General information for g4605.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 g4605 is located on chr_2: 3472937..3474222 (- 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 | g4605 | g4605.t1 | TTS | g4605.t1 | 3471705 | 3471705 |
| chr_2 | g4605 | g4605.t1 | isoform | g4605.t1 | 3472061 | 3473629 |
| chr_2 | g4605 | g4605.t1 | exon | g4605.t1.exon1 | 3472061 | 3472374 |
| chr_2 | g4605 | g4605.t1 | cds | g4605.t1.CDS1 | 3472061 | 3472374 |
| chr_2 | g4605 | g4605.t1 | exon | g4605.t1.exon2 | 3472433 | 3472476 |
| chr_2 | g4605 | g4605.t1 | cds | g4605.t1.CDS2 | 3472433 | 3472476 |
| chr_2 | g4605 | g4605.t1 | exon | g4605.t1.exon3 | 3472530 | 3472938 |
| chr_2 | g4605 | g4605.t1 | cds | g4605.t1.CDS3 | 3472530 | 3472938 |
| chr_2 | g4605 | g4605.t1 | exon | g4605.t1.exon4 | 3473350 | 3473629 |
| chr_2 | g4605 | g4605.t1 | cds | g4605.t1.CDS4 | 3473350 | 3473629 |
| chr_2 | g4605 | g4605.t1 | TSS | g4605.t1 | 3473651 | 3473651 |
Sequences
>g4605.t1 Gene=g4605 Length=1047
ATGAAGTCATTTTCAATATTACTATTATGTGGTGTTTTGTTTATTGTCATGCTGATCTAC
AACATTCAGTATTTAAAGAATAGCGATTATTCAATTATAGATATTGGAAAATTTGAAGAA
ATAGAAATTGAAGAAGAAAAAGAAGATCTAAGATTTGTTAAAAATATTGAAAGCAGCTCA
ACACTCTTACTTAATGGTGAAAATGTATTTTTTGTTGAAACACAAAATTCAACACAACAT
ATCTTGAATGATCGTCAAGCGTGCAGTATTGAGTCTGCTGCTTTAATGAATCCTAATGCA
TTAATTATTGTGACATTTGTAACACCAAAACATTTTGTCGATTTGAATGAAACACGAGCG
ATTGAAATATTGCGACAATATTCGAACATAATTTTCAGATTTGTAAATTTGAAAAGTTTC
TCAAAGAACACTCCACTAGAGAATTGGATCAAAAGTGGCAAATTGAGCAATTCAAAATTT
GTTGTGTCACATACATCGGATGTGCTACGCTATTTGCTGTTGTATAAATATTCGGGATTA
TATCTTGACACAGATGTCATAGTCACATATCCGTATGGTCGAATAAATATTGAGAATTAT
GCATGTGCAGAGAGTCATAAATTCCTCAATGGTGCCATTTTAAAACTTACCGGTGAAAGT
GGACGACAAATAGCTGAAAGCTTTATGCAAGATCTTATTGCGAATTTTGATGGCAATGTA
TGGGGCAAAAATGGCCCAGAATTATTGACGCGAGTGATTAAGAAAATGTGCAACATCTCA
TACTTTAATTCAACTCAAAAATGCAAAAACTTTACCATTCTTGAGACAGAAAAATGTTAC
GGCATTGGTTGGGAAGAATGGGTAAAGTTTTTTGAGCCACACAAACTTGATAGCGTGCGA
AGACACACAAAAAACTCGTATTATGTGCACTTATGGAATAAATTCAGTAAAACTCGTAAA
TTAGAGAAAAACTCAACAGCAGGCTTAAATGAAATTTTAAGAAAATTTTGTCCCAGAGTT
TACAAGTCTCTCGACAATTTCTTCTAA
>g4605.t1 Gene=g4605 Length=348
MKSFSILLLCGVLFIVMLIYNIQYLKNSDYSIIDIGKFEEIEIEEEKEDLRFVKNIESSS
TLLLNGENVFFVETQNSTQHILNDRQACSIESAALMNPNALIIVTFVTPKHFVDLNETRA
IEILRQYSNIIFRFVNLKSFSKNTPLENWIKSGKLSNSKFVVSHTSDVLRYLLLYKYSGL
YLDTDVIVTYPYGRINIENYACAESHKFLNGAILKLTGESGRQIAESFMQDLIANFDGNV
WGKNGPELLTRVIKKMCNISYFNSTQKCKNFTILETEKCYGIGWEEWVKFFEPHKLDSVR
RHTKNSYYVHLWNKFSKTRKLEKNSTAGLNEILRKFCPRVYKSLDNFF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4605.t1 | Gene3D | G3DSA:3.90.550.20 | - | 78 | 334 | 3.7E-9 |
| 3 | g4605.t1 | PANTHER | PTHR12042 | LACTOSYLCERAMIDE 4-ALPHA-GALACTOSYLTRANSFERASE ALPHA- 1,4-GALACTOSYLTRANSFERASE | 61 | 346 | 1.0E-69 |
| 1 | g4605.t1 | Pfam | PF04488 | Glycosyltransferase sugar-binding region containing DXD motif | 84 | 198 | 3.4E-15 |
| 2 | g4605.t1 | Pfam | PF04572 | Alpha 1,4-glycosyltransferase conserved region | 219 | 343 | 2.4E-38 |
| 8 | g4605.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 9 | g4605.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 10 | g4605.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 16 | - |
| 11 | g4605.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 21 | - |
| 7 | g4605.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 348 | - |
| 5 | g4605.t1 | SUPERFAMILY | SSF53448 | Nucleotide-diphospho-sugar transferases | 58 | 343 | 5.25E-37 |
| 4 | g4605.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 5 | 24 | - |
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.
