General information for g13451.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Cytidine deaminase.
Parent gene
- The parent gene g13451 is located on chr_1: 30216759..30217230 (+ 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 | g13451 | g13451.t4 | TSS | g13451.t4 | 30216476 | 30216476 |
| chr_1 | g13451 | g13451.t4 | isoform | g13451.t4 | 30216480 | 30217230 |
| chr_1 | g13451 | g13451.t4 | exon | g13451.t4.exon1 | 30216480 | 30216580 |
| chr_1 | g13451 | g13451.t4 | cds | g13451.t4.CDS1 | 30216529 | 30216580 |
| chr_1 | g13451 | g13451.t4 | exon | g13451.t4.exon2 | 30216641 | 30216697 |
| chr_1 | g13451 | g13451.t4 | cds | g13451.t4.CDS2 | 30216641 | 30216697 |
| chr_1 | g13451 | g13451.t4 | exon | g13451.t4.exon3 | 30216759 | 30216821 |
| chr_1 | g13451 | g13451.t4 | cds | g13451.t4.CDS3 | 30216759 | 30216821 |
| chr_1 | g13451 | g13451.t4 | exon | g13451.t4.exon4 | 30216878 | 30217023 |
| chr_1 | g13451 | g13451.t4 | cds | g13451.t4.CDS4 | 30216878 | 30217023 |
| chr_1 | g13451 | g13451.t4 | exon | g13451.t4.exon5 | 30217092 | 30217230 |
| chr_1 | g13451 | g13451.t4 | cds | g13451.t4.CDS5 | 30217092 | 30217127 |
| chr_1 | g13451 | g13451.t4 | TTS | g13451.t4 | 30217346 | 30217346 |
Sequences
>g13451.t4 Gene=g13451 Length=506
TTTCTCTCAGCTTTTCGTGAGAACGGATCAAAAAAGTATTCACTCAGAAATGGAAGTCAA
TGGCACTAATCATCAAAAGATCGTGAATATTGACGATTTAGACGTTGGTGATCAAGATTT
GATAAGAAAAGCAGTTGAGGCGAGGAATTTTGCATACTGTCCATATTCAAATTTTGCTGT
GGGGAGTGCATTGAGAACTAACACTGGTGAAATTTTTACAGGATGTAATGTTGAGAATGT
TGCCCATTCTCCTGGAGTTTGTGCCGAAAGAACAGCTATTGTAAAAGCTGTTAGTGAAGG
ATTTACAAAATTTGATGCAATTGCAGTAGTTGCATATTTAGAAAATGATTTTTGCACACC
ATGTGGCACAAGCTCTTTCGGAATTTGCATCACCGGATATTAAAGTGTTTGTTGCTAAAC
CAGTTGCTATTAGAGTATTGTGTACTTCAGTTCAAGAACTTCTTCCATATCGTTTTTCTC
CTGATAAATTGCAAAAACAATTGTAA
>g13451.t4 Gene=g13451 Length=117
MEVNGTNHQKIVNIDDLDVGDQDLIRKAVEARNFAYCPYSNFAVGSALRTNTGEIFTGCN
VENVAHSPGVCAERTAIVKAVSEGFTKFDAIAVVAYLENDFCTPCGTSSFGICITGY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g13451.t4 | CDD | cd01283 | cytidine_deaminase | 25 | 106 | 0.000 |
| 5 | g13451.t4 | Gene3D | G3DSA:3.40.140.10 | Cytidine Deaminase | 8 | 108 | 0.000 |
| 2 | g13451.t4 | PANTHER | PTHR11644:SF24 | CYTIDINE DEAMINASE | 12 | 107 | 0.000 |
| 3 | g13451.t4 | PANTHER | PTHR11644 | CYTIDINE DEAMINASE | 12 | 107 | 0.000 |
| 1 | g13451.t4 | Pfam | PF08211 | Cytidine and deoxycytidylate deaminase zinc-binding region | 16 | 98 | 0.000 |
| 6 | g13451.t4 | ProSiteProfiles | PS51747 | Cytidine and deoxycytidylate deaminases domain profile. | 19 | 117 | 22.636 |
| 4 | g13451.t4 | SUPERFAMILY | SSF53927 | Cytidine deaminase-like | 16 | 107 | 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:0009972 | cytidine deamination | BP |
| GO:0004126 | cytidine deaminase activity | MF |
| GO:0008270 | zinc ion binding | MF |
| GO:0003824 | catalytic activity | 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.
