Gene loci information

Transcript annotation

  • This transcript has been annotated as 2-hydroxyacylsphingosine 1-beta-galactosyltransferase.

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_3 g3643 g3643.t2 TTS g3643.t2 27152250 27152250
chr_3 g3643 g3643.t2 isoform g3643.t2 27152297 27153406
chr_3 g3643 g3643.t2 exon g3643.t2.exon1 27152297 27152759
chr_3 g3643 g3643.t2 cds g3643.t2.CDS1 27152297 27152759
chr_3 g3643 g3643.t2 exon g3643.t2.exon2 27152819 27153406
chr_3 g3643 g3643.t2 cds g3643.t2.CDS2 27152819 27153354
chr_3 g3643 g3643.t2 TSS g3643.t2 NA NA

Sequences

>g3643.t2 Gene=g3643 Length=1051
AGAATCCCCAGCATCTTATGTACCAAATCCTTTCTTAAAATATACTGATAAAATGTCATT
TGGAGAAAGACTTTGGAATTCAGCATTTTCTCTTGTTGAGCGATTTATTTATCATTTCTA
TCATTTACCAAATCATCGTAAACGTTACAAAAAATATTTCCCAGATGCTAAACGCAGTTT
TGAAGAAATGTATAAGGGATCATCTATAATATTTTCTAATACTCATGTCAGTTCTTCAAC
GGTCCGTCCATTTATGCCTAATGTAATAGAAATAGCTGGTATCCATATGAAACCTGCTCA
ACTTTTACCAAAGGACATACAAGAATTCCTTGATTCAGCTACAGATGGTGCAATTCTATT
CTCCATGGGATCATTCATTCAAAGTAAAATGTGGCCGGTAGAGAAGCGTGATGCATTGAT
AAAAGCTTTCGGAAAATTAAATCTTAAAGTAATATGGAAGTATGAGAATGAAACATTACC
TAATAATCCTGGTAATATCAAAATAAGTTCGTGGTTGCCACAAAGAGATATTTTGGCTCA
CAAAAATATAAAACTGTTTATCACACATGGTGGACTATTAGGAACAACTGAAGCATTAGT
TGAAGGTGTACCTGTTTTAGGATTACCAATTTTTGGAGATCAAAAAATGAACATGGCAAA
GACAGTGCTTCGTGGCTATGGTTTACAAATCTCTTTTCAAGATATAGAAGAACAAAGAGT
ATCGGATGCTATTAATGAGCTTTTAACAAATCCAAAATACAAAGAGAATGCAATGACTGT
TTCAAAGAGATTTATTGACAGACCAATGACACCGCAAGAATCTGTTGTTTATTGGACGGA
ATATGTAGCAAGGCATGATGGTGCACATCATTTAAGAGCATATTCCACTCAATTAAATTT
TATAGAATTTCATATGTTTGATGTTTATGGGGCTCTTATTTTAATTGCACTTGTTATAAT
GTACATTCAATTTTTAGTATTGAGGGCAATTTTAAGGAAAATTTTTAAAAGAAAAAATTC
TAAAAGTGAAAATAAAATTAAAAAAAATTGA

>g3643.t2 Gene=g3643 Length=332
MSFGERLWNSAFSLVERFIYHFYHLPNHRKRYKKYFPDAKRSFEEMYKGSSIIFSNTHVS
SSTVRPFMPNVIEIAGIHMKPAQLLPKDIQEFLDSATDGAILFSMGSFIQSKMWPVEKRD
ALIKAFGKLNLKVIWKYENETLPNNPGNIKISSWLPQRDILAHKNIKLFITHGGLLGTTE
ALVEGVPVLGLPIFGDQKMNMAKTVLRGYGLQISFQDIEEQRVSDAINELLTNPKYKENA
MTVSKRFIDRPMTPQESVVYWTEYVARHDGAHHLRAYSTQLNFIEFHMFDVYGALILIAL
VIMYIQFLVLRAILRKIFKRKNSKSENKIKKN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g3643.t2 CDD cd03784 GT1_Gtf-like 28 261 4.19985E-49
5 g3643.t2 Gene3D G3DSA:3.40.50.2000 Glycogen Phosphorylase B; 80 248 2.2E-43
2 g3643.t2 PANTHER PTHR48043 EG:EG0003.4 PROTEIN-RELATED 1 313 1.8E-96
3 g3643.t2 PANTHER PTHR48043:SF59 UDP-GLUCURONOSYLTRANSFERASE 1 313 1.8E-96
1 g3643.t2 Pfam PF00201 UDP-glucoronosyl and UDP-glucosyl transferase 1 321 1.1E-71
7 g3643.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 290 -
8 g3643.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 291 314 -
6 g3643.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 315 332 -
11 g3643.t2 ProSitePatterns PS00375 UDP-glycosyltransferases signature. 154 197 -
4 g3643.t2 SUPERFAMILY SSF53756 UDP-Glycosyltransferase/glycogen phosphorylase 1 274 8.03E-79
10 g3643.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 292 314 -

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:0008194 UDP-glycosyltransferase 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. There were no conditions that were differentially expressed