Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Cytidine deaminase.

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 g13451 g13451.t12 TSS g13451.t12 30216476 30216476
chr_1 g13451 g13451.t12 isoform g13451.t12 30216529 30217230
chr_1 g13451 g13451.t12 exon g13451.t12.exon1 30216529 30216580
chr_1 g13451 g13451.t12 cds g13451.t12.CDS1 30216529 30216580
chr_1 g13451 g13451.t12 exon g13451.t12.exon2 30216641 30216679
chr_1 g13451 g13451.t12 cds g13451.t12.CDS2 30216641 30216679
chr_1 g13451 g13451.t12 exon g13451.t12.exon3 30216759 30216821
chr_1 g13451 g13451.t12 cds g13451.t12.CDS3 30216759 30216821
chr_1 g13451 g13451.t12 exon g13451.t12.exon4 30216878 30217023
chr_1 g13451 g13451.t12 cds g13451.t12.CDS4 30216878 30217023
chr_1 g13451 g13451.t12 exon g13451.t12.exon5 30217084 30217230
chr_1 g13451 g13451.t12 cds g13451.t12.CDS5 30217084 30217230
chr_1 g13451 g13451.t12 TTS g13451.t12 30217346 30217346

Sequences

>g13451.t12 Gene=g13451 Length=447
ATGGAAGTCAATGGCACTAATCATCAAAAGATCGTGAATATTGACGATTTAGACGTTGGT
GATCAAGATTTGATAAGAAAAGCAGTTGAGGGTCCATATTCAAATTTTGCTGTGGGGAGT
GCATTGAGAACTAACACTGGTGAAATTTTTACAGGATGTAATGTTGAGAATGTTGCCCAT
TCTCCTGGAGTTTGTGCCGAAAGAACAGCTATTGTAAAAGCTGTTAGTGAAGGATTTACA
AAATTTGATGCAATTGCAGTAGTTGCATATTTAGAAAATGATTTTTGCACACCATGTGGC
GTATGCAGACAAGCTCTTTCGGAATTTGCATCACCGGATATTAAAGTGTTTGTTGCTAAA
CCAGTTGCTATTAGAGTATTGTGTACTTCAGTTCAAGAACTTCTTCCATATCGTTTTTCT
CCTGATAAATTGCAAAAACAATTGTAA

>g13451.t12 Gene=g13451 Length=148
MEVNGTNHQKIVNIDDLDVGDQDLIRKAVEGPYSNFAVGSALRTNTGEIFTGCNVENVAH
SPGVCAERTAIVKAVSEGFTKFDAIAVVAYLENDFCTPCGVCRQALSEFASPDIKVFVAK
PVAIRVLCTSVQELLPYRFSPDKLQKQL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g13451.t12 CDD cd01283 cytidine_deaminase 32 121 3.0814E-37
4 g13451.t12 Gene3D G3DSA:3.40.140.10 Cytidine Deaminase 16 148 1.4E-43
2 g13451.t12 PANTHER PTHR11644 CYTIDINE DEAMINASE 30 147 4.9E-38
1 g13451.t12 Pfam PF00383 Cytidine and deoxycytidylate deaminase zinc-binding region 28 113 7.8E-14
6 g13451.t12 ProSitePatterns PS00903 Cytidine and deoxycytidylate deaminases zinc-binding region signature. 65 106 -
7 g13451.t12 ProSiteProfiles PS51747 Cytidine and deoxycytidylate deaminases domain profile. 13 142 22.259
3 g13451.t12 SUPERFAMILY SSF53927 Cytidine deaminase-like 26 144 1.62E-38
8 g13451.t12 TIGRFAM TIGR01354 cyt_deam_tetra: cytidine deaminase 30 143 5.7E-36

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:0016787 hydrolase activity MF
GO:0009972 cytidine deamination BP
GO:0004126 cytidine deaminase activity MF
GO:0008270 zinc ion binding MF
GO:0003824 catalytic activity MF

KEGG

Orthology

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.

Raw TPM values