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.t10 TSS g877.t10 6618107 6618107
chr_3 g877 g877.t10 isoform g877.t10 6618133 6620155
chr_3 g877 g877.t10 exon g877.t10.exon1 6618133 6618367
chr_3 g877 g877.t10 cds g877.t10.CDS1 6618133 6618367
chr_3 g877 g877.t10 exon g877.t10.exon2 6618433 6618718
chr_3 g877 g877.t10 cds g877.t10.CDS2 6618433 6618718
chr_3 g877 g877.t10 exon g877.t10.exon3 6619057 6619626
chr_3 g877 g877.t10 cds g877.t10.CDS3 6619057 6619626
chr_3 g877 g877.t10 exon g877.t10.exon4 6619684 6620155
chr_3 g877 g877.t10 cds g877.t10.CDS4 6619684 6620155
chr_3 g877 g877.t10 TTS g877.t10 6620992 6620992

Sequences

>g877.t10 Gene=g877 Length=1563
ATGAAGCTCTCTTTAGCATTAATTGTTGTTTTTATCAATGGAATATTTGGTTTTAAAGTG
TTGGGAATTTTGCCTTTTGGCAGCAAGTCACATTTTGCAATTGGACATGCAATTTTGAAA
AGTTTAGCAGAAGCTGGACATAATGTAACGTCGATTTCACCATATCCATTAAAAGAACCT
ATGGAAAATTACAAAGATATCAGCACAGAAGATTACGTTGAAGTATTTTTTAAAAATAAT
GCTGTGAATATGTTTGCTTTTGAAAATACTCCTATCGTCAATAAAATTATGGAATTAATA
TTTATTTATTGGATTAATCGAAATGGCAATGAAGTTGTGAAATATCATGCAGTTCATCCT
AAAGTTATTGAATTTATGAACACTTATGAGAAGTTTGATATTTGCTTTATGGAAATTTTT
AATTATGATGCATTACTTGGAATTGCCGAACATGTTGGTTGCAAAGTTATTTCGTATACC
ACAACAGCTGTTGTTAAATGGGCTGATGATATGACTGGAAATGTACCAAGACCGTATGTT
CAATATTCAGATAAAATGTCATTCAGAGAACGACTTATGAATACATTTTACGCTCACATT
GAAGACATAGTTTATGAATTCATCATAAAACCAAACCAAAGAAGACTTTATGAGAAATAT
TTCCCAAATGCAACTAAAACATTTGACGAGATGTACAAAGATACTTCAATGATTTTCATG
AACACTCACATTTCACTGACAGCACCTCGTCCGTATTTACCAAGTTTTGTAGAAATTGGA
GGAATTCATATTCAACCTGTAAAAAAGTTGCCAAAAGTATTTCAAAATTTCTTAGATTCA
GCGACTGATGGTGTGATTTTATTTTCAATGGGTTCAGTAATTCGATCATACCAATGGCCA
GTTGAGAAACGTGAAGCATTCGTTAAAGTTTTTGGCAAATTGAAGCAAAAAGTACTTTGG
AAATATGAAAATGACACATTACCAAATAAACCTGATAATGTTATGATTAGTTCATGGTTG
CCACAAAGAGACATTTTGGCTCATCCTAATGTAAAAGCTTATATCTGTCATGGCGGACTA
TTAGGAACAACTGAAGCAGTTTATGAAGGAGTCCCTGTGCTTGGTATACCAATATTCGGA
GACCAAAAGACAATCATGGCTAAAGCAGTTACTCGTGGCTATGGATTGCAAGTTTATTTC
AAAGATGTTTCTGAAGAAACAATTGGTTCTGCCTTGGATGAATTATTGAACAATCCAATG
TACAAAGAAAATGCAAAAATTATTTCAACACGCTTTAAAGATCGACCAATGACACCACAA
CAATCAGTAGTTTATTGGACTGAATATGTTCATAGACACGGTGGAGCACCACACTTGAAA
GCTGCTGGAAATGATTTGGATTTTATCGCATTTCATATGATTGATGTTTATGCTGTTTTG
TTTTTTGGTGGAATTTCTTTCATTTTCATTAATTATTTGATTATTAAGTGGATTTTTATG
AAATTTTCTGGAAAACCAAAGAAGACAGAAAAGAAAAATGAGAAGAAGCTTAAAAAGAAA
TAA

>g877.t10 Gene=g877 Length=520
MKLSLALIVVFINGIFGFKVLGILPFGSKSHFAIGHAILKSLAEAGHNVTSISPYPLKEP
MENYKDISTEDYVEVFFKNNAVNMFAFENTPIVNKIMELIFIYWINRNGNEVVKYHAVHP
KVIEFMNTYEKFDICFMEIFNYDALLGIAEHVGCKVISYTTTAVVKWADDMTGNVPRPYV
QYSDKMSFRERLMNTFYAHIEDIVYEFIIKPNQRRLYEKYFPNATKTFDEMYKDTSMIFM
NTHISLTAPRPYLPSFVEIGGIHIQPVKKLPKVFQNFLDSATDGVILFSMGSVIRSYQWP
VEKREAFVKVFGKLKQKVLWKYENDTLPNKPDNVMISSWLPQRDILAHPNVKAYICHGGL
LGTTEAVYEGVPVLGIPIFGDQKTIMAKAVTRGYGLQVYFKDVSEETIGSALDELLNNPM
YKENAKIISTRFKDRPMTPQQSVVYWTEYVHRHGGAPHLKAAGNDLDFIAFHMIDVYAVL
FFGGISFIFINYLIIKWIFMKFSGKPKKTEKKNEKKLKKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g877.t10 CDD cd03784 GT1_Gtf-like 19 446 1.06074E-62
5 g877.t10 Gene3D G3DSA:3.40.50.2000 Glycogen Phosphorylase B; 265 434 6.2E-44
2 g877.t10 PANTHER PTHR48043 EG:EG0003.4 PROTEIN-RELATED 17 484 2.0E-128
3 g877.t10 PANTHER PTHR48043:SF114 DOROTHY, ISOFORM A-RELATED 17 484 2.0E-128
1 g877.t10 Pfam PF00201 UDP-glucoronosyl and UDP-glucosyl transferase 30 508 5.7E-80
8 g877.t10 Phobius SIGNAL_PEPTIDE Signal peptide region 1 17 -
9 g877.t10 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
10 g877.t10 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 12 -
12 g877.t10 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 13 17 -
7 g877.t10 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 18 475 -
11 g877.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 476 499 -
6 g877.t10 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 500 520 -
16 g877.t10 ProSitePatterns PS00375 UDP-glycosyltransferases signature. 339 382 -
4 g877.t10 SUPERFAMILY SSF53756 UDP-Glycosyltransferase/glycogen phosphorylase 20 459 4.19E-99
15 g877.t10 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 5 27 -
14 g877.t10 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 478 500 -

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