General information for g4604.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Lactosylceramide 4-alpha-galactosyltransferase.
Parent gene
- The parent gene g4604 is located on chr_2: 3467585..3468700 (- 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_2 | g4604 | g4604.t1 | TTS | g4604.t1 | 3467315 | 3467315 |
| chr_2 | g4604 | g4604.t1 | isoform | g4604.t1 | 3467585 | 3468700 |
| chr_2 | g4604 | g4604.t1 | exon | g4604.t1.exon1 | 3467585 | 3467939 |
| chr_2 | g4604 | g4604.t1 | cds | g4604.t1.CDS1 | 3467585 | 3467939 |
| chr_2 | g4604 | g4604.t1 | exon | g4604.t1.exon2 | 3467993 | 3468404 |
| chr_2 | g4604 | g4604.t1 | cds | g4604.t1.CDS2 | 3467993 | 3468404 |
| chr_2 | g4604 | g4604.t1 | exon | g4604.t1.exon3 | 3468457 | 3468700 |
| chr_2 | g4604 | g4604.t1 | cds | g4604.t1.CDS3 | 3468457 | 3468700 |
| chr_2 | g4604 | g4604.t1 | TSS | g4604.t1 | 3468730 | 3468730 |
Sequences
>g4604.t1 Gene=g4604 Length=1011
ATGAATCAAATAAAATTTAAGAAACCTGTTGTATTATTATTTGCAATAATTGCTTTCCTT
ATAATTTATAGTGTTCTCATAAGTTTCATGTCAATTGAATGTGATCAAGCTATAATTATT
TCAGACGGTTTTAGAGAAATTCCATCTAATTTAATGTCTAGCCGAAATATTTATTTTTTG
GAGACACACAATACAAGTGATCATTTTTTAACAACTAGGGCTGCTTGTTCTATTGAATCA
GCTGCTCTGATGAACCCAAATACAAACATTTTTGTTCTCTTTCTCTCACCTTCAAAATAC
ACTCGACTCAAAAATTGGTCTCAATTTCAAGGAATTTTGAATTATAAAAATATTCATTTA
AAATATTTTAATACAGAAGATTTTACCAAAGACACAGTTATTGACGATTGGATTAATAAA
GGTTTATTGAGCAGTTCATGGTATCAAGTTGTACACACATCTGACATTTTAAGATATGCT
TTGCTTTATAAATATTCAGGAATTTATTTAGATCTCGATGTTATTGTAAGAAAATCATTA
GATGAAATTGAATTTGAAAACTTTGCATGCTTTCAAGATGATAGAGAAATTGTCAATAAC
GCAATTTTGAAGATTACCAATGATGATGGTGGAGTTTTAGGGAAAATGCTTCTCAATGAA
GTAATTTCTCATTTTGATGGTTTCGATTGGTCAATGAATGGTCCAAAACTACTAACTAGA
GTACTAAAAAATTACTGTGATGTAACAGATTTTCTTTCAACAAGTAAATGTGGAAATTTT
ACTATTCTTACTCAAGAACTTTGTTATCCAATTCCTTGGCAAAAATGGGATGATTATTTT
ACAGAGCAAGATTCACAAAAAGTTATGGAATCAGTTGAAAATTCTTATTTCGTTCACTTT
TGGAATAGAAAATCAGAAGGAAAAATGTTAGAAAAAAGAAGTCACGCTGCTTTCAATCAA
CTTGCATCAAAATATTGTCCACATGTGTATGCAACCAATGTTTTGATTTAA
>g4604.t1 Gene=g4604 Length=336
MNQIKFKKPVVLLFAIIAFLIIYSVLISFMSIECDQAIIISDGFREIPSNLMSSRNIYFL
ETHNTSDHFLTTRAACSIESAALMNPNTNIFVLFLSPSKYTRLKNWSQFQGILNYKNIHL
KYFNTEDFTKDTVIDDWINKGLLSSSWYQVVHTSDILRYALLYKYSGIYLDLDVIVRKSL
DEIEFENFACFQDDREIVNNAILKITNDDGGVLGKMLLNEVISHFDGFDWSMNGPKLLTR
VLKNYCDVTDFLSTSKCGNFTILTQELCYPIPWQKWDDYFTEQDSQKVMESVENSYFVHF
WNRKSEGKMLEKRSHAAFNQLASKYCPHVYATNVLI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4604.t1 | Gene3D | G3DSA:3.90.550.20 | - | 94 | 326 | 2.2E-9 |
| 3 | g4604.t1 | PANTHER | PTHR12042 | LACTOSYLCERAMIDE 4-ALPHA-GALACTOSYLTRANSFERASE ALPHA- 1,4-GALACTOSYLTRANSFERASE | 33 | 331 | 3.9E-67 |
| 1 | g4604.t1 | Pfam | PF04488 | Glycosyltransferase sugar-binding region containing DXD motif | 73 | 186 | 9.4E-15 |
| 2 | g4604.t1 | Pfam | PF04572 | Alpha 1,4-glycosyltransferase conserved region | 213 | 331 | 2.9E-35 |
| 7 | g4604.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 9 | g4604.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 32 | - |
| 8 | g4604.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 33 | 336 | - |
| 5 | g4604.t1 | SUPERFAMILY | SSF53448 | Nucleotide-diphospho-sugar transferases | 50 | 333 | 2.25E-32 |
| 4 | g4604.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 9 | 31 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K01988 (lactosylceramide 4-alpha-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