGAT
GAGAAAAAAGAGATGAAGAAGGGAAACACTTAAAAAACATATTAAAATCATAATTAATAG
TTTGTAATAGTAATAATTTTTAACTTTCCTTTTTATCTTTTTCTATGTAACGACAAAGTG
TTATATACCAAAAAATTTCCACGGAATGAGCTGCTCAGTCTACTGTTGCATAATTAGAAT
ATTGCAACTATTTTCTAAATGGCACTTCTTAAATTAGTTTTTTATGTCAATAGAGTTAGA
ATTTTTTTTTTTTTGACTTTTATATATAGGAGACAATATTCTCCTAAAAATTTCACTGAG
TTATTTAAAAGTTGTGTTTCCTGTCAACAATTTCCCTTATGAATTATTTGTAAAGAAAGG
TCATTTCTTTCATATGTGTGTATAGTTATCTATGTAATTTGTTTTCTGTGACCTATCTTT
TGAAAGAAGATAAAAAATCTTAAATTTTTGTGCCATTAGAATTTCGTCAAGAATTAGAAG
TATAACTATAACATTTTTTGCGTTTCAAACTCTATGTGGATTTATTAATTACTATATTAT
AATGTATTGACTGTGTTTTCATTTAATTTTTCAATTTTCTAATGATAGTTTTTCTTTGTT
TTACACATACACATAAATACCTGTCAAAATTGTTGTATTATTGAATCTTAATAATTTCTT
ATAAAAACTTGAATGTACCGAAAAAAGCAAATGTTACATCAATTTTGATTTTTTTTGAAT
TATAGACTAATTTGTTTCATTATTACAAAATTTCCCAAAAAAACTTGCTGAATTACTGTA
AAATTCAATTTGCTTATGTGTGAATGTATGAAATGAATGATCAGGAAATTTCCAAAAATT
ATTTTAAGATAAATAAAAGCAAATGGGAATGAGAAAGAAATTATTTGTATGGTGCATAAA
TAAAACAGTAAAAAAATATCACTAAAGCTGTATTTGACGATGAAAAATCTGATGCTGATT
TTATGAAGGATTGATACTTTACTGAATCATTAAAGAGCGTCACTTTCGTTTTCTAAATGT
CTCAGTCAAGTGTTTAAATATTAACTTTTCTTCTTCTTCTTTGTTTTCCTTCTTTCTCCA
TGTGTAAACCATACCTATAAAAGAAAAGTGTTTCACACACATACCAAAACACGCGCGGTT
TTTCATGTCTCTGTAAATAACAAAAAATGAAGTGTCTCTCATCATAAATATATATAATTC
ATCAGATACTAATTTGTTATTTTTGTCGAGAAAAAATTAGTATGTATGCAAGTATATGTA
AAAAATTTTAACCAAAAGGAATTGCATAAAAACTTGCTTAGTCACATTAGCCAAAATATC
ATCATTAATTTCTCATTTTCACCAAATAGTAAGGACAGATGTAACTGAAAAATGTAATTA
TTAGGTTGTTTTTGTATACAAAATTTCCTGCAACAACTGAGTGTAAAAAACAATAAAAAT
AGAAAATTTAAAAAGAATTGTTTAATTTTTATTGATATGTATTGTTATAAAATAAAATTT
GCCTCAAAATAATTTTTTTACAGTTATAGTATATTTGACTATGT
>g10957.t9 Gene=g10957 Length=371
MLNKKYNENDVRQLFTGHGTIEECTVLRDPNGQSKGCAFVTFSSKQAAIGAIKALHQSQT
MEGCSAPLVVKFADTQKEKDAKRIHTMQTNLWSFAAAINNPLAQSPISITSPVTASSAVN
TSPYLATDAATAASLPAATSLQLLQQIQAIGLQQQLLHGLSAQAETPQPATVPSATANLS
SLASPASAAGLLAPITVQNLLTLAAMSQQPLASATANQPSPLHNAPAPTRSSTATADGLA
SQLAATAPSAMSQFTSPFSATHLTNPTMAAAVANAAGKQVEGPEGCNLFIYHLPQEFTDT
DLASTFMPFGHVVSAKVFIDKQTNLSKCFGFVSFDNVTSAQTAIQSMHGFQIGTKRLKVQ
LKRSKDASKPY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g10957.t9 | Gene3D | G3DSA:3.30.70.330 | - | 1 | 83 | 5.7E-23 |
| 9 | g10957.t9 | Gene3D | G3DSA:3.30.70.330 | - | 249 | 363 | 7.0E-30 |
| 8 | g10957.t9 | MobiDBLite | mobidb-lite | consensus disorder prediction | 212 | 237 | - |
| 3 | g10957.t9 | PANTHER | PTHR24012 | RNA BINDING PROTEIN | 1 | 358 | 1.2E-74 |
| 4 | g10957.t9 | PANTHER | PTHR24012:SF716 | CUGBP ELAV-LIKE FAMILY MEMBER 6 | 1 | 358 | 1.2E-74 |
| 1 | g10957.t9 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 2 | 61 | 2.4E-13 |
| 2 | g10957.t9 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 288 | 358 | 3.8E-17 |
| 12 | g10957.t9 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 1 | 75 | 13.345 |
| 11 | g10957.t9 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 286 | 364 | 16.517 |
| 7 | g10957.t9 | SMART | SM00360 | rrm1_1 | 2 | 71 | 1.9E-11 |
| 6 | g10957.t9 | SMART | SM00360 | rrm1_1 | 287 | 360 | 1.6E-22 |
| 5 | g10957.t9 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 2 | 367 | 1.29E-40 |
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.
