General information for g11384.t5
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Chondroitin sulfate synthase 3.
Parent gene
- The parent gene g11384 is located on chr_1: 15889093..15890377 (+ 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 | g11384 | g11384.t5 | isoform | g11384.t5 | 15888197 | 15889093 |
| chr_1 | g11384 | g11384.t5 | exon | g11384.t5.exon1 | 15888197 | 15889093 |
| chr_1 | g11384 | g11384.t5 | cds | g11384.t5.CDS1 | 15888560 | 15889093 |
| chr_1 | g11384 | g11384.t5 | TTS | g11384.t5 | 15889309 | 15889309 |
| chr_1 | g11384 | g11384.t5 | TSS | g11384.t5 | NA | NA |
Sequences
>g11384.t5 Gene=g11384 Length=897
GTTATTCTCAAGCCTTCAGAGAATGTTGATCTCATAGTATCATTATTCATCAATAATAGC
ACCGATCCAAACATATCCTCTATTTTACAACTGATTGATTATCTTAACAACAAATATCAC
CGACAATCAATAGTTTCTATAAAACTTTATGGTGAATTTTCTAGAGGTGTAGCCATCAAC
ACAGCAATTCAATCGTCAAAAATTTCCAATAACGACATAATTTTTCTCATTGATGTTGAT
ATAATTTTTACATCACTCACAATTAGACGAATAAGACAAAATACAATAAGGAATAAACAA
ATTTACTTGCCAATTGTATTTAGTGAATATAATCCAGATATAGTTTCTTTAAATCGACCA
CCAATGCCAAAATTAAATGGTGGAAATAATTTTTTGTCAAATTATCGTATAATGTCAAAA
TATTACATGTTTTATGCTAATCAAACAGCAGACTTTGTAAACAATGAAAGTGGTTATTTC
CGTGAATTCGGTTATGGTTTAGTTTCAATCTACAAATGTGATATTATGAATAGTAAAATA
AATGGCTTTGTAACTGATGTTAAGGGATGGGGACTTGAGGATGTAAAATTCTTAGAAAGA
ATTCTCACTGCAAGCTATCAAGTTCAGAATCAGTATATTTTATCAGTTGCCGAAGGCAAT
GAGATGAAAAACATTTCTAGCCATAATTTAGACATTTTTCGATCACCCGACTCATCGCTG
TGGCACATTTTCCATAATATTGCATGTGATAGCAATTTAGAAAAGAATCAATATAAAATG
TGTCTTGGTACATCTGCAAGTACACTAGGCAATTTCCGTTTATTGAAAGAAAAGTACATT
CTTCAAAATGATTTTATGGAGTTTATGAGTAGAATTAAAGAAATAGTTGCAAATTAA
>g11384.t5 Gene=g11384 Length=177
MPKLNGGNNFLSNYRIMSKYYMFYANQTADFVNNESGYFREFGYGLVSIYKCDIMNSKIN
GFVTDVKGWGLEDVKFLERILTASYQVQNQYILSVAEGNEMKNISSHNLDIFRSPDSSLW
HIFHNIACDSNLEKNQYKMCLGTSASTLGNFRLLKEKYILQNDFMEFMSRIKEIVAN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g11384.t5 | Gene3D | G3DSA:3.90.550.10 | Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A | 8 | 163 | 3.0e-07 |
| 2 | g11384.t5 | PANTHER | PTHR12369 | CHONDROITIN SYNTHASE | 32 | 163 | 0.0e+00 |
| 3 | g11384.t5 | PANTHER | PTHR12369:SF11 | HEXOSYLTRANSFERASE | 32 | 163 | 0.0e+00 |
| 1 | g11384.t5 | Pfam | PF05679 | Chondroitin N-acetylgalactosaminyltransferase | 32 | 153 | 0.0e+00 |
| 4 | g11384.t5 | SUPERFAMILY | SSF53448 | Nucleotide-diphospho-sugar transferases | 37 | 145 | 9.6e-06 |
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:0032580 | Golgi cisterna membrane | CC |
| GO:0008376 | acetylgalactosaminyltransferase activity | MF |
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.
