General information for g13375.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as N-acetylgalactosaminyltransferase 4.
Parent gene
- The parent gene g13375 is located on chr_1: 29595421..29598439 (+ 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_1 | g13375 | g13375.t1 | isoform | g13375.t1 | 29595421 | 29598439 |
| chr_1 | g13375 | g13375.t1 | exon | g13375.t1.exon1 | 29595421 | 29595836 |
| chr_1 | g13375 | g13375.t1 | cds | g13375.t1.CDS1 | 29595421 | 29595836 |
| chr_1 | g13375 | g13375.t1 | exon | g13375.t1.exon2 | 29596645 | 29596948 |
| chr_1 | g13375 | g13375.t1 | cds | g13375.t1.CDS2 | 29596645 | 29596948 |
| chr_1 | g13375 | g13375.t1 | exon | g13375.t1.exon3 | 29597042 | 29597287 |
| chr_1 | g13375 | g13375.t1 | cds | g13375.t1.CDS3 | 29597042 | 29597287 |
| chr_1 | g13375 | g13375.t1 | exon | g13375.t1.exon4 | 29597384 | 29597632 |
| chr_1 | g13375 | g13375.t1 | cds | g13375.t1.CDS4 | 29597384 | 29597632 |
| chr_1 | g13375 | g13375.t1 | exon | g13375.t1.exon5 | 29597701 | 29598150 |
| chr_1 | g13375 | g13375.t1 | cds | g13375.t1.CDS5 | 29597701 | 29598150 |
| chr_1 | g13375 | g13375.t1 | exon | g13375.t1.exon6 | 29598209 | 29598439 |
| chr_1 | g13375 | g13375.t1 | cds | g13375.t1.CDS6 | 29598209 | 29598439 |
| chr_1 | g13375 | g13375.t1 | TSS | g13375.t1 | NA | NA |
| chr_1 | g13375 | g13375.t1 | TTS | g13375.t1 | NA | NA |
Sequences
>g13375.t1 Gene=g13375 Length=1896
ATGCTTCTCTACCTTAGCGGAAAGTTTAACAAATTGGATTTCATCTCATTAGCATTCATA
CTGACAGCTTTATTTGTGAGCGTCACATTAATAAGAAATTATTTTGACACACAAATTTCC
ACGCTCAAAACGGAAGTGCTGCTATATAAAGACGCATTAGGCTCATTCAAAAAGAAACTT
TCTGTGCCACGTTACCCTTTTGCAAGGAATTATGATCGCGAAGACTATCACGATTATGAA
TTTATAATATCAGAAGAAGGTCGAAGTGGTCCAGGCGAGAACGGTTTGCCTTATTATCTT
ATAAATGATAAACTTGTAGAAGAAAATAGACGATTATATGAACAAATTGGATTTCATGGA
TTGGTTAGCGATCATATTTCGGTTAATCGCTCATTGCCAGATGTGAGACACGAAAAATGC
AAGAAGAAAAAGTATCTCAAGCAGTTATCAAAAGTTTCAATAATAATAGTATTCTATAAT
GAACATACTAGCATGCTCAAACGAACACTTCATTCAGTTTATAATCGTACGCCACACAAA
CTTATTAACGAAATAATTTTAGTAAACGACAATAGTACGTCACCAGAACTTTATGAACCG
TTTGAGGAATACGTCATAACTAATTTTGCTGATTTTGTGAAAATTCGTGTTCTAAATGAG
CGTCGCGGTATGATTATAGGACGAATGGAAGGTGCACGATTTGCAAAAGGCGAAGTTCTC
GTCTTTCTTGATGCTCATGTTGAAGTAAATGTCAATTGGTTACCGCCTTTACTCGAACCA
ATTGCCCTCAATCCAAAAATAATTACAACTCCCATAGTCGATATACTTGATTCAGCAACA
TTCGCATACTTAAAGCGGGACAATGGTGGACGTGGGATCTTCAATTGGGATTTGGAATAT
CGACGCGTATCACGAAGGCCAGAAGATAAAATTCGACCAGAAACGCCCTTTCTAACACCC
GTGATGGTAGGTTCAGTATTTGCAATTAATCGACAATATTTTTGGGATATGGGTGCATAT
GATGGACAATTGAGAGTAGCGCAAGGCGAGCAATTTGAAATGTCCCTTAAAGCTCATTTA
TGTGGTCAAGGAATTGTCGAATGTCCATGTAGTCGTGTCGGCAACATCAAACGTAACAAA
AACTATTATAAAAGTTTCGAAAATGGCACAGATTTTGCTGCTCGTAATCTCAAGAGGATT
GTCGAAGTTTGGTTTGATGAATATCAAAATGTTGTTTTAAATCGACATCCAGAGAGATAT
AAATCTGTCGATGCTGGCAATCTTGCAAGAGAACGAACAATAAGATTAGGATTGCATTGT
AGACCATTTCAATTTTTCTTGGAATTTGTTGCACCTGAAATTTTAGAAAGATATCCAGTT
GAAAATCCCGGATATTTTGTAAGAGGTGCAATAAGAAGTAAATCAAATCCAAAATTTTGT
TTAGAAGCAACAAATGTTGGAAATTTAGTTGATGGAATAAGTGAAAAATTGATAGTTAAA
GATTGCAGTGGAGATTATGTGAATCCACAAGATCCAAGACAAGCATTTACTTTGACTTAT
CAAAGAAATATTCAACTTTACATTTATGATTATTGCATTGACAATACTTTAAATCTCAAT
ATTTGTCATTTCCAAGGTGGAAATCAATTATGGCAATATAATTTAGATACATCACAACTT
ATTAACCCTTTAAAAAATGCCACAACTTGTCTTACTTTAGATTCAAATTCACAAAAATTA
TTAATGGATGAGTGCAATGAGGACAACATCAATCAAAAGTGGAATTGGGGCGAAAAGAAC
TTGACAGCTTTAAGAAGTTGGGAAAATTTTGGAGTTGAACTAACGTCACTCAATTTAGGT
GTAGGTGAAAAAGATGAAGAGGAAGATGATTATTAA
>g13375.t1 Gene=g13375 Length=631
MLLYLSGKFNKLDFISLAFILTALFVSVTLIRNYFDTQISTLKTEVLLYKDALGSFKKKL
SVPRYPFARNYDREDYHDYEFIISEEGRSGPGENGLPYYLINDKLVEENRRLYEQIGFHG
LVSDHISVNRSLPDVRHEKCKKKKYLKQLSKVSIIIVFYNEHTSMLKRTLHSVYNRTPHK
LINEIILVNDNSTSPELYEPFEEYVITNFADFVKIRVLNERRGMIIGRMEGARFAKGEVL
VFLDAHVEVNVNWLPPLLEPIALNPKIITTPIVDILDSATFAYLKRDNGGRGIFNWDLEY
RRVSRRPEDKIRPETPFLTPVMVGSVFAINRQYFWDMGAYDGQLRVAQGEQFEMSLKAHL
CGQGIVECPCSRVGNIKRNKNYYKSFENGTDFAARNLKRIVEVWFDEYQNVVLNRHPERY
KSVDAGNLARERTIRLGLHCRPFQFFLEFVAPEILERYPVENPGYFVRGAIRSKSNPKFC
LEATNVGNLVDGISEKLIVKDCSGDYVNPQDPRQAFTLTYQRNIQLYIYDYCIDNTLNLN
ICHFQGGNQLWQYNLDTSQLINPLKNATTCLTLDSNSQKLLMDECNEDNINQKWNWGEKN
LTALRSWENFGVELTSLNLGVGEKDEEEDDY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g13375.t1 | CDD | cd00161 | RICIN | 469 | 596 | 3.79445E-14 |
| 7 | g13375.t1 | Gene3D | G3DSA:3.90.550.10 | Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A | 70 | 461 | 4.1E-131 |
| 6 | g13375.t1 | Gene3D | G3DSA:2.80.10.50 | - | 462 | 610 | 4.4E-19 |
| 3 | g13375.t1 | PANTHER | PTHR11675 | N-ACETYLGALACTOSAMINYLTRANSFERASE | 103 | 600 | 5.9E-126 |
| 2 | g13375.t1 | Pfam | PF00535 | Glycosyl transferase family 2 | 153 | 337 | 1.6E-26 |
| 1 | g13375.t1 | Pfam | PF00652 | Ricin-type beta-trefoil lectin domain | 469 | 594 | 2.5E-14 |
| 8 | g13375.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 10 | g13375.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 35 | - |
| 9 | g13375.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 36 | 631 | - |
| 14 | g13375.t1 | ProSiteProfiles | PS50231 | Lectin domain of ricin B chain profile. | 467 | 597 | 14.574 |
| 13 | g13375.t1 | SMART | SM00458 | ricin_3 | 468 | 597 | 1.2E-5 |
| 5 | g13375.t1 | SUPERFAMILY | SSF53448 | Nucleotide-diphospho-sugar transferases | 129 | 453 | 5.2E-45 |
| 4 | g13375.t1 | SUPERFAMILY | SSF50370 | Ricin B-like lectins | 463 | 597 | 4.31E-17 |
| 12 | g13375.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 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 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.
