Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Acidic mammalian chitinase.

Parent gene

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 g11075 g11075.t3 TSS g11075.t3 13789172 13789172
chr_1 g11075 g11075.t3 isoform g11075.t3 13789220 13790606
chr_1 g11075 g11075.t3 exon g11075.t3.exon1 13789220 13789280
chr_1 g11075 g11075.t3 exon g11075.t3.exon2 13789455 13789681
chr_1 g11075 g11075.t3 exon g11075.t3.exon3 13789744 13790606
chr_1 g11075 g11075.t3 cds g11075.t3.CDS1 13790061 13790606
chr_1 g11075 g11075.t3 TTS g11075.t3 13790706 13790706

Sequences

>g11075.t3 Gene=g11075 Length=1151
ATGAAAAACTTGTTGGGCTTTTTGATTTTGAGTTCAATTTTCTTTGCTGCATTTGCTGCA
ACTATTGGGGAACGTGGTCACATTATCGAACTGGTGATGCACATTTTAGTATTGATAACA
TTGATTTGGCTCTTTGCACACATTTTGTTTATTCATTCTTGGGAGCTACTCCTGAAGGGC
ATGTTATTCATTTAGATCCAGTTGTTGATCTTGAACTTGGTTATATTTCAAGATTTACAG
CATTAAAAAGTAGAAGTCCTCAAACGAAATTCTTGTTCAGTGTTGGAGGTTATTCATTTG
GTTCTGAAATTTTCTCACGCCTTGCTTCAACTGCTGCAACTCGCGCTACATTTGCACAAA
GTGTGCTTGCAAAAATCAATGAATTTAATTTTGATGGCTTTGATCTCGATTGGGAATGGC
CAGGACAACGAAATGGAAGCAGTCCTAATGATCGAGATAATTTTGTTCTTCTTTGTGCTG
AAATTCATCGTGTGCTGCAACCAGCTGGAAAAGAATTTGGCATTGCAGTGGCAGCAGTGG
AAAGCTCTGCAGCAATTTCTTATGATGTTCCAAGAGTGCAAGCAAATGTTGATTTCATTT
TTCTTATGACTTATGACATGCATGGATCATGGAACTCTTTTACTGGAATTCATGCAGCAT
TGTATGCTGGTCCAGCTGATACAAATTCATTTCTACAGACATTAAATGTACATGCATCAG
TAACATGGTGGTTAAATCAAGGCACACCACGTAATAAATTAGTTGTTGGTATGCCGTCTT
ATGGTCGAAGTTTTACACTTCGAAGTGCAGCTAATAATGCTATTGGAGCTCCTGCAACTG
GGGCCGGTAATCCTGGTTTTTTATTAAACGAACCTGGTTTTCTTGGTTATAATGAAATTT
GTCAAATGGTCAGAACTTGGGGATATACAAGAGTTTGGCAATCACAACAATTAGTTCCAT
ATGCATTCAATGGAAATCAATGGGTTGGCTATGATGATACTGAATCAATAAGACACAAAT
TACAATACATAATCGATAATAATCTTGCTGGCTCTATGTGGTGGTCAATTGAGACGGAAG
ATTTTCATAATCGTTGCGGAAATGGAAATTCACCATTAATTCGATTAGCTCAAGAAATGA
TGAATTGGTAG

>g11075.t3 Gene=g11075 Length=181
MTYDMHGSWNSFTGIHAALYAGPADTNSFLQTLNVHASVTWWLNQGTPRNKLVVGMPSYG
RSFTLRSAANNAIGAPATGAGNPGFLLNEPGFLGYNEICQMVRTWGYTRVWQSQQLVPYA
FNGNQWVGYDDTESIRHKLQYIIDNNLAGSMWWSIETEDFHNRCGNGNSPLIRLAQEMMN
W

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g11075.t3 Gene3D G3DSA:3.20.20.80 Glycosidases 1 176 0.0e+00
8 g11075.t3 Gene3D G3DSA:3.10.50.10 - 58 129 0.0e+00
2 g11075.t3 PANTHER PTHR11177 CHITINASE 1 173 0.0e+00
3 g11075.t3 PANTHER PTHR11177:SF360 CHITINASE 12-RELATED 1 173 0.0e+00
1 g11075.t3 Pfam PF00704 Glycosyl hydrolases family 18 1 156 0.0e+00
6 g11075.t3 SMART SM00636 2g34 1 158 1.6e-05
5 g11075.t3 SUPERFAMILY SSF51445 (Trans)glycosidases 1 176 0.0e+00
4 g11075.t3 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.

Raw TPM values