General information for g4600.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 g4600 is located on chr_2: 3454678..3455841 (- 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 | g4600 | g4600.t1 | isoform | g4600.t1 | 3454678 | 3455841 |
| chr_2 | g4600 | g4600.t1 | exon | g4600.t1.exon1 | 3454678 | 3455029 |
| chr_2 | g4600 | g4600.t1 | cds | g4600.t1.CDS1 | 3454678 | 3455029 |
| chr_2 | g4600 | g4600.t1 | exon | g4600.t1.exon2 | 3455083 | 3455494 |
| chr_2 | g4600 | g4600.t1 | cds | g4600.t1.CDS2 | 3455083 | 3455494 |
| chr_2 | g4600 | g4600.t1 | exon | g4600.t1.exon3 | 3455583 | 3455841 |
| chr_2 | g4600 | g4600.t1 | cds | g4600.t1.CDS3 | 3455583 | 3455841 |
| chr_2 | g4600 | g4600.t1 | TSS | g4600.t1 | NA | NA |
| chr_2 | g4600 | g4600.t1 | TTS | g4600.t1 | NA | NA |
Sequences
>g4600.t1 Gene=g4600 Length=1023
ATGAATCACAATAAACTCAAAAAAATTTTAATTTTAATTCTTATAAAATTTCTCATAGTT
TTTATAATTCATCGATTTTATTTATATCAGCAATGGTTTCAAGACGAGTGCAATAAAAAT
ACTGCAATTATAATTGAAAATAATTTTAATCAAGTTCCTATTGAAATGCTAAAAAACGAA
ACAATTTATTTTCTTGAAACACACAATTCAAGTGATCATGAACTCACAGCTAGACAGGCA
TGTGCTATAGAATCAGCAGCTTATATGAATCCAAACACTAACGTTTTTGTTCTTTTTTTA
TCGTCATCAAATCACATTCGTCTCAAAAATTGGTCACAATTTCAAAGAATTTTAGATTAT
AAAAATATTCATTTAAAGTATTTTCATATGGATGATATAATAAAAGGTACTGTAGTTGAG
GATTTTTTGACTCATGATATGATACTAAATTCAAAATGGAAAGAACTTCATATAAGTGAC
ATATTAAGATATGCTTTGCTTCGTACATATTCGGGAGTATATTTAGATTTAGACATAATT
GTGAAAAGGCCGTTAGATGAAATTAAACTAAAGAACTTTGTCTGTCTGGAAGATAAAAAC
AGTATTAACAATGCAATAATAAAGTTTAGTGATGTTGATATTGCTTACAAAATAGGCAAT
TGGTTACTTGAGGGTGTGATAAAAAATTTCGATGGAAAACAATGGACAATTGGACCGAGA
CTCTTAACAAAAGTCATAAAAAGATATTGCAATATTACTGATTTTATAAACACAACAGAA
TGCAATGGAATAAATATCTTACCAATTGAAAAATGTTATGCAATAGAAGGATATCAATGG
AAATATTTTATTCAAGAATTTCGTTCAGATCAAGTTATGAGTGCTGTAGAGAATTCACAT
TTTGTTCATCTTTGGAATTATCAAAGCGACAAAAGACTTGTTAAAACTGGAAAATCTGTA
GCATTAAATTTTTTAGCAGCGGAGTATTGTCCACTAGTATTTGAATCAAATTTATACATT
TAG
>g4600.t1 Gene=g4600 Length=340
MNHNKLKKILILILIKFLIVFIIHRFYLYQQWFQDECNKNTAIIIENNFNQVPIEMLKNE
TIYFLETHNSSDHELTARQACAIESAAYMNPNTNVFVLFLSSSNHIRLKNWSQFQRILDY
KNIHLKYFHMDDIIKGTVVEDFLTHDMILNSKWKELHISDILRYALLRTYSGVYLDLDII
VKRPLDEIKLKNFVCLEDKNSINNAIIKFSDVDIAYKIGNWLLEGVIKNFDGKQWTIGPR
LLTKVIKRYCNITDFINTTECNGINILPIEKCYAIEGYQWKYFIQEFRSDQVMSAVENSH
FVHLWNYQSDKRLVKTGKSVALNFLAAEYCPLVFESNLYI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4600.t1 | Gene3D | G3DSA:3.90.550.20 | - | 72 | 258 | 8.2E-11 |
| 3 | g4600.t1 | PANTHER | PTHR12042 | LACTOSYLCERAMIDE 4-ALPHA-GALACTOSYLTRANSFERASE ALPHA- 1,4-GALACTOSYLTRANSFERASE | 41 | 335 | 1.6E-53 |
| 1 | g4600.t1 | Pfam | PF04488 | Glycosyltransferase sugar-binding region containing DXD motif | 77 | 190 | 3.3E-13 |
| 2 | g4600.t1 | Pfam | PF04572 | Alpha 1,4-glycosyltransferase conserved region | 222 | 335 | 2.0E-23 |
| 7 | g4600.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 8 | - |
| 9 | g4600.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 9 | 29 | - |
| 8 | g4600.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 30 | 340 | - |
| 5 | g4600.t1 | SUPERFAMILY | SSF53448 | Nucleotide-diphospho-sugar transferases | 71 | 333 | 7.17E-22 |
| 4 | g4600.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 9 | 28 | - |
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 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