General information for g10957.t3
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.t3 | TSS | g10957.t3 | 13010776 | 13010776 |
| chr_1 | g10957 | g10957.t3 | isoform | g10957.t3 | 13011021 | 13020051 |
| chr_1 | g10957 | g10957.t3 | exon | g10957.t3.exon1 | 13011021 | 13011250 |
| chr_1 | g10957 | g10957.t3 | cds | g10957.t3.CDS1 | 13011021 | 13011250 |
| chr_1 | g10957 | g10957.t3 | exon | g10957.t3.exon2 | 13011883 | 13012002 |
| chr_1 | g10957 | g10957.t3 | cds | g10957.t3.CDS2 | 13011883 | 13012002 |
| chr_1 | g10957 | g10957.t3 | exon | g10957.t3.exon3 | 13012187 | 13012446 |
| chr_1 | g10957 | g10957.t3 | cds | g10957.t3.CDS3 | 13012187 | 13012446 |
| chr_1 | g10957 | g10957.t3 | exon | g10957.t3.exon4 | 13012723 | 13012805 |
| chr_1 | g10957 | g10957.t3 | cds | g10957.t3.CDS4 | 13012723 | 13012805 |
| chr_1 | g10957 | g10957.t3 | exon | g10957.t3.exon5 | 13013335 | 13013383 |
| chr_1 | g10957 | g10957.t3 | cds | g10957.t3.CDS5 | 13013335 | 13013383 |
| chr_1 | g10957 | g10957.t3 | exon | g10957.t3.exon6 | 13017145 | 13017323 |
| chr_1 | g10957 | g10957.t3 | cds | g10957.t3.CDS6 | 13017145 | 13017323 |
| chr_1 | g10957 | g10957.t3 | exon | g10957.t3.exon7 | 13017396 | 13017711 |
| chr_1 | g10957 | g10957.t3 | cds | g10957.t3.CDS7 | 13017396 | 13017711 |
| chr_1 | g10957 | g10957.t3 | exon | g10957.t3.exon8 | 13019346 | 13019564 |
| chr_1 | g10957 | g10957.t3 | cds | g10957.t3.CDS8 | 13019346 | 13019564 |
| chr_1 | g10957 | g10957.t3 | exon | g10957.t3.exon9 | 13019624 | 13020051 |
| chr_1 | g10957 | g10957.t3 | cds | g10957.t3.CDS9 | 13019624 | 13020051 |
| chr_1 | g10957 | g10957.t3 | TTS | g10957.t3 | 13020747 | 13020747 |
Sequences
>g10957.t3 Gene=g10957 Length=1884
ATGAATTTAGCATCGCTAGAAATGTTAAATACCTTAGAGACGCTTGCGGACAGATTATCG
TCGGGCCAGCAAACAAAAATCATTCTCGATAATAATGGAAATAAAGTTAATTGCAACAAT
AACAAACAGCAACATCATCCCTATCAGAAAGATTCTAATTACAACAATAGATCATCGCCA
AATAATAATAATAACAATAATAACAGCATTAATACAAAATATAATGAAAACCTAAAAATG
ATGAATCTTCGATATAATTACGATTATATTCCTTCGACATTTCAATATTATGGCGCCTAT
CGTAAAAATTTAAATCGCTATTATGGTGGTTGTGGAGTGGACTATTTCAATGACTTAACG
GCATTGAATAATAATAACGCTCATACAATCAATCAGAATCAGATCAATAGCATGCATTTA
AAGGACAATAATGTAAAGGATGTAGGATCGGATATGGAGCAAGATCAACCAGATGCAGAC
TATATAAAGATGTTTGTTGGACAAGTGCCACGGGAAATGGATGAAGCGCAATTGCGAGAA
ATGTTTGAAGTTTATGGCCGTGTACATACGATTAATGTTTTGCGAGATAAAGCTACAGGC
ATGAGTAAAGGATGCTGTTTTGTGACGTTTTATAAACGAAAAGCTGCATTATTGGCGCAA
GATGCTCTTCATAATATTAAAATTTTAGATGGGATGCATCATCCAATACAAATGAAGCCG
GCTGATAGCGAAAATCGCAATGAGCGAAAACTATTTGTTGGCATGCTTAATAAAAAATAC
AATGAGAATGATGTGAGACAATTATTTACGGGACACGGGACAATTGAAGAGTGTACAGTT
TTGCGAGATCCGAATGGACAGAGCAAAGGATGTGCTTTTGTGACATTTTCAAGCAAACAA
GCAGCTATTGGTGCTATTAAGGCACTTCATCAAAGTCAGACTATGGAAGGATGTTCCGCA
CCACTTGTTGTGAAATTTGCCGACACTCAAAAAGAGAAAGATGCCAAAAGGATTCATACG
ATGCAAACAAATCTGTGGAGTTTTGCTGCGGCCATTAATAATCCTTTGGCTCAGAGTCCA
ATATCAATTACTTCGCCTGTAACTGCTAGTTCGGCAGTAAATACTAGTCCTTATTTGGCT
ACTGATGCTGCAACTGCTGCATCTCTTCCAGCTGCAACTTCTTTACAATTATTACAACAA
ATTCAGGCTATTGGTTTGCAGCAACAATTATTGCATGGACTTAGTGCTCAGGCTGAAACT
CCACAACCAGCAACAGTACCATCAGCAACTGCAAATCTTTCGTCACTAGCATCTCCTGCA
TCAGCAGCGGGACTGTTGGCTCCAATTACTGTTCAAAATCTTCTAACATTAGCTGCAATG
TCACAACAACCGTTGGCAAGTGCCACTGCTAATCAACCTTCGCCTTTGCACAATGCACCA
GCACCAACAAGTTTATGGTCAAGTACTGCAACTGCTGATGGACTAGCGTCACAATTAGCA
GCAACAGCTCCATCAGCAATGTCGCAATTTACTTCACCATTTAGTGCAACACATTTAACT
AATCCTACGATGGCAGCGGCAGTCGCCAATGCGGCTGGAAAACAAGTCGAAGGTCCTGAA
GGCTGTAACTTATTCATTTATCACCTGCCGCAAGAATTTACTGATACCGATTTGGCATCA
ACTTTCATGCCATTTGGTCATGTAGTGTCCGCAAAGGTGTTCATTGATAAGCAAACCAAT
TTAAGTAAATGCTTTGGATTCGTGTCATTTGATAATGTTACATCAGCTCAAACAGCAATT
CAATCTATGCACGGCTTCCAAATTGGTACAAAGCGTTTAAAAGTGCAACTGAAACGATCC
AAAGATGCCTCAAAGCCATATTAA
>g10957.t3 Gene=g10957 Length=627
MNLASLEMLNTLETLADRLSSGQQTKIILDNNGNKVNCNNNKQQHHPYQKDSNYNNRSSP
NNNNNNNNSINTKYNENLKMMNLRYNYDYIPSTFQYYGAYRKNLNRYYGGCGVDYFNDLT
ALNNNNAHTINQNQINSMHLKDNNVKDVGSDMEQDQPDADYIKMFVGQVPREMDEAQLRE
MFEVYGRVHTINVLRDKATGMSKGCCFVTFYKRKAALLAQDALHNIKILDGMHHPIQMKP
ADSENRNERKLFVGMLNKKYNENDVRQLFTGHGTIEECTVLRDPNGQSKGCAFVTFSSKQ
AAIGAIKALHQSQTMEGCSAPLVVKFADTQKEKDAKRIHTMQTNLWSFAAAINNPLAQSP
ISITSPVTASSAVNTSPYLATDAATAASLPAATSLQLLQQIQAIGLQQQLLHGLSAQAET
PQPATVPSATANLSSLASPASAAGLLAPITVQNLLTLAAMSQQPLASATANQPSPLHNAP
APTSLWSSTATADGLASQLAATAPSAMSQFTSPFSATHLTNPTMAAAVANAAGKQVEGPE
GCNLFIYHLPQEFTDTDLASTFMPFGHVVSAKVFIDKQTNLSKCFGFVSFDNVTSAQTAI
QSMHGFQIGTKRLKVQLKRSKDASKPY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g10957.t3 | CDD | cd12636 | RRM2_Bruno_like | 248 | 328 | 5.51742E-50 |
| 12 | g10957.t3 | CDD | cd12640 | RRM3_Bruno_like | 538 | 616 | 9.79038E-48 |
| 8 | g10957.t3 | Gene3D | G3DSA:3.30.70.330 | - | 149 | 245 | 5.5E-24 |
| 9 | g10957.t3 | Gene3D | G3DSA:3.30.70.330 | - | 246 | 337 | 8.2E-28 |
| 10 | g10957.t3 | Gene3D | G3DSA:3.30.70.330 | - | 506 | 619 | 1.8E-29 |
| 16 | g10957.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 44 | 69 | - |
| 4 | g10957.t3 | PANTHER | PTHR24012 | RNA BINDING PROTEIN | 141 | 614 | 6.5E-131 |
| 5 | g10957.t3 | PANTHER | PTHR24012:SF686 | CUGBP ELAV-LIKE FAMILY MEMBER 1 | 141 | 614 | 6.5E-131 |
| 3 | g10957.t3 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 165 | 228 | 1.5E-14 |
| 1 | g10957.t3 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 251 | 315 | 2.3E-15 |
| 2 | g10957.t3 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 544 | 614 | 8.4E-17 |
| 18 | g10957.t3 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 162 | 243 | 15.067 |
| 19 | g10957.t3 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 249 | 329 | 15.716 |
| 17 | g10957.t3 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 542 | 620 | 16.517 |
| 14 | g10957.t3 | SMART | SM00360 | rrm1_1 | 163 | 239 | 1.1E-17 |
| 13 | g10957.t3 | SMART | SM00360 | rrm1_1 | 250 | 325 | 1.1E-19 |
| 15 | g10957.t3 | SMART | SM00360 | rrm1_1 | 543 | 616 | 1.6E-22 |
| 7 | g10957.t3 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 165 | 623 | 2.65E-44 |
| 6 | g10957.t3 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 230 | 338 | 3.94E-24 |
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 transcript has been annotated with K02177 (bruno)
Pathway
- This transcript belongs to the following pathways
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