General information for g3.t1
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 g3 is located on chr_3: 24939..25171 (- 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_3 | g3 | g3.t1 | TTS | g3.t1 | 23861 | 23861 |
| chr_3 | g3 | g3.t1 | isoform | g3.t1 | 23930 | 25171 |
| chr_3 | g3 | g3.t1 | exon | g3.t1.exon1 | 23930 | 24149 |
| chr_3 | g3 | g3.t1 | cds | g3.t1.CDS1 | 23930 | 24149 |
| chr_3 | g3 | g3.t1 | exon | g3.t1.exon2 | 24535 | 24830 |
| chr_3 | g3 | g3.t1 | cds | g3.t1.CDS2 | 24535 | 24830 |
| chr_3 | g3 | g3.t1 | exon | g3.t1.exon3 | 24935 | 25171 |
| chr_3 | g3 | g3.t1 | cds | g3.t1.CDS3 | 24935 | 25171 |
| chr_3 | g3 | g3.t1 | TSS | g3.t1 | 25209 | 25209 |
Sequences
>g3.t1 Gene=g3 Length=753
ATGTCATCAGAAAATATTCAATCACCAATTGCTTTAGAATTGCGAGAAGCAGAATTTCAG
GATGATGCAGAGCCTTTGGTTTATTATGGGCATTGGGATAAAATTGGTGGAAGTGCAGAA
ATGATAAATACAGGCAGTTCAGCAATGATTACTTTGCCTAATCGTAACCGTAAACCCTTC
ATAACTGGAGGTCCATTAAAGGGAAAATATATTTTTGAACAATTGCATTTTCATTGGGGT
GATTGCAATGAATACGGATGCGAACATTTGCTAGAAGGCAACACTTATAGTATGGAGGCA
CATGCTGTACATTATAACGAAAAGTATAAAAATTTCCAGGAAGCTGTGACGAAACCAGAT
GGATTAGCGGTTACAGGCTTTTTTATTCATGGTTTGGGTGATAAAGACTGTACTGAATTC
AAAAAAATTTCTGATGGGATTGAACGCATTACAAAACCAGGTGGAAAAACACGTCTCGGC
GCAGACTGCTTATCGTTTCTTAAACTTCAGGAACTGAGCAAACATTATTATAACTATGTT
GGATCGCTTACTACACCACCATACAATGAAGTTGTTCAATGGATCGTTTATAGAACTCCA
ATTTACGTCTCGGAAAAACAAATTGCAGCTTTTAGATCACTAAAGTGTCATGATGAAACA
AAGTGTATTGTGAACAATTATCGTGATATTCAGCAACCTACACGCTCTCCAAAAATTATC
TTTACTCGCAATACTCTTAAATCGAAATTGTAA
>g3.t1 Gene=g3 Length=250
MSSENIQSPIALELREAEFQDDAEPLVYYGHWDKIGGSAEMINTGSSAMITLPNRNRKPF
ITGGPLKGKYIFEQLHFHWGDCNEYGCEHLLEGNTYSMEAHAVHYNEKYKNFQEAVTKPD
GLAVTGFFIHGLGDKDCTEFKKISDGIERITKPGGKTRLGADCLSFLKLQELSKHYYNYV
GSLTTPPYNEVVQWIVYRTPIYVSEKQIAAFRSLKCHDETKCIVNNYRDIQQPTRSPKII
FTRNTLKSKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3.t1 | CDD | cd00326 | alpha_CA | 7 | 231 | 0.000 |
| 6 | g3.t1 | Gene3D | G3DSA:3.10.200.10 | Carbonic Anhydrase II | 1 | 239 | 0.000 |
| 2 | g3.t1 | PANTHER | PTHR18952:SF114 | LD36568P | 3 | 246 | 0.000 |
| 3 | g3.t1 | PANTHER | PTHR18952 | CARBONIC ANHYDRASE | 3 | 246 | 0.000 |
| 1 | g3.t1 | Pfam | PF00194 | Eukaryotic-type carbonic anhydrase | 4 | 232 | 0.000 |
| 7 | g3.t1 | ProSiteProfiles | PS51144 | Alpha-carbonic anhydrases profile. | 1 | 243 | 50.257 |
| 5 | g3.t1 | SMART | SM01057 | Carb_anhydrase_2a | 1 | 241 | 0.000 |
| 4 | g3.t1 | SUPERFAMILY | SSF51069 | Carbonic anhydrase | 4 | 232 | 0.000 |
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:0008270 | zinc ion binding | MF |
| GO:0004089 | carbonate dehydratase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01672 (carbonic anhydrase)
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