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.t6 TSS g5955.t6 13008557 13008557
chr_2 g5955 g5955.t6 isoform g5955.t6 13008875 13015259
chr_2 g5955 g5955.t6 exon g5955.t6.exon1 13008875 13008908
chr_2 g5955 g5955.t6 cds g5955.t6.CDS1 13008875 13008908
chr_2 g5955 g5955.t6 exon g5955.t6.exon2 13014051 13014314
chr_2 g5955 g5955.t6 cds g5955.t6.CDS2 13014051 13014314
chr_2 g5955 g5955.t6 exon g5955.t6.exon3 13014465 13014628
chr_2 g5955 g5955.t6 cds g5955.t6.CDS3 13014465 13014628
chr_2 g5955 g5955.t6 exon g5955.t6.exon4 13014867 13015259
chr_2 g5955 g5955.t6 cds g5955.t6.CDS4 13014867 13015259
chr_2 g5955 g5955.t6 TTS g5955.t6 13015402 13015402

Sequences

>g5955.t6 Gene=g5955 Length=855
ATGAGCAACGATTGGGGATATACAACCAAAAATGGACCAGAGAAGTGGGCTGAAAAATTT
CCACTTGCGGCAGGAACAAGGCAATCACCGGTAAACATCATAACGTCAAAAACTCAACAG
AGCACTGATTTAGTAGTCAATCCATTGAGATGGACATATGTTGCTGACAATGTTAAATGC
TTGATTAATCCTGGATATTGCTGGAGAGTTGATGTCAAGGGTGAAGGATCAGAATTGACA
GGTGGACCACTTAATAATGATAAATATGTTATTGAACAGGTAAATTTTATATTCATTTCT
CATTGGGGATGCTCAAATGGTCGAGGAAGTGAACATACTGTTGATGGGACTTCATTTTCT
GCTGAACTGCATATTGTTCATTGGAATTCAAGCAAATACAATTCGTTCCAAGAAGCAGCA
GGACATCCTGACGGTCTTGCAGTTTTGGGAGTATTTTTGAAAGTCGGTGAAAAACATGAA
GAATTGGATAAAATAGCTCGTTTGATGCCATATATTTCACACAAGGGAGATCGAGTGACA
TTGAATTCACTTGATATTGCAAAATTGCTACCAGAAAACCGAGCATATTGGACATATGAA
GGTTCACTGACTACACCTCCATTTAATGAAAGTGTCACATGGATTTTATTTAAAGAACCA
ATGTATGTCTCACAAGAACAATTAGATTTATTCCGTGAGTTACGTCGATATGATGTGAAT
GAAGAATGCCCATATGATGAGCAAAATTGGCTTGTTTATGACTCAGTTGAAGAAAAAGCT
GGAAAAATTGTCAACAATTTCAGACCACCACTACCACTTGGAAATCGTGAACTACGCGAA
ACTGGAGAACACTAA

>g5955.t6 Gene=g5955 Length=284
MSNDWGYTTKNGPEKWAEKFPLAAGTRQSPVNIITSKTQQSTDLVVNPLRWTYVADNVKC
LINPGYCWRVDVKGEGSELTGGPLNNDKYVIEQVNFIFISHWGCSNGRGSEHTVDGTSFS
AELHIVHWNSSKYNSFQEAAGHPDGLAVLGVFLKVGEKHEELDKIARLMPYISHKGDRVT
LNSLDIAKLLPENRAYWTYEGSLTTPPFNESVTWILFKEPMYVSQEQLDLFRELRRYDVN
EECPYDEQNWLVYDSVEEKAGKIVNNFRPPLPLGNRELRETGEH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g5955.t6 Gene3D G3DSA:3.10.200.10 Carbonic Anhydrase II 1 281 2.1E-85
2 g5955.t6 PANTHER PTHR18952 CARBONIC ANHYDRASE 2 257 1.5E-75
3 g5955.t6 PANTHER PTHR18952:SF120 CARBONIC ANHYDRASE 2 2 257 1.5E-75
1 g5955.t6 Pfam PF00194 Eukaryotic-type carbonic anhydrase 4 279 7.0E-81
6 g5955.t6 ProSitePatterns PS00162 Alpha-carbonic anhydrases signature. 110 126 -
8 g5955.t6 ProSiteProfiles PS51144 Alpha-carbonic anhydrases profile. 3 282 58.595
5 g5955.t6 SMART SM01057 Carb_anhydrase_2a 5 282 2.5E-105
4 g5955.t6 SUPERFAMILY SSF51069 Carbonic anhydrase 4 279 9.29E-78

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5955/g5955.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5955.t6.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. There were no conditions that were differentially expressed