Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Carbonic anhydrase 2.

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_2 g5955 g5955.t12 TSS g5955.t12 13008557 13008557
chr_2 g5955 g5955.t12 isoform g5955.t12 13008875 13015645
chr_2 g5955 g5955.t12 exon g5955.t12.exon1 13008875 13008908
chr_2 g5955 g5955.t12 exon g5955.t12.exon2 13014051 13014309
chr_2 g5955 g5955.t12 exon g5955.t12.exon3 13014465 13014628
chr_2 g5955 g5955.t12 exon g5955.t12.exon4 13014867 13015645
chr_2 g5955 g5955.t12 cds g5955.t12.CDS1 13014909 13015259
chr_2 g5955 g5955.t12 TTS g5955.t12 13015608 13015608

Sequences

>g5955.t12 Gene=g5955 Length=1236
ATGAGCAACGATTGGGGATATACAACCAAAAATGGACCAGAGAAGTGGGCTGAAAAATTT
CCACTTGCGGCAGGAACAAGGCAATCACCGGTAAACATCATAACGTCAAAAACTCAACAG
AGCACTGATTTAGTAGTCAATCCATTGAGATGGACATATGTTGCTGACAATGTTAAATGC
TTGATTAATCCTGGATATTGCTGGAGAGTTGATGTCAAGGGTGAAGGATCAGAATTGACA
GGTGGACCACTTAATAATGATAAATATGTTATTGAACAGGTAAATTTTATATTCTCATTG
GGGATGCTCAAATGGTCGAGGAAGTGAACATACTGTTGATGGGACTTCATTTTCTGCTGA
ACTGCATATTGTTCATTGGAATTCAAGCAAATACAATTCGTTCCAAGAAGCAGCAGGACA
TCCTGACGGTCTTGCAGTTTTGGGAGTATTTTTGAAAGTCGGTGAAAAACATGAAGAATT
GGATAAAATAGCTCGTTTGATGCCATATATTTCACACAAGGGAGATCGAGTGACATTGAA
TTCACTTGATATTGCAAAATTGCTACCAGAAAACCGAGCATATTGGACATATGAAGGTTC
ACTGACTACACCTCCATTTAATGAAAGTGTCACATGGATTTTATTTAAAGAACCAATGTA
TGTCTCACAAGAACAATTAGATTTATTCCGTGAGTTACGTCGATATGATGTGAATGAAGA
ATGCCCATATGATGAGCAAAATTGGCTTGTTTATGACTCAGTTGAAGAAAAAGCTGGAAA
AATTGTCAACAATTTCAGACCACCACTACCACTTGGAAATCGTGAACTACGCGAAACTGG
AGAACACTAAATAATTATCTACATAGAGATGCTTTAAGCTATATTGCAACACTATTTTGT
AATTTTAATCACAGGAAATTTTCAATATGATGAAAAATATTATTGCCTTTATGATTTGTT
GAACAAATGTAATAAAAAAAGTTGTTTTCCTATAAAACACCTGTTTAAATTTTAGCAATT
GACCTTTAATAAAGGAATTAACAGTTAACTTGAGGCAAATGCATACAATATATATATTGA
GAGAAAGAATGAGAAAAGGTGCTAGCTACCTATTATTGTATAGAAATGTAGACTTTATTA
TGACGATATTGAATTAATCGAATAAAAATTGTTTTATGACTTTTCATTTTTATTCTAAAT
TTCGAAAAATCTACTTAACTAGATAATTTTAATTCC

>g5955.t12 Gene=g5955 Length=116
MPYISHKGDRVTLNSLDIAKLLPENRAYWTYEGSLTTPPFNESVTWILFKEPMYVSQEQL
DLFRELRRYDVNEECPYDEQNWLVYDSVEEKAGKIVNNFRPPLPLGNRELRETGEH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g5955.t12 CDD cd00326 alpha_CA 1 111 0.0000
6 g5955.t12 Gene3D G3DSA:3.10.200.10 Carbonic Anhydrase II 1 115 0.0000
2 g5955.t12 PANTHER PTHR18952 CARBONIC ANHYDRASE 4 112 0.0000
3 g5955.t12 PANTHER PTHR18952:SF141 CARBONIC ANHYDRASE 1 4 112 0.0000
1 g5955.t12 Pfam PF00194 Eukaryotic-type carbonic anhydrase 2 111 0.0000
7 g5955.t12 ProSiteProfiles PS51144 Alpha-carbonic anhydrases profile. 1 114 26.2130
5 g5955.t12 SMART SM01057 Carb_anhydrase_2a 1 114 0.0022
4 g5955.t12 SUPERFAMILY SSF51069 Carbonic anhydrase 1 111 0.0000

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5955/g5955.t12; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5955.t12.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0008270 zinc ion binding MF
GO:0004089 carbonate dehydratase 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. There were no conditions that were differentially expressed