Gene loci information

Transcript annotation

  • This transcript has been annotated as CUGBP Elav-like family member 1.

Parent gene

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.t7 TSS g10957.t7 13011717 13011717
chr_1 g10957 g10957.t7 isoform g10957.t7 13011883 13017306
chr_1 g10957 g10957.t7 exon g10957.t7.exon1 13011883 13012002
chr_1 g10957 g10957.t7 cds g10957.t7.CDS1 13011890 13012002
chr_1 g10957 g10957.t7 exon g10957.t7.exon2 13012187 13012446
chr_1 g10957 g10957.t7 cds g10957.t7.CDS2 13012187 13012446
chr_1 g10957 g10957.t7 exon g10957.t7.exon3 13012723 13012805
chr_1 g10957 g10957.t7 cds g10957.t7.CDS3 13012723 13012805
chr_1 g10957 g10957.t7 exon g10957.t7.exon4 13013335 13013383
chr_1 g10957 g10957.t7 cds g10957.t7.CDS4 13013335 13013383
chr_1 g10957 g10957.t7 exon g10957.t7.exon5 13017145 13017306
chr_1 g10957 g10957.t7 cds g10957.t7.CDS5 13017145 13017305
chr_1 g10957 g10957.t7 TTS g10957.t7 NA NA

Sequences

>g10957.t7 Gene=g10957 Length=674
CCTAAAAATGATGAATCTTCGATATAATTACGATTATATTCCTTCGACATTTCAATATTA
TGGCGCCTATCGTAAAAATTTAAATCGCTATTATGGTGGTTGTGGAGTGGACTATTTCAA
TGACTTAACGGCATTGAATAATAATAACGCTCATACAATCAATCAGAATCAGATCAATAG
CATGCATTTAAAGGACAATAATGTAAAGGATGTAGGATCGGATATGGAGCAAGATCAACC
AGATGCAGACTATATAAAGATGTTTGTTGGACAAGTGCCACGGGAAATGGATGAAGCGCA
ATTGCGAGAAATGTTTGAAGTTTATGGCCGTGTACATACGATTAATGTTTTGCGAGATAA
AGCTACAGGCATGAGTAAAGGATGCTGTTTTGTGACGTTTTATAAACGAAAAGCTGCATT
ATTGGCGCAAGATGCTCTTCATAATATTAAAATTTTAGATGGGATGCATCATCCAATACA
AATGAAGCCGGCTGATAGCGAAAATCGCAATGAGCGAAAACTATTTGTTGGCATGCTTAA
TAAAAAATACAATGAGAATGATGTGAGACAATTATTTACGGGACACGGGACAATTGAAGA
GTGTACAGTTTTGCGAGATCCGAATGGACAGAGCAAAGGATGTGCTTTTGTGACATTTTC
AAGCAAACAAGCAG

>g10957.t7 Gene=g10957 Length=222
MMNLRYNYDYIPSTFQYYGAYRKNLNRYYGGCGVDYFNDLTALNNNNAHTINQNQINSMH
LKDNNVKDVGSDMEQDQPDADYIKMFVGQVPREMDEAQLREMFEVYGRVHTINVLRDKAT
GMSKGCCFVTFYKRKAALLAQDALHNIKILDGMHHPIQMKPADSENRNERKLFVGMLNKK
YNENDVRQLFTGHGTIEECTVLRDPNGQSKGCAFVTFSSKQA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g10957.t7 Gene3D G3DSA:3.30.70.330 - 69 165 0.000
8 g10957.t7 Gene3D G3DSA:3.30.70.330 - 166 222 0.000
3 g10957.t7 PANTHER PTHR24012 RNA BINDING PROTEIN 61 221 0.000
4 g10957.t7 PANTHER PTHR24012:SF686 CUGBP ELAV-LIKE FAMILY MEMBER 1 61 221 0.000
2 g10957.t7 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 86 149 0.000
1 g10957.t7 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 172 220 0.000
11 g10957.t7 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 83 164 15.067
10 g10957.t7 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 170 222 13.550
7 g10957.t7 SMART SM00360 rrm1_1 84 160 0.000
6 g10957.t7 SMART SM00360 rrm1_1 171 221 0.100
5 g10957.t7 SUPERFAMILY SSF54928 RNA-binding domain, RBD 81 221 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