General information for g3643.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 2-hydroxyacylsphingosine 1-beta-galactosyltransferase.
Parent gene
- The parent gene g3643 is located on chr_3: 27152297..27155113 (- 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_3 | g3643 | g3643.t4 | TTS | g3643.t4 | 27152250 | 27152250 |
| chr_3 | g3643 | g3643.t4 | isoform | g3643.t4 | 27152297 | 27154390 |
| chr_3 | g3643 | g3643.t4 | exon | g3643.t4.exon1 | 27152297 | 27152759 |
| chr_3 | g3643 | g3643.t4 | cds | g3643.t4.CDS1 | 27152297 | 27152759 |
| chr_3 | g3643 | g3643.t4 | exon | g3643.t4.exon2 | 27152819 | 27153406 |
| chr_3 | g3643 | g3643.t4 | cds | g3643.t4.CDS2 | 27152819 | 27153406 |
| chr_3 | g3643 | g3643.t4 | exon | g3643.t4.exon3 | 27153888 | 27154158 |
| chr_3 | g3643 | g3643.t4 | cds | g3643.t4.CDS3 | 27153888 | 27154158 |
| chr_3 | g3643 | g3643.t4 | exon | g3643.t4.exon4 | 27154220 | 27154390 |
| chr_3 | g3643 | g3643.t4 | cds | g3643.t4.CDS4 | 27154220 | 27154301 |
| chr_3 | g3643 | g3643.t4 | TSS | g3643.t4 | 27154486 | 27154486 |
Sequences
>g3643.t4 Gene=g3643 Length=1493
GTTTGATTCCATTTGGTAGCAAATCTCATTTTGCTATAGGAAACAGTATTTTAAGAACAC
TTCAAAATGCTGGTCATGATGTTACAGTTATGACTGCATTTCCTTCTAAGAAGCAAGAAC
AAAACTATCGTGAAATTAAATTAACTAAAATTATGGAAGTTTTCGACCGAGGTGACGAAG
TTAATCCATTTATTTTTGGTCAGTTACCAGCTATTATGACATTTTTTTTGATATCAAAAA
TGAACACTGATGTTGTTGACTTGTTTATGCAAGAGCTAGAAGTTCAAAAGTTTCTTGAAG
AAGATAAAAGCAAATATGATATTTGTTTGTTTGAAATTTTTATGGTAGATGCATTATTAG
GAATTCCAGAGAGATATGGTTGTCATTTGATTTCATACACAACATTTGCAGCAGTTAGAT
GGACTGATGATATGACAGGATTAGAATCCCCAGCATCTTATGTACCAAATCCTTTCTTAA
AATATACTGATAAAATGTCATTTGGAGAAAGACTTTGGAATTCAGCATTTTCTCTTGTTG
AGCGATTTATTTATCATTTCTATCATTTACCAAATCATCGTAAACGTTACAAAAAATATT
TCCCAGATGCTAAACGCAGTTTTGAAGAAATGTATAAGGGATCATCTATAATATTTTCTA
ATACTCATGTCAGTTCTTCAACGGTCCGTCCATTTATGCCTAATGTAATAGAAATAGCTG
GTATCCATATGAAACCTGCTCAACTTTTACCAAAGGACATACAAGAATTCCTTGATTCAG
CTACAGATGGTGCAATTCTATTCTCCATGGGATCATTCATTCAAAGTAAAATGTGGCCGG
TAGAGAAGCGTGATGCATTGATAAAAGCTTTCGGAAAATTAAATCTTAAAGTAATATGGA
AGTATGAGAATGAAACATTACCTAATAATCCTGGTAATATCAAAATAAGTTCGTGGTTGC
CACAAAGAGATATTTTGGCTCACAAAAATATAAAACTGTTTATCACACATGGTGGACTAT
TAGGAACAACTGAAGCATTAGTTGAAGGTGTACCTGTTTTAGGATTACCAATTTTTGGAG
ATCAAAAAATGAACATGGCAAAGACAGTGCTTCGTGGCTATGGTTTACAAATCTCTTTTC
AAGATATAGAAGAACAAAGAGTATCGGATGCTATTAATGAGCTTTTAACAAATCCAAAAT
ACAAAGAGAATGCAATGACTGTTTCAAAGAGATTTATTGACAGACCAATGACACCGCAAG
AATCTGTTGTTTATTGGACGGAATATGTAGCAAGGCATGATGGTGCACATCATTTAAGAG
CATATTCCACTCAATTAAATTTTATAGAATTTCATATGTTTGATGTTTATGGGGCTCTTA
TTTTAATTGCACTTGTTATAATGTACATTCAATTTTTAGTATTGAGGGCAATTTTAAGGA
AAATTTTTAAAAGAAAAAATTCTAAAAGTGAAAATAAAATTAAAAAAAATTGA
>g3643.t4 Gene=g3643 Length=467
MTAFPSKKQEQNYREIKLTKIMEVFDRGDEVNPFIFGQLPAIMTFFLISKMNTDVVDLFM
QELEVQKFLEEDKSKYDICLFEIFMVDALLGIPERYGCHLISYTTFAAVRWTDDMTGLES
PASYVPNPFLKYTDKMSFGERLWNSAFSLVERFIYHFYHLPNHRKRYKKYFPDAKRSFEE
MYKGSSIIFSNTHVSSSTVRPFMPNVIEIAGIHMKPAQLLPKDIQEFLDSATDGAILFSM
GSFIQSKMWPVEKRDALIKAFGKLNLKVIWKYENETLPNNPGNIKISSWLPQRDILAHKN
IKLFITHGGLLGTTEALVEGVPVLGLPIFGDQKMNMAKTVLRGYGLQISFQDIEEQRVSD
AINELLTNPKYKENAMTVSKRFIDRPMTPQESVVYWTEYVARHDGAHHLRAYSTQLNFIE
FHMFDVYGALILIALVIMYIQFLVLRAILRKIFKRKNSKSENKIKKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g3643.t4 | CDD | cd03784 | GT1_Gtf-like | 23 | 396 | 9.21564E-51 |
| 5 | g3643.t4 | Gene3D | G3DSA:3.40.50.2000 | Glycogen Phosphorylase B; | 215 | 383 | 4.8E-43 |
| 2 | g3643.t4 | PANTHER | PTHR48043 | EG:EG0003.4 PROTEIN-RELATED | 4 | 440 | 1.9E-113 |
| 3 | g3643.t4 | PANTHER | PTHR48043:SF114 | DOROTHY, ISOFORM A-RELATED | 4 | 440 | 1.9E-113 |
| 1 | g3643.t4 | Pfam | PF00201 | UDP-glucoronosyl and UDP-glucosyl transferase | 103 | 456 | 3.0E-78 |
| 7 | g3643.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 425 | - |
| 8 | g3643.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 426 | 449 | - |
| 6 | g3643.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 450 | 467 | - |
| 11 | g3643.t4 | ProSitePatterns | PS00375 | UDP-glycosyltransferases signature. | 289 | 332 | - |
| 4 | g3643.t4 | SUPERFAMILY | SSF53756 | UDP-Glycosyltransferase/glycogen phosphorylase | 38 | 409 | 2.27E-91 |
| 10 | g3643.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 427 | 449 | - |
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 transcript has been annotated with K04628 (ceramide galactosyltransferase)
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. There were no conditions that were differentially expressed