General information for g3024.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 g3024 is located on chr_3: 22180956..22182891 (- 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_3 | g3024 | g3024.t1 | isoform | g3024.t1 | 22180956 | 22182891 |
| chr_3 | g3024 | g3024.t1 | exon | g3024.t1.exon1 | 22180956 | 22181197 |
| chr_3 | g3024 | g3024.t1 | cds | g3024.t1.CDS1 | 22180956 | 22181197 |
| chr_3 | g3024 | g3024.t1 | exon | g3024.t1.exon2 | 22181260 | 22182717 |
| chr_3 | g3024 | g3024.t1 | cds | g3024.t1.CDS2 | 22181260 | 22182717 |
| chr_3 | g3024 | g3024.t1 | exon | g3024.t1.exon3 | 22182888 | 22182891 |
| chr_3 | g3024 | g3024.t1 | cds | g3024.t1.CDS3 | 22182888 | 22182891 |
| chr_3 | g3024 | g3024.t1 | TSS | g3024.t1 | NA | NA |
| chr_3 | g3024 | g3024.t1 | TTS | g3024.t1 | NA | NA |
Sequences
>g3024.t1 Gene=g3024 Length=1704
ATGATGTTATTAAATGCATTTCACACATTAAAGAGAGTGAAACATGAGTTAAAACTAAAA
GATTGGAATGATTATGAAATAATTAAACGTGATTCACTGAGAGTTGGTTTTGGAGAGCAC
GGTAAAGGTGAAAAGTTAATCGATGCAAACGACATTGAAAAAAATGCAGCATTATTCGAA
GAATATGGAATGTCAGTGTTGATTAGTGATAAAATTTCAGTAAATCGATCGATTCCAGAT
TTTAGACATCAAGTATGTAAAACAAGAAAATATTTAAAAGATTTACCAAAAGTTAGTATT
ATAATAATTTTCAATGATGAAGCTTTTAGTGTATTTAAAAGAACATTACATAGTTTATAT
AATCGTACACCATTGGAACTTGTTGAAGAAGTTATTTTAGTCAATGACAACAGCTCAAAA
AGTTATCTTTATGATGATTTAAAAAATTACATCGATGAACATTTTAAAAATCTCAAATTT
AATATTATAAATTTAAAAAAGCGTCATGGATTAATGCAAGCTAGAGTTTTAGGTGCAAAG
GCTGCTAAAAGTGAATTAATTTTTATTATGGAATCACATTGTGAAATGACTTATAATTGG
CTACCTCCACTTATTCAGCCATTAATTGAGGCTAGTAACCATCGTGTTGTTACCGTACCT
ATAATTGATAACATCGAATGGCAATATATGGATTACTATGAGAACGATAATGGAAATAAA
GGTAGTCGTGGAATTTTCACATGGGATTTAGAGTATTACAAACTCAAACGATTACCAGTG
TCTAATGTTGATAAAGAGCTTGATCCTTTTCCTATACCGGTACTTACCGGTGGGATTTTT
ATGATCCGCAAAAATTACTTTTTTGAAATCGGACCTTATGATGAAAAATTAATTATTTGG
GGAGCTGAAAATATAGAAATGAGTTTAAAAGTAAATTTATGTGGTGGTAAAATTTTAGAA
GTTCCTTGTAGCCATATTGGCCATATGTTTCGAGCATTTACAAAATCACGAACTCATGAA
AGTGGCATTGATTTTGAAGCATTCAATCGAAAGAGAGTTGTGGAAGTTTGGTTTGATAAT
TATAAAGAAGCAGTTTATATGCGTAACAAAGAAAGATATGCATACATCGATGTTGGTGAC
TTAAGTGAAGCAAGACAAGTTAAAGAACGATTAAATTGCAAACCATTTGAATACTTTCTC
AAAGATATCGCTCCAGATATGATTGAAAATTTTCCACCTGACCAGTTTCCATTCGCGTAT
GGAAGGATTGAATTACTTGATGAAAATCTTTGCCTGCATATTAATGTTGGACCAAATCCA
GGAGAAATGACGAAAGTTGAATTATATGAATGTCAGAAACCAACAGTTGCGAATCAAAAT
TTAGAATTGAGCTGGTATCGTGATATTAGACTGAGAGATGTAAATATTTGCATTGATGTT
TATGAAATTTCTGCTGTTACTTGTCATTTATCTGGAGGGAATCAACTCTTTAAATATGAT
TTTCGTACTAAGCAAATAAAAAACATGAATAATAAATTATGCATAGAGGGTAATGCTGAA
GAGAGAACTTTAAAGCTAACAAAATGCGATGAAATGTTAAAGAGTCAGAAGTGGATTTTC
AGTGATTTTGTTAATGCTACTGCATTGCAAAACTGGTATGAATCTGGAAGAAAATTCAAA
GATGACAATAGTGTCTTTTGGTAG
>g3024.t1 Gene=g3024 Length=567
MMLLNAFHTLKRVKHELKLKDWNDYEIIKRDSLRVGFGEHGKGEKLIDANDIEKNAALFE
EYGMSVLISDKISVNRSIPDFRHQVCKTRKYLKDLPKVSIIIIFNDEAFSVFKRTLHSLY
NRTPLELVEEVILVNDNSSKSYLYDDLKNYIDEHFKNLKFNIINLKKRHGLMQARVLGAK
AAKSELIFIMESHCEMTYNWLPPLIQPLIEASNHRVVTVPIIDNIEWQYMDYYENDNGNK
GSRGIFTWDLEYYKLKRLPVSNVDKELDPFPIPVLTGGIFMIRKNYFFEIGPYDEKLIIW
GAENIEMSLKVNLCGGKILEVPCSHIGHMFRAFTKSRTHESGIDFEAFNRKRVVEVWFDN
YKEAVYMRNKERYAYIDVGDLSEARQVKERLNCKPFEYFLKDIAPDMIENFPPDQFPFAY
GRIELLDENLCLHINVGPNPGEMTKVELYECQKPTVANQNLELSWYRDIRLRDVNICIDV
YEISAVTCHLSGGNQLFKYDFRTKQIKNMNNKLCIEGNAEERTLKLTKCDEMLKSQKWIF
SDFVNATALQNWYESGRKFKDDNSVFW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g3024.t1 | CDD | cd00161 | RICIN | 421 | 540 | 0.000000 |
| 8 | g3024.t1 | Gene3D | G3DSA:3.90.550.10 | Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A | 16 | 414 | 0.000000 |
| 7 | g3024.t1 | Gene3D | G3DSA:2.80.10.50 | - | 417 | 546 | 0.000000 |
| 3 | g3024.t1 | PANTHER | PTHR11675 | N-ACETYLGALACTOSAMINYLTRANSFERASE | 49 | 543 | 0.000000 |
| 2 | g3024.t1 | Pfam | PF00535 | Glycosyl transferase family 2 | 99 | 287 | 0.000000 |
| 1 | g3024.t1 | Pfam | PF00652 | Ricin-type beta-trefoil lectin domain | 420 | 538 | 0.000000 |
| 9 | g3024.t1 | ProSiteProfiles | PS50231 | Lectin domain of ricin B chain profile. | 483 | 540 | 10.978000 |
| 6 | g3024.t1 | SMART | SM00458 | ricin_3 | 418 | 541 | 0.000052 |
| 5 | g3024.t1 | SUPERFAMILY | SSF53448 | Nucleotide-diphospho-sugar transferases | 75 | 406 | 0.000000 |
| 4 | g3024.t1 | SUPERFAMILY | SSF50370 | Ricin B-like lectins | 413 | 541 | 0.000000 |
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