General information for g6225.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable chitinase 2.
Parent gene
- The parent gene g6225 is located on chr_2: 15405802..15408236 (- 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 | g6225 | g6225.t1 | TTS | g6225.t1 | 15405429 | 15405429 |
| chr_2 | g6225 | g6225.t1 | isoform | g6225.t1 | 15405802 | 15408236 |
| chr_2 | g6225 | g6225.t1 | exon | g6225.t1.exon1 | 15405802 | 15406144 |
| chr_2 | g6225 | g6225.t1 | cds | g6225.t1.CDS1 | 15405802 | 15406144 |
| chr_2 | g6225 | g6225.t1 | exon | g6225.t1.exon2 | 15406811 | 15407433 |
| chr_2 | g6225 | g6225.t1 | cds | g6225.t1.CDS2 | 15406811 | 15407433 |
| chr_2 | g6225 | g6225.t1 | exon | g6225.t1.exon3 | 15407803 | 15407815 |
| chr_2 | g6225 | g6225.t1 | cds | g6225.t1.CDS3 | 15407803 | 15407815 |
| chr_2 | g6225 | g6225.t1 | exon | g6225.t1.exon4 | 15407893 | 15408018 |
| chr_2 | g6225 | g6225.t1 | cds | g6225.t1.CDS4 | 15407893 | 15408018 |
| chr_2 | g6225 | g6225.t1 | exon | g6225.t1.exon5 | 15408109 | 15408236 |
| chr_2 | g6225 | g6225.t1 | cds | g6225.t1.CDS5 | 15408109 | 15408236 |
| chr_2 | g6225 | g6225.t1 | TSS | g6225.t1 | NA | NA |
Sequences
>g6225.t1 Gene=g6225 Length=1233
ATGAAAAATATTTTTTTATTAGATCCATGGCAAGATTTAGAAGATGATGGTGGCAAAGGA
GGCTATAAAAGATTGACAGCGTTCAAGCGCACAAATAGTCACCTGAAAGTGCTATTGGCT
ATTGGAGGGTGGAACGAAGGAAGCCGTAACTACTCAGAATTAGCCGGTGACCCGCGTCGT
AGAGGACGTTTTGTGAAACAAGCGTCGGAATTTGTGAGAAAATTTGATTTTGATGGCTTG
GATTTAGATTGGGAGTATCCTACACAGCGCAATGGATCGCAGCAAGACAAAGAGAGCTTT
GTGTTATTGGTTAAGGAGCTCTCGGTGGAATTTAAAAAGCATAATCTCTACCTCTCTAGC
GCTTTTGGTGCGTCAAAGAAGATAATTGACTCAGCGTACAATGTAAAGGCTCTTGCGCCA
TATTTGGACTCATTTCATATCATGTGCTATGATTATTTTGGTAGTTGGGATAAAAAAGTT
GGTCTTAATGCACCATTAGAAACTGATGATGATTTAAATGTAAAATTTTCAATTGATTAT
TTCTTGAAACTTGGTGCACCAGCTGAAAAAATTATGATGGGTTTGCCATTTTATGGTCGA
ACATTTTTAGCGAATACAAATGGTGATTTAGGTGATGAAACTGATGATTTGGGATTTTCT
GGACCTTATACCAGAGAGAATGGATTTATGGGATATAACGAAATTTGTCAAGCATTGAGT
ACAAGTTCAGAATGGCGATCTGATTGGCATGCTGAATCATCTGAGGCTATTGCAAGAGTT
AAATATGCTAATGAAACACAGACACGCGTTGTTTCATATGATTCATCTAGGTCCATTGCT
AACAAAGTCCATTATGCGATTAGAAAAGGTCTGGGAGGATTAATGGTTTGGTCCATTGAT
ACTGACGATTTCAGAGGCGAATGTGATGAAAAGATAAATTTTGACACATTCAGTGACTTT
AGAGCACAACCAAAAGTGAAGTTAAATATTCCAAAGAGAATGGAACGAAACTATCCATTA
TTGAGGACCTTAAATGATGCTATTGTTGTAACGCTTGACGAGTTAAGACAAGAGGAGAAT
TTAATGAAAGAGAATGAAGTGAATGTGAATGAGAACAATAAGGATAATATGGTTGGAAAC
AAAAACAATAGTCTTTCAAAAACCGCAACACCTGTAGCATTTTCCTCAACTGTTTTATGC
CTTTTTGCTGTTCTATCGAAGTTATTGCTGTAA
>g6225.t1 Gene=g6225 Length=410
MKNIFLLDPWQDLEDDGGKGGYKRLTAFKRTNSHLKVLLAIGGWNEGSRNYSELAGDPRR
RGRFVKQASEFVRKFDFDGLDLDWEYPTQRNGSQQDKESFVLLVKELSVEFKKHNLYLSS
AFGASKKIIDSAYNVKALAPYLDSFHIMCYDYFGSWDKKVGLNAPLETDDDLNVKFSIDY
FLKLGAPAEKIMMGLPFYGRTFLANTNGDLGDETDDLGFSGPYTRENGFMGYNEICQALS
TSSEWRSDWHAESSEAIARVKYANETQTRVVSYDSSRSIANKVHYAIRKGLGGLMVWSID
TDDFRGECDEKINFDTFSDFRAQPKVKLNIPKRMERNYPLLRTLNDAIVVTLDELRQEEN
LMKENEVNVNENNKDNMVGNKNNSLSKTATPVAFSSTVLCLFAVLSKLLL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g6225.t1 | Coils | Coil | Coil | 352 | 375 | - |
| 6 | g6225.t1 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 8 | 311 | 4.5E-98 |
| 7 | g6225.t1 | Gene3D | G3DSA:3.10.50.10 | - | 197 | 273 | 4.5E-98 |
| 2 | g6225.t1 | PANTHER | PTHR11177:SF344 | CHITINASE 2-RELATED | 3 | 344 | 3.8E-94 |
| 3 | g6225.t1 | PANTHER | PTHR11177 | CHITINASE | 3 | 344 | 3.8E-94 |
| 1 | g6225.t1 | Pfam | PF00704 | Glycosyl hydrolases family 18 | 4 | 302 | 1.3E-71 |
| 10 | g6225.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 391 | - |
| 11 | g6225.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 392 | 409 | - |
| 9 | g6225.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 410 | 410 | - |
| 12 | g6225.t1 | ProSitePatterns | PS01095 | Chitinases family 18 active site. | 77 | 85 | - |
| 13 | g6225.t1 | SMART | SM00636 | 2g34 | 1 | 302 | 4.3E-86 |
| 5 | g6225.t1 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 3 | 317 | 1.66E-74 |
| 4 | g6225.t1 | SUPERFAMILY | SSF54556 | Chitinase insertion domain | 198 | 249 | 3.51E-10 |
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:0004553 | hydrolase activity, hydrolyzing O-glycosyl compounds | MF |
| GO:0008061 | chitin binding | MF |
| GO:0005975 | carbohydrate metabolic process | BP |
KEGG
Orthology
- This transcript has been annotated with K01183 (chitinase)
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.
