General information for g5955.t17
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Carbonic anhydrase 2.
Parent gene
- The parent gene g5955 is located on chr_2: 13014880..13015645 (+ 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_2 | g5955 | g5955.t17 | isoform | g5955.t17 | 13014216 | 13015259 |
| chr_2 | g5955 | g5955.t17 | exon | g5955.t17.exon1 | 13014216 | 13014295 |
| chr_2 | g5955 | g5955.t17 | exon | g5955.t17.exon2 | 13014465 | 13014616 |
| chr_2 | g5955 | g5955.t17 | exon | g5955.t17.exon3 | 13014819 | 13015259 |
| chr_2 | g5955 | g5955.t17 | cds | g5955.t17.CDS1 | 13014909 | 13015259 |
| chr_2 | g5955 | g5955.t17 | TTS | g5955.t17 | 13015402 | 13015402 |
| chr_2 | g5955 | g5955.t17 | TSS | g5955.t17 | NA | NA |
Sequences
>g5955.t17 Gene=g5955 Length=673
GCTGGAGAGTTGATGTCAAGGGTGAAGGATCAGAATTGACAGGTGGACCACTTAATAATG
ATAAATATGTTATTGAACAGCTCATTGGGGATGCTCAAATGGTCGAGGAAGTGAACATAC
TGTTGATGGGACTTCATTTTCTGCTGAACTGCATATTGTTCATTGGAATTCAAGCAAATA
CAATTCGTTCCAAGAAGCAGCAGGACATCCTGACGGTCTTGCAGTTTTGGGACGAATTTT
AAAAATTATTAACTAATTGAAACAATGTGTGATCTCGCAGGTCGGTGAAAAACATGAAGA
ATTGGATAAAATAGCTCGTTTGATGCCATATATTTCACACAAGGGAGATCGAGTGACATT
GAATTCACTTGATATTGCAAAATTGCTACCAGAAAACCGAGCATATTGGACATATGAAGG
TTCACTGACTACACCTCCATTTAATGAAAGTGTCACATGGATTTTATTTAAAGAACCAAT
GTATGTCTCACAAGAACAATTAGATTTATTCCGTGAGTTACGTCGATATGATGTGAATGA
AGAATGCCCATATGATGAGCAAAATTGGCTTGTTTATGACTCAGTTGAAGAAAAAGCTGG
AAAAATTGTCAACAATTTCAGACCACCACTACCACTTGGAAATCGTGAACTACGCGAAAC
TGGAGAACACTAA
>g5955.t17 Gene=g5955 Length=116
MPYISHKGDRVTLNSLDIAKLLPENRAYWTYEGSLTTPPFNESVTWILFKEPMYVSQEQL
DLFRELRRYDVNEECPYDEQNWLVYDSVEEKAGKIVNNFRPPLPLGNRELRETGEH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5955.t17 | CDD | cd00326 | alpha_CA | 1 | 111 | 0.0000 |
| 6 | g5955.t17 | Gene3D | G3DSA:3.10.200.10 | Carbonic Anhydrase II | 1 | 115 | 0.0000 |
| 2 | g5955.t17 | PANTHER | PTHR18952 | CARBONIC ANHYDRASE | 4 | 112 | 0.0000 |
| 3 | g5955.t17 | PANTHER | PTHR18952:SF141 | CARBONIC ANHYDRASE 1 | 4 | 112 | 0.0000 |
| 1 | g5955.t17 | Pfam | PF00194 | Eukaryotic-type carbonic anhydrase | 2 | 111 | 0.0000 |
| 7 | g5955.t17 | ProSiteProfiles | PS51144 | Alpha-carbonic anhydrases profile. | 1 | 114 | 26.2130 |
| 5 | g5955.t17 | SMART | SM01057 | Carb_anhydrase_2a | 1 | 114 | 0.0022 |
| 4 | g5955.t17 | 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.t17; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5955.t17.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.
