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 g877 g877.t18 TSS g877.t18 6618107 6618107
chr_3 g877 g877.t18 isoform g877.t18 6618133 6620998
chr_3 g877 g877.t18 exon g877.t18.exon1 6618133 6618371
chr_3 g877 g877.t18 exon g877.t18.exon2 6618433 6618718
chr_3 g877 g877.t18 cds g877.t18.CDS1 6618447 6618718
chr_3 g877 g877.t18 exon g877.t18.exon3 6619039 6619626
chr_3 g877 g877.t18 cds g877.t18.CDS2 6619039 6619626
chr_3 g877 g877.t18 exon g877.t18.exon4 6619684 6620998
chr_3 g877 g877.t18 cds g877.t18.CDS3 6619684 6620155
chr_3 g877 g877.t18 TTS g877.t18 6620992 6620992

Sequences

>g877.t18 Gene=g877 Length=2428
ATGAAGCTCTCTTTAGCATTAATTGTTGTTTTTATCAATGGAATATTTGGTTTTAAAGTG
TTGGGAATTTTGCCTTTTGGCAGCAAGTCACATTTTGCAATTGGACATGCAATTTTGAAA
AGTTTAGCAGAAGCTGGACATAATGTAACGTCGATTTCACCATATCCATTAAAAGAACCT
ATGGAAAATTACAAAGATATCAGCACAGAAGATTACGTTGAAGTATTTTTTAAAAGTGAA
TAATGCTGTGAATATGTTTGCTTTTGAAAATACTCCTATCGTCAATAAAATTATGGAATT
AATATTTATTTATTGGATTAATCGAAATGGCAATGAAGTTGTGAAATATCATGCAGTTCA
TCCTAAAGTTATTGAATTTATGAACACTTATGAGAAGTTTGATATTTGCTTTATGGAAAT
TTTTAATTATGATGCATTACTTGGAATTGCCGAACATGTTGGTTGCAAAGTTATTTCGTA
TACCACAACAGCTGTTGTTAAATGGGCTGATGATATGACTGGAAACGTTTCACCACCATC
ATATGTACCAAGACCGTATGTTCAATATTCAGATAAAATGTCATTCAGAGAACGACTTAT
GAATACATTTTACGCTCACATTGAAGACATAGTTTATGAATTCATCATAAAACCAAACCA
AAGAAGACTTTATGAGAAATATTTCCCAAATGCAACTAAAACATTTGACGAGATGTACAA
AGATACTTCAATGATTTTCATGAACACTCACATTTCACTGACAGCACCTCGTCCGTATTT
ACCAAGTTTTGTAGAAATTGGAGGAATTCATATTCAACCTGTAAAAAAGTTGCCAAAAGT
ATTTCAAAATTTCTTAGATTCAGCGACTGATGGTGTGATTTTATTTTCAATGGGTTCAGT
AATTCGATCATACCAATGGCCAGTTGAGAAACGTGAAGCATTCGTTAAAGTTTTTGGCAA
ATTGAAGCAAAAAGTACTTTGGAAATATGAAAATGACACATTACCAAATAAACCTGATAA
TGTTATGATTAGTTCATGGTTGCCACAAAGAGACATTTTGGCTCATCCTAATGTAAAAGC
TTATATCTGTCATGGCGGACTATTAGGAACAACTGAAGCAGTTTATGAAGGAGTCCCTGT
GCTTGGTATACCAATATTCGGAGACCAAAAGACAATCATGGCTAAAGCAGTTACTCGTGG
CTATGGATTGCAAGTTTATTTCAAAGATGTTTCTGAAGAAACAATTGGTTCTGCCTTGGA
TGAATTATTGAACAATCCAATGTACAAAGAAAATGCAAAAATTATTTCAACACGCTTTAA
AGATCGACCAATGACACCACAACAATCAGTAGTTTATTGGACTGAATATGTTCATAGACA
CGGTGGAGCACCACACTTGAAAGCTGCTGGAAATGATTTGGATTTTATCGCATTTCATAT
GATTGATGTTTATGCTGTTTTGTTTTTTGGTGGAATTTCTTTCATTTTCATTAATTATTT
GATTATTAAGTGGATTTTTATGAAATTTTCTGGAAAACCAAAGAAGACAGAAAAGAAAAA
TGAGAAGAAGCTTAAAAAGAAATAAACAAGAAATAATAGAATATTTCAACCATTAGCTGT
GACCAGTAAAATTTCAATCAGGGAACTGAGTTCTGTTCATATCGAATGAAAAATATTTTT
GAACAAATTTTAAAAGAAATCTCTGAATTCATTTATTTATTTACATTTAAGATTATGGCT
TAATATTTTGCAACAATTAAAAACTTAGTTCATTAAAAAGTGTTCCTTACATTTTTCATT
ATTTTATATTTTATTATTTCTTGAAAAATTATTTAAGTTCAAAATAATTTCCTTAAAATT
CCATGTAAAGCTATAAACAGTGATATTTTCTTTTACTTTTGCTCAATTAAATTTTATTAT
TTATTTTCTAGCTATATTTTCATTTTAATTAAAGTTCATTTTCCTAAAAAAATTTTTGGC
AAAAGAAATCATGAAATTTTCAAAAAACATGAAAGAATGAGAGTGATTGTAAATTTAATG
AAAAACTCTAGGTGATTTTTATTGAATATTGAAGGAACAATTTAGAAATTAAGTTTTAAA
TTTTCTAAAAATAAAACTTTTTCCTTTTGATTAATTTATCAAAAAAAAAAATTTATTGAA
TCAAAAACTTTTCAGACAGAATATTAAAATTATTTACACATCAGCTTAAGCAAAAAAGGA
AAAGTTTATCATAAGTTAAATAAAAAATAAAACTTTCTCTTTTCAATCGTAGTCAAATAG
TAGAAACTAAAATTCAATATTTATTCAGTCGTTTTTAAAGAAAAATAAAAAAGAAAAATT
GAATAAAATGATAAATTGCAACAAGCAATAAATTTTTTTTTCCATGCAATGATGTTGAAA
AATAAATAAGATAAATTGTAATAAAATA

>g877.t18 Gene=g877 Length=443
MFAFENTPIVNKIMELIFIYWINRNGNEVVKYHAVHPKVIEFMNTYEKFDICFMEIFNYD
ALLGIAEHVGCKVISYTTTAVVKWADDMTGNVSPPSYVPRPYVQYSDKMSFRERLMNTFY
AHIEDIVYEFIIKPNQRRLYEKYFPNATKTFDEMYKDTSMIFMNTHISLTAPRPYLPSFV
EIGGIHIQPVKKLPKVFQNFLDSATDGVILFSMGSVIRSYQWPVEKREAFVKVFGKLKQK
VLWKYENDTLPNKPDNVMISSWLPQRDILAHPNVKAYICHGGLLGTTEAVYEGVPVLGIP
IFGDQKTIMAKAVTRGYGLQVYFKDVSEETIGSALDELLNNPMYKENAKIISTRFKDRPM
TPQQSVVYWTEYVHRHGGAPHLKAAGNDLDFIAFHMIDVYAVLFFGGISFIFINYLIIKW
IFMKFSGKPKKTEKKNEKKLKKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g877.t18 CDD cd03784 GT1_Gtf-like 37 369 4.27358E-54
5 g877.t18 Gene3D G3DSA:3.40.50.2000 Glycogen Phosphorylase B; 188 357 4.4E-44
2 g877.t18 PANTHER PTHR48043 EG:EG0003.4 PROTEIN-RELATED 8 408 9.2E-119
3 g877.t18 PANTHER PTHR48043:SF114 DOROTHY, ISOFORM A-RELATED 8 408 9.2E-119
1 g877.t18 Pfam PF00201 UDP-glucoronosyl and UDP-glucosyl transferase 46 431 3.5E-83
7 g877.t18 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 398 -
8 g877.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 399 422 -
6 g877.t18 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 423 443 -
11 g877.t18 ProSitePatterns PS00375 UDP-glycosyltransferases signature. 262 305 -
4 g877.t18 SUPERFAMILY SSF53756 UDP-Glycosyltransferase/glycogen phosphorylase 32 382 2.13E-93
10 g877.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 401 423 -

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

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.

Raw TPM values