Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t1 TSS g5955.t1 13008557 13008557
chr_2 g5955 g5955.t1 isoform g5955.t1 13008875 13015259
chr_2 g5955 g5955.t1 exon g5955.t1.exon1 13008875 13008908
chr_2 g5955 g5955.t1 cds g5955.t1.CDS1 13008875 13008908
chr_2 g5955 g5955.t1 exon g5955.t1.exon2 13014051 13014295
chr_2 g5955 g5955.t1 cds g5955.t1.CDS2 13014051 13014295
chr_2 g5955 g5955.t1 exon g5955.t1.exon3 13014399 13014405
chr_2 g5955 g5955.t1 cds g5955.t1.CDS3 13014399 13014405
chr_2 g5955 g5955.t1 exon g5955.t1.exon4 13014465 13014628
chr_2 g5955 g5955.t1 cds g5955.t1.CDS4 13014465 13014628
chr_2 g5955 g5955.t1 exon g5955.t1.exon5 13014867 13015259
chr_2 g5955 g5955.t1 cds g5955.t1.CDS5 13014867 13015259
chr_2 g5955 g5955.t1 TTS g5955.t1 13015402 13015402

Sequences

>g5955.t1 Gene=g5955 Length=843
ATGAGCAACGATTGGGGATATACAACCAAAAATGGACCAGAGAAGTGGGCTGAAAAATTT
CCACTTGCGGCAGGAACAAGGCAATCACCGGTAAACATCATAACGTCAAAAACTCAACAG
AGCACTGATTTAGTAGTCAATCCATTGAGATGGACATATGTTGCTGACAATGTTAAATGC
TTGATTAATCCTGGATATTGCTGGAGAGTTGATGTCAAGGGTGAAGGATCAGAATTGACA
GGTGGACCACTTAATAATGATAAATATGTTATTGAACAGTTTCATGCTCATTGGGGATGC
TCAAATGGTCGAGGAAGTGAACATACTGTTGATGGGACTTCATTTTCTGCTGAACTGCAT
ATTGTTCATTGGAATTCAAGCAAATACAATTCGTTCCAAGAAGCAGCAGGACATCCTGAC
GGTCTTGCAGTTTTGGGAGTATTTTTGAAAGTCGGTGAAAAACATGAAGAATTGGATAAA
ATAGCTCGTTTGATGCCATATATTTCACACAAGGGAGATCGAGTGACATTGAATTCACTT
GATATTGCAAAATTGCTACCAGAAAACCGAGCATATTGGACATATGAAGGTTCACTGACT
ACACCTCCATTTAATGAAAGTGTCACATGGATTTTATTTAAAGAACCAATGTATGTCTCA
CAAGAACAATTAGATTTATTCCGTGAGTTACGTCGATATGATGTGAATGAAGAATGCCCA
TATGATGAGCAAAATTGGCTTGTTTATGACTCAGTTGAAGAAAAAGCTGGAAAAATTGTC
AACAATTTCAGACCACCACTACCACTTGGAAATCGTGAACTACGCGAAACTGGAGAACAC
TAA

>g5955.t1 Gene=g5955 Length=280
MSNDWGYTTKNGPEKWAEKFPLAAGTRQSPVNIITSKTQQSTDLVVNPLRWTYVADNVKC
LINPGYCWRVDVKGEGSELTGGPLNNDKYVIEQFHAHWGCSNGRGSEHTVDGTSFSAELH
IVHWNSSKYNSFQEAAGHPDGLAVLGVFLKVGEKHEELDKIARLMPYISHKGDRVTLNSL
DIAKLLPENRAYWTYEGSLTTPPFNESVTWILFKEPMYVSQEQLDLFRELRRYDVNEECP
YDEQNWLVYDSVEEKAGKIVNNFRPPLPLGNRELRETGEH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g5955.t1 Gene3D G3DSA:3.10.200.10 Carbonic Anhydrase II 1 277 1.3E-89
2 g5955.t1 PANTHER PTHR18952 CARBONIC ANHYDRASE 4 276 7.8E-80
3 g5955.t1 PANTHER PTHR18952:SF141 CARBONIC ANHYDRASE 1 4 276 7.8E-80
1 g5955.t1 Pfam PF00194 Eukaryotic-type carbonic anhydrase 4 275 7.4E-85
6 g5955.t1 ProSitePatterns PS00162 Alpha-carbonic anhydrases signature. 106 122 -
8 g5955.t1 ProSiteProfiles PS51144 Alpha-carbonic anhydrases profile. 3 278 64.084
5 g5955.t1 SMART SM01057 Carb_anhydrase_2a 5 278 1.3E-111
4 g5955.t1 SUPERFAMILY SSF51069 Carbonic anhydrase 4 275 2.49E-81

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5955/g5955.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5955.t1.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

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