General information for g12825.t3
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.t3 | isoform | g12825.t3 | 26443183 | 26444301 |
| chr_1 | g12825 | g12825.t3 | exon | g12825.t3.exon1 | 26443183 | 26443922 |
| chr_1 | g12825 | g12825.t3 | cds | g12825.t3.CDS1 | 26443377 | 26443922 |
| chr_1 | g12825 | g12825.t3 | exon | g12825.t3.exon2 | 26443982 | 26444120 |
| chr_1 | g12825 | g12825.t3 | cds | g12825.t3.CDS2 | 26443982 | 26444120 |
| chr_1 | g12825 | g12825.t3 | exon | g12825.t3.exon3 | 26444189 | 26444301 |
| chr_1 | g12825 | g12825.t3 | cds | g12825.t3.CDS3 | 26444189 | 26444301 |
| chr_1 | g12825 | g12825.t3 | TTS | g12825.t3 | 26445079 | 26445079 |
| chr_1 | g12825 | g12825.t3 | TSS | g12825.t3 | NA | NA |
Sequences
>g12825.t3 Gene=g12825 Length=992
AGTATCCTGCACAAAGAGATACTACATATGGAAGTGCTGATAAAGAAAATTTTGTGGAAC
TTTTAAAAGTACTTAAAAGTAAATTAAGCTCAAATGGAAAATTACTAACCATTGCAGTTG
GAGCAACAGCTTCTTCTGCATCAGTTTCGTATGACATTCCAAATGTTGCTGCAAATGTTG
ATTTTATCAATCTTATGTCATATGATCTGCATGGTTTGTGGGATTCAAAAACTGGCATCA
ATTCGCCACTTTATTCGGGACCAAGTGATGTCAGTTCATATGAAAAACAATTAAATGTAG
ACTCAATTGTTAATTATTGGTTAAATCAAGGATGTCCAAAGAGTAAATTAATTGTCGGAA
TACCACTTTATGGACGAACTTTCACATTAGCAAATTCGAATAATAATGGTGTGGGTGCTC
CTATATATGGTGGAGGAGAAATGGGTTCATTTGTTCCAGAGTCTGGCTTTTTAGGATATA
ATGAGATATGCTACAATATAAATAATAAAGGTTGGAGAAGATTTTGGGAAGACACACAAA
AAGTTCCTTATGCAGTTAGTGGCAATCAATGGGTTGGATATGATGATGCAGAATCATTAT
CTTATAAATTGAATTACATCAAAAACAGAGATTTAGGTGGTGCCATGTTTTGGTCAATTG
AGACTGATGATTTTGCAAATATTTGTGATAAAGGCAAATTTCCTTTGATAAAAGCTGCTT
TTAGTGCATTGATTAATAATTCGCCTGTTCCAATTACTACTGATAAACCAAATCCAACTG
AAAATAATGGTGTGACAACCACTACAACAACAACTCAAAAATCAAATAGTGGCTCAATTT
GTTCAAATGGTGATGGCATATATCCAGATCCATTAGATTGCAACAAATTTTATATATGTG
CTGCTAATGTTCCGTACCATCAATCGTGTGGTGTTGGCTTGAATTTTAATCCAAATGGAT
ATTGTGACTGGCCTTATAATTTTTCATGCTAG
>g12825.t3 Gene=g12825 Length=265
MSYDLHGLWDSKTGINSPLYSGPSDVSSYEKQLNVDSIVNYWLNQGCPKSKLIVGIPLYG
RTFTLANSNNNGVGAPIYGGGEMGSFVPESGFLGYNEICYNINNKGWRRFWEDTQKVPYA
VSGNQWVGYDDAESLSYKLNYIKNRDLGGAMFWSIETDDFANICDKGKFPLIKAAFSALI
NNSPVPITTDKPNPTENNGVTTTTTTTQKSNSGSICSNGDGIYPDPLDCNKFYICAANVP
YHQSCGVGLNFNPNGYCDWPYNFSC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g12825.t3 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 1 | 175 | 0.0e+00 |
| 12 | g12825.t3 | Gene3D | G3DSA:3.10.50.10 | - | 58 | 129 | 0.0e+00 |
| 10 | g12825.t3 | Gene3D | G3DSA:2.170.140.10 | Antimicrobial Protein | 206 | 265 | 0.0e+00 |
| 3 | g12825.t3 | PANTHER | PTHR11177 | CHITINASE | 1 | 244 | 0.0e+00 |
| 4 | g12825.t3 | PANTHER | PTHR11177:SF248 | CHITOTRIOSIDASE-1 | 1 | 244 | 0.0e+00 |
| 2 | g12825.t3 | Pfam | PF00704 | Glycosyl hydrolases family 18 | 1 | 158 | 0.0e+00 |
| 1 | g12825.t3 | Pfam | PF01607 | Chitin binding Peritrophin-A domain | 216 | 265 | 0.0e+00 |
| 13 | g12825.t3 | ProSiteProfiles | PS50940 | Chitin-binding type-2 domain profile. | 213 | 265 | 1.3e+01 |
| 8 | g12825.t3 | SMART | SM00636 | 2g34 | 1 | 158 | 2.2e-05 |
| 9 | g12825.t3 | SMART | SM00494 | chi_10 | 214 | 264 | 0.0e+00 |
| 7 | g12825.t3 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 1 | 197 | 0.0e+00 |
| 5 | g12825.t3 | SUPERFAMILY | SSF54556 | Chitinase insertion domain | 59 | 129 | 0.0e+00 |
| 6 | g12825.t3 | SUPERFAMILY | SSF57625 | Invertebrate chitin-binding proteins | 213 | 265 | 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 |
| GO:0005576 | extracellular region | CC |
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.
