General information for g8450.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as CUGBP Elav-like family member 4.
Parent gene
- The parent gene g8450 is located on chr_2: 30718936..30746231 (+ 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_2 | g8450 | g8450.t1 | isoform | g8450.t1 | 30718936 | 30746231 |
| chr_2 | g8450 | g8450.t1 | exon | g8450.t1.exon1 | 30718936 | 30719041 |
| chr_2 | g8450 | g8450.t1 | cds | g8450.t1.CDS1 | 30718936 | 30719041 |
| chr_2 | g8450 | g8450.t1 | exon | g8450.t1.exon2 | 30729960 | 30730039 |
| chr_2 | g8450 | g8450.t1 | cds | g8450.t1.CDS2 | 30729960 | 30730039 |
| chr_2 | g8450 | g8450.t1 | exon | g8450.t1.exon3 | 30741805 | 30742048 |
| chr_2 | g8450 | g8450.t1 | cds | g8450.t1.CDS3 | 30741805 | 30742048 |
| chr_2 | g8450 | g8450.t1 | exon | g8450.t1.exon4 | 30742202 | 30742333 |
| chr_2 | g8450 | g8450.t1 | cds | g8450.t1.CDS4 | 30742202 | 30742333 |
| chr_2 | g8450 | g8450.t1 | exon | g8450.t1.exon5 | 30742392 | 30742490 |
| chr_2 | g8450 | g8450.t1 | cds | g8450.t1.CDS5 | 30742392 | 30742490 |
| chr_2 | g8450 | g8450.t1 | exon | g8450.t1.exon6 | 30744178 | 30744252 |
| chr_2 | g8450 | g8450.t1 | cds | g8450.t1.CDS6 | 30744178 | 30744252 |
| chr_2 | g8450 | g8450.t1 | exon | g8450.t1.exon7 | 30745668 | 30745826 |
| chr_2 | g8450 | g8450.t1 | cds | g8450.t1.CDS7 | 30745668 | 30745826 |
| chr_2 | g8450 | g8450.t1 | exon | g8450.t1.exon8 | 30746104 | 30746231 |
| chr_2 | g8450 | g8450.t1 | cds | g8450.t1.CDS8 | 30746104 | 30746231 |
| chr_2 | g8450 | g8450.t1 | TTS | g8450.t1 | 30746396 | 30746396 |
| chr_2 | g8450 | g8450.t1 | TSS | g8450.t1 | NA | NA |
Sequences
>g8450.t1 Gene=g8450 Length=1023
ATGCTCAGTAAGCAACAAAATGAAGAGGATGTGAGACAACTGTTCAACACATTTGGAACT
ATCGAAGAGTGTACTATTTTACGTGGACCAGACGGCGCAAGCAAAGGTTGTGCATTTGTG
AAATTTAGCTCACATCCAGAGGCTCAAGCAGCTATTACGAGTTTACACGGTAGTCAAACT
ATGCCGGGAGCATCCTCGAGCTTAGTTGTGAAATTTGCCGATACTGAGAAAGAAAGACAA
ATAAGACGCATGCAGCAAATGGCTGGCCACATGAATTTATTAAGTCCTTTTGTATTTAAT
CAGTTTGGACCATATAACGCTTACGCTCAAACGCAACAACAGGCTGCATTAATGGCGGCT
GCAACTGCGCAAGGCACTTACATGAATCCTATGGCCGCTTTAGCTACCCAAATACCTCAC
GCTTTAGGTGGACAACCTGTTAATGCATCTTTGCCATCCCCAACTATGCCAACATTTAAT
ATGGCTGCTGCTCAACCAAACGGTCAACCAGCAGGCGCAGAGGCTGTTTATTCAAATGGT
ATACCTCATACGTATCCTGGACATGCACTACAATTGTCGATACCAGCACAAGGACTGGCG
AATGGTGATGCTGCATTGCCGCATGCTACTTATCCTGGAATTCAACCCTATCCTGGCGTT
GCATATCCTGCAGTCTATGGACAATTTCCGCAAGCTATTCCTCAGCCAATTGCTGCTGTT
CCAGCTCAACGTGAAGGATGTTCCATTTCTGGACCTGAAGGCTGTAACCTGTTTATCTAT
CATTTGCCCCAAGAATTTGGTGATGGTGAATTGATGCAAATGTTTATGCCATTTGGCACG
GTTATTAGTTCTAAAGTGTTTATCGATCGCGCTACAAATCAAAGTAAATGTTTTGGTTTT
GTTTCATTTGATAATCCTGCCAGTGCTCAAGCAGCTATTCAAGCGATGAATGGTTTCCAA
ATCGGAATGAAAAGACTGAAGGTTCAGTTGAAAAGACCTAAAGATGCCAATCGACCTTAT
TAA
>g8450.t1 Gene=g8450 Length=340
MLSKQQNEEDVRQLFNTFGTIEECTILRGPDGASKGCAFVKFSSHPEAQAAITSLHGSQT
MPGASSSLVVKFADTEKERQIRRMQQMAGHMNLLSPFVFNQFGPYNAYAQTQQQAALMAA
ATAQGTYMNPMAALATQIPHALGGQPVNASLPSPTMPTFNMAAAQPNGQPAGAEAVYSNG
IPHTYPGHALQLSIPAQGLANGDAALPHATYPGIQPYPGVAYPAVYGQFPQAIPQPIAAV
PAQREGCSISGPEGCNLFIYHLPQEFGDGELMQMFMPFGTVISSKVFIDRATNQSKCFGF
VSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPKDANRPY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g8450.t1 | CDD | cd12635 | RRM2_CELF3_4_5_6 | 1 | 74 | 0.000 |
| 13 | g8450.t1 | CDD | cd12639 | RRM3_CELF3_4_5_6 | 251 | 329 | 0.000 |
| 9 | g8450.t1 | Gene3D | G3DSA:3.30.70.330 | - | 1 | 83 | 0.000 |
| 8 | g8450.t1 | Gene3D | G3DSA:3.30.70.330 | - | 230 | 332 | 0.000 |
| 3 | g8450.t1 | PANTHER | PTHR24012 | RNA BINDING PROTEIN | 1 | 327 | 0.000 |
| 4 | g8450.t1 | PANTHER | PTHR24012:SF716 | CUGBP ELAV-LIKE FAMILY MEMBER 6 | 1 | 327 | 0.000 |
| 1 | g8450.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 2 | 60 | 0.000 |
| 2 | g8450.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 257 | 327 | 0.000 |
| 11 | g8450.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 1 | 75 | 14.675 |
| 10 | g8450.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 255 | 333 | 16.773 |
| 7 | g8450.t1 | SMART | SM00360 | rrm1_1 | 2 | 71 | 0.000 |
| 6 | g8450.t1 | SMART | SM00360 | rrm1_1 | 256 | 329 | 0.000 |
| 5 | g8450.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 2 | 337 | 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 transcript has been annotated with K13207 (CUG-BP- and ETR3-like factor)
Pathway
This gene does not belong to any 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