General information for g12825.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Acidic mammalian chitinase.
Parent gene
- The parent gene g12825 is located on chr_1: 26444301..26445087 (+ 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_1 | g12825 | g12825.t2 | isoform | g12825.t2 | 26443132 | 26444301 |
| chr_1 | g12825 | g12825.t2 | exon | g12825.t2.exon1 | 26443132 | 26444301 |
| chr_1 | g12825 | g12825.t2 | cds | g12825.t2.CDS1 | 26443377 | 26443928 |
| chr_1 | g12825 | g12825.t2 | TTS | g12825.t2 | 26445079 | 26445079 |
| chr_1 | g12825 | g12825.t2 | TSS | g12825.t2 | NA | NA |
Sequences
>g12825.t2 Gene=g12825 Length=1170
GGTATGAAAAATAAAATTTTTTTGAAAATTTTATTTCTAATTATTTTAATTAGTATCCTG
CACAAAGAGATACTACATATGGAAGTGCTGATAAAGAAAATTTTGTGGAACTTTTAAAAG
TACTTAAAAGTAAATTAAGCTCAAATGGAAAATTACTAACCATTGCAGTTGGAGCAACAG
CTTCTTCTGCATCAGTTTCGTATGACATTCCAAATGTTGCTGCAAATGTTGATTTTATCA
ATCTTATGTCATATGATCTGCATGGTTTGTGGGATTCAAAAACTGGCATCAATTCGCCAC
TTTATTCGGGACCAAGTGATGTCAGTTCATATGAAAAACAATTAAATGTAGACTCAATTG
TTAATTATTGGTTAAATCAAGGATGTCCAAAGAGTAAATTAATTGTCGGAATACCACTTT
ATGGACGAACTTTCACATTAGCAAATTCGAATAATAATGGTGTGGGTGCTCCTATATATG
GTGGAGGAGAAATGGGTTCATTTGTTCCAGAGTCTGGCTTTTTAGGATATAATGAGATAT
GCTACAATATAAATAATAAAGGTTGGAGAAGATTTTGGGAAGACACACAAAAAGTTCCTT
ATGCAGTTAGTGGCAATCAATGGGTTGGATATGATGATGCAGAATCATTATCTTATAAAT
TGAATTACATCAAAAACAGAGATTTAGGTGGTGCCATGTTTTGGTCAATTGAGACTGATG
ATTTTGCAAATATTTGTGATAAAGGCAAATTTCCTTTGATAAAAGCTGCTTTTAGTGCAT
TGATTAATAATGTATGAAGTCAATTTTATAAAAAAAGAAAAGATTTTTTTTAAAGAAATT
CTATTTTTAGTCGCCTGTTCCAATTACTACTGATAAACCAAATCCAACTGAAAATAATGG
TGTGACAACCACTACAACAACAACTCAAAAATCAAATAGTGGCTCAATTTGTTCAAATGG
TGATGGCATATATCCAGATCCATTAGATTGTATGTAGATGATTGAAAATTTCTTTGATAT
AAAATTTATAATTTTTTTGTGATTAAAACTTTTTTAGGCAACAAATTTTATATATGTGCT
GCTAATGTTCCGTACCATCAATCGTGTGGTGTTGGCTTGAATTTTAATCCAAATGGATAT
TGTGACTGGCCTTATAATTTTTCATGCTAG
>g12825.t2 Gene=g12825 Length=183
MSYDLHGLWDSKTGINSPLYSGPSDVSSYEKQLNVDSIVNYWLNQGCPKSKLIVGIPLYG
RTFTLANSNNNGVGAPIYGGGEMGSFVPESGFLGYNEICYNINNKGWRRFWEDTQKVPYA
VSGNQWVGYDDAESLSYKLNYIKNRDLGGAMFWSIETDDFANICDKGKFPLIKAAFSALI
NNV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g12825.t2 | Gene3D | G3DSA:3.10.50.10 | - | 62 | 129 | 0.0e+00 |
| 2 | g12825.t2 | PANTHER | PTHR11177 | CHITINASE | 1 | 176 | 0.0e+00 |
| 3 | g12825.t2 | PANTHER | PTHR11177:SF217 | OVIDUCT-SPECIFIC GLYCOPROTEIN | 1 | 176 | 0.0e+00 |
| 1 | g12825.t2 | Pfam | PF00704 | Glycosyl hydrolases family 18 | 1 | 158 | 0.0e+00 |
| 6 | g12825.t2 | SMART | SM00636 | 2g34 | 1 | 158 | 2.2e-05 |
| 5 | g12825.t2 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 1 | 179 | 0.0e+00 |
| 4 | g12825.t2 | SUPERFAMILY | SSF54556 | Chitinase insertion domain | 59 | 129 | 0.0e+00 |
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:0008061 | chitin binding | MF |
| GO:0005975 | carbohydrate metabolic process | BP |
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.
