General information for g11974.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 g11974 is located on chr_1: 20116572..20119121 (+ 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 | g11974 | g11974.t1 | TSS | g11974.t1 | 20116542 | 20116542 |
| chr_1 | g11974 | g11974.t1 | isoform | g11974.t1 | 20116572 | 20119121 |
| chr_1 | g11974 | g11974.t1 | exon | g11974.t1.exon1 | 20116572 | 20118149 |
| chr_1 | g11974 | g11974.t1 | cds | g11974.t1.CDS1 | 20116572 | 20118149 |
| chr_1 | g11974 | g11974.t1 | exon | g11974.t1.exon2 | 20118927 | 20119121 |
| chr_1 | g11974 | g11974.t1 | cds | g11974.t1.CDS2 | 20118927 | 20119121 |
| chr_1 | g11974 | g11974.t1 | TTS | g11974.t1 | 20119217 | 20119217 |
Sequences
>g11974.t1 Gene=g11974 Length=1773
ATGCGAATCACGTTAAATCGTCGTGGTTTTATCTTTCTCATCATTTTACTTTCATTTAGC
TATTTAATCTACATAATTCAGCCACAAACTTTTATCAAATCAAATTTTAAAACCAATGAA
ATTACTCGAAATTGGAATGACTTCGAATTTATGGCATATGAAACGTCAAGAATTGGTCCA
GGTGAACAAGGTGAAGCAGTGTTTCTAATTGACCCTGAAGAAATTCGACAAAACGAAAAG
TTATATGAAAAAACCGGATTTAATGTGCTTGTGTCAAACAAAATTTCTGTCAATCGCTCA
CTACCACAAGTTGTTCATCCTGATTGCTATAAGATTGAGTATCTTCGTAAATTGCCATCT
GTCTCTGTAATAATAATTTTTCACAATGAAGTTTTTAGTGTGCTGCTTCGTACGATTCAT
AGTATTTTTAACAGAACACCCAAAGAATTGCTGCATGAAATTATTTTAGTCAATGACAAC
AGCACAGAAGTAGAACTATACGAAAAACTTCAGAATTATGTGCGGGAAAATTTTCCAAAG
AATTTAATAAAAATCAAGAATTTACCAAAACGTTCGGGTTTAATTGTTGCACGAATGGAA
GGTGCACGTGAAGCAACAGCTGAAGTTCTTGTTTTCTTTGATTCACATGTTGAAGTTCAT
AATAATTGGCTGCCGCCTTTACTTGAACCAATTGTAATTAATCCAAATATTTCAACACTT
CCAATTATTGATTATTTTCACTATGAAACTTTCGCTTATTTACCAAATCAAGAATTTAAT
TTTGGCACAAGAGGCATCATTGATTGGTATCTGGATTTTCATGAAGTGCCAAAGCTAAAA
GTTGATCAATTAGAAAATTTGAGACCATTTCCAAATCCAATTATGCTTGGTTGCGCATTT
GCTATTAATAGAGAATTTTTTCTCTATGAACTCGGTGGATATGATGAAGAATTGAGAATT
TGGAATGGTGAAAATTATGAATTGAGTTTCAAACTGTGGATGTGTCGAGATGGAGTTTTT
ACTGTACCGTGCTCAAGAATTGCTCATTCATTTCGTCAACATAATCCAACTAGAAAATTC
AGTGATGATTATGTGGCAAGAAATTTTAAAAGAATTGCTGAAGTGTGGCTTGATGAATTT
AAGACTCTTCCTTATGAGCTTGAGCCAGAGAGATATGCAGTAGTTGATGCAGGTGATTTG
TCGTTTCAACATAAGATACGTGAAAGACTTCAGTGCAAATCATTTCGTTGGTTTCTCAAA
AATATCGCCTATGATATGGCTCTTGCTTATCCACCAATGATTCACGTTCCTCATTTTGCA
TCTGGAGCAATTCAAAGCGTTGCAAACCCTAGAGCATGCTTAGATAATTATGGAAGTCTT
TTTGATTCACAAATTGGAACTTATGAATGTGCAAATGATCTAAATGAGCCAGGGACTAAT
CAAAAATTCATTTACTCATTTTATAAAGACATACGTCAGGACCATGGACGACACAAATTT
TGTCTCGATGCATACAATCTTTTAATGACCGATTGCAATCAAGTGGATTTTGGAAATCAA
TATTGGAATTACAATTTGCAAACAAAAGAAATCTCAATAAAGTCAATGGCTGATGAAAGA
CAGTGTCTCACACTGGTGCTTGTTAACATGACACTTTTACTCAGTGATTGCAATGGTGAA
ATGAATCAACAATGGAATTTTGCATACATCAATGAAACTGCTTTTGCAAAGTTTGATGAA
ATTTTTGGATATGAAAGTATTGTTCATTTATGA
>g11974.t1 Gene=g11974 Length=590
MRITLNRRGFIFLIILLSFSYLIYIIQPQTFIKSNFKTNEITRNWNDFEFMAYETSRIGP
GEQGEAVFLIDPEEIRQNEKLYEKTGFNVLVSNKISVNRSLPQVVHPDCYKIEYLRKLPS
VSVIIIFHNEVFSVLLRTIHSIFNRTPKELLHEIILVNDNSTEVELYEKLQNYVRENFPK
NLIKIKNLPKRSGLIVARMEGAREATAEVLVFFDSHVEVHNNWLPPLLEPIVINPNISTL
PIIDYFHYETFAYLPNQEFNFGTRGIIDWYLDFHEVPKLKVDQLENLRPFPNPIMLGCAF
AINREFFLYELGGYDEELRIWNGENYELSFKLWMCRDGVFTVPCSRIAHSFRQHNPTRKF
SDDYVARNFKRIAEVWLDEFKTLPYELEPERYAVVDAGDLSFQHKIRERLQCKSFRWFLK
NIAYDMALAYPPMIHVPHFASGAIQSVANPRACLDNYGSLFDSQIGTYECANDLNEPGTN
QKFIYSFYKDIRQDHGRHKFCLDAYNLLMTDCNQVDFGNQYWNYNLQTKEISIKSMADER
QCLTLVLVNMTLLLSDCNGEMNQQWNFAYINETAFAKFDEIFGYESIVHL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g11974.t1 | CDD | cd02510 | pp-GalNAc-T | 122 | 423 | 1.34762E-134 |
| 11 | g11974.t1 | CDD | cd00161 | RICIN | 442 | 567 | 3.86947E-16 |
| 7 | g11974.t1 | Gene3D | G3DSA:3.90.550.10 | Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A | 40 | 433 | 3.3E-140 |
| 6 | g11974.t1 | Gene3D | G3DSA:2.80.10.50 | - | 437 | 573 | 1.8E-19 |
| 3 | g11974.t1 | PANTHER | PTHR11675 | N-ACETYLGALACTOSAMINYLTRANSFERASE | 72 | 572 | 1.9E-135 |
| 2 | g11974.t1 | Pfam | PF00535 | Glycosyl transferase family 2 | 122 | 307 | 2.2E-26 |
| 1 | g11974.t1 | Pfam | PF00652 | Ricin-type beta-trefoil lectin domain | 441 | 565 | 6.2E-13 |
| 8 | g11974.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 8 | - |
| 10 | g11974.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 9 | 26 | - |
| 9 | g11974.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 27 | 590 | - |
| 15 | g11974.t1 | ProSiteProfiles | PS50231 | Lectin domain of ricin B chain profile. | 440 | 568 | 17.71 |
| 14 | g11974.t1 | SMART | SM00458 | ricin_3 | 441 | 568 | 3.8E-8 |
| 5 | g11974.t1 | SUPERFAMILY | SSF53448 | Nucleotide-diphospho-sugar transferases | 98 | 425 | 7.22E-50 |
| 4 | g11974.t1 | SUPERFAMILY | SSF50370 | Ricin B-like lectins | 436 | 567 | 1.28E-18 |
| 13 | g11974.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 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.
