General information for g4335.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 g4335 is located on chr_2: 1387099..1388902 (+ 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 | g4335 | g4335.t1 | TSS | g4335.t1 | 1384676 | 1384676 |
| chr_2 | g4335 | g4335.t1 | isoform | g4335.t1 | 1385208 | 1388321 |
| chr_2 | g4335 | g4335.t1 | exon | g4335.t1.exon1 | 1385208 | 1385258 |
| chr_2 | g4335 | g4335.t1 | cds | g4335.t1.CDS1 | 1385208 | 1385258 |
| chr_2 | g4335 | g4335.t1 | exon | g4335.t1.exon2 | 1385682 | 1386332 |
| chr_2 | g4335 | g4335.t1 | cds | g4335.t1.CDS2 | 1385682 | 1386332 |
| chr_2 | g4335 | g4335.t1 | exon | g4335.t1.exon3 | 1386724 | 1387174 |
| chr_2 | g4335 | g4335.t1 | cds | g4335.t1.CDS3 | 1386724 | 1387174 |
| chr_2 | g4335 | g4335.t1 | exon | g4335.t1.exon4 | 1387237 | 1387276 |
| chr_2 | g4335 | g4335.t1 | cds | g4335.t1.CDS4 | 1387237 | 1387276 |
| chr_2 | g4335 | g4335.t1 | exon | g4335.t1.exon5 | 1387341 | 1387364 |
| chr_2 | g4335 | g4335.t1 | cds | g4335.t1.CDS5 | 1387341 | 1387364 |
| chr_2 | g4335 | g4335.t1 | exon | g4335.t1.exon6 | 1387431 | 1387461 |
| chr_2 | g4335 | g4335.t1 | cds | g4335.t1.CDS6 | 1387431 | 1387461 |
| chr_2 | g4335 | g4335.t1 | exon | g4335.t1.exon7 | 1387518 | 1387712 |
| chr_2 | g4335 | g4335.t1 | cds | g4335.t1.CDS7 | 1387518 | 1387712 |
| chr_2 | g4335 | g4335.t1 | exon | g4335.t1.exon8 | 1387771 | 1387837 |
| chr_2 | g4335 | g4335.t1 | cds | g4335.t1.CDS8 | 1387771 | 1387837 |
| chr_2 | g4335 | g4335.t1 | exon | g4335.t1.exon9 | 1387921 | 1388321 |
| chr_2 | g4335 | g4335.t1 | cds | g4335.t1.CDS9 | 1387921 | 1388321 |
| chr_2 | g4335 | g4335.t1 | TTS | g4335.t1 | 1388421 | 1388421 |
Sequences
>g4335.t1 Gene=g4335 Length=1911
ATGTCAATGAACCGGTTTCTATTAAGATTAAAATCACTTCTTCGATTACAGGTCTTAAAA
AGCCGAAAAAGTTTCACATATTTTATCAAATTTGTTGGTTCATTTCTAATAATATGCTTA
ATTGTAATGATATCAGCCTACAAATTTATTCAACGAAATAATCATCCGCTTGCCATCACA
CAAAATTATATTTATATTGAGCCCATTTCCTCCTTCTTTCGTCGTGAACACAATCTTAAT
GGAGAGAAAATAGATTGGCATGATTATGAATATTTGCAACGAGAAAAAGAGCAATTTGGA
AAGCCAGGTGAAAATGGACAGCCGGTGTATGCAGAACCTGGTGAGGAAGAGCTCGATAAA
CAGCTATTTGATGTAAATGGCTACAATGGTCTCATTTCTGATAAAATTGCATTAAACAGA
AGTGTTGCTGACTATAGGCACCAACAGTGCAAAAAAATAAAGTATCTTAAAGAACTTCCA
TCAGTATCAATTGTCATTCCATTTTACAATGATCATCTTTCTACTTTGTTGAGGACAGTC
TATTCAGTAATAAATAGAAGTCCAAAAGAACTACTAAAAGAAGTAATTCTAGTCAATGAT
CATTCCACAAAAGACTTTCTCTATGGAGAATTAGAAGAATATATAGAGAAGCATTTGAAA
CACATTGTTAAACTTTATGTTTTACCTCGACGCTCTGGATTGATTTGGGCACGCTTAGCT
GGTGCTCGTGCTGCGAGTGGCGATGTGTTACTTTTCCTCGATTCACATACTGAAGCGTCA
ACAAATTTCTTGCCACCACTTATTGAACCAATTGCTAAAGATTATCGTACATGTGTTTGT
CCTTTTGTTGATGTAATTGATTTCAAGACTTTTGCCTATCATCCACAAGGCGATGGAAGT
AGAGGAATTTTCGATTGGAACGGAATGCATTATCATCATATGCCACTAAGACCTGGTGAT
CAAGAACATCCATGGTCACTTTATGAAAATCCTGTCATGGTCGGTGGATTGTTTGCAATA
TCAGCTAAATTCTTTTGGGAACTGGGCGGTTATGACCCAGGTCTAGATATCTGGGGAGGT
GAACAATACGAATTGAGTTTTAAAATTTGGCTTTGTGGTGGCAAAATGTATGATGCACCG
TGCTCAAGAATTGGTCATGTTTTTAGAGGTGGAATGCCATTTCCTAATGATCGCAAAGGA
ATTGATTTCATAACAATAAATTACAAGCGTGTAGCGGAAGTATGGTTGGACGAATACAAA
GAGTATTTGTATAAAAGAGATCCTGACCGATATGCACGAGTGAGTGCTGGAGACTTAAGC
TATCAATTTTATATTAAAAAGAGGCAACAATGCAAACCATTCAAATATTTTTTGGATGTG
GTAGCACCAGATATGAAGGAACGATATCCACTAGAGGAACCACCAGAATTTGCTTCAGGC
GCTATTCAATCGATGGCCGATGAAAAGTTTTGCATCGATAAACTGAATCGTCCGAAAGAG
CAACCTTTAGGAATTTATTATTGTGGTGAAAACAAGAAACGTCCACAGAACAATCAACAT
TTTATATTGCGTTATTATCGTGATATTGCTGATGCTGATATGGAATCATGCTTTGATTCA
TTTGGTGTAGGTGAAAAAAGAGAACTAAAAACATTCTCGTGCCATCATGGACAGGGAAAT
CAATATTTCCGATATGATTTAAATACAAAGCAAATATTTCATGGACCAGTTCGTAACAAG
CATTGTGTTGAAGTTAATATAGGAACTCAATCAGTTTATGTGACAACATGCAATGATAAA
AAATTGGAACAGAAATGGAAATGGGGTTTTGTCAATGAAACAAACATTCGAAATTGGGCA
ACATATGGTTCACCTATAATGGATGCACAAGAAGTAAAAGATTTATCCTGA
>g4335.t1 Gene=g4335 Length=636
MSMNRFLLRLKSLLRLQVLKSRKSFTYFIKFVGSFLIICLIVMISAYKFIQRNNHPLAIT
QNYIYIEPISSFFRREHNLNGEKIDWHDYEYLQREKEQFGKPGENGQPVYAEPGEEELDK
QLFDVNGYNGLISDKIALNRSVADYRHQQCKKIKYLKELPSVSIVIPFYNDHLSTLLRTV
YSVINRSPKELLKEVILVNDHSTKDFLYGELEEYIEKHLKHIVKLYVLPRRSGLIWARLA
GARAASGDVLLFLDSHTEASTNFLPPLIEPIAKDYRTCVCPFVDVIDFKTFAYHPQGDGS
RGIFDWNGMHYHHMPLRPGDQEHPWSLYENPVMVGGLFAISAKFFWELGGYDPGLDIWGG
EQYELSFKIWLCGGKMYDAPCSRIGHVFRGGMPFPNDRKGIDFITINYKRVAEVWLDEYK
EYLYKRDPDRYARVSAGDLSYQFYIKKRQQCKPFKYFLDVVAPDMKERYPLEEPPEFASG
AIQSMADEKFCIDKLNRPKEQPLGIYYCGENKKRPQNNQHFILRYYRDIADADMESCFDS
FGVGEKRELKTFSCHHGQGNQYFRYDLNTKQIFHGPVRNKHCVEVNIGTQSVYVTTCNDK
KLEQKWKWGFVNETNIRNWATYGSPIMDAQEVKDLS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g4335.t1 | CDD | cd02510 | pp-GalNAc-T | 163 | 462 | 2.65423E-155 |
| 12 | g4335.t1 | CDD | cd00161 | RICIN | 480 | 608 | 3.16599E-15 |
| 8 | g4335.t1 | Gene3D | G3DSA:3.90.550.10 | Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A | 81 | 472 | 5.5E-149 |
| 7 | g4335.t1 | Gene3D | G3DSA:2.80.10.50 | - | 473 | 622 | 2.9E-23 |
| 3 | g4335.t1 | PANTHER | PTHR11675:SF41 | POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 10 | 81 | 617 | 6.7E-146 |
| 4 | g4335.t1 | PANTHER | PTHR11675 | N-ACETYLGALACTOSAMINYLTRANSFERASE | 81 | 617 | 6.7E-146 |
| 2 | g4335.t1 | Pfam | PF00535 | Glycosyl transferase family 2 | 163 | 348 | 1.2E-28 |
| 1 | g4335.t1 | Pfam | PF00652 | Ricin-type beta-trefoil lectin domain | 479 | 606 | 7.6E-17 |
| 9 | g4335.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 24 | - |
| 11 | g4335.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 25 | 47 | - |
| 10 | g4335.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 48 | 636 | - |
| 16 | g4335.t1 | ProSiteProfiles | PS50231 | Lectin domain of ricin B chain profile. | 478 | 609 | 13.146 |
| 15 | g4335.t1 | SMART | SM00458 | ricin_3 | 479 | 609 | 2.5E-6 |
| 6 | g4335.t1 | SUPERFAMILY | SSF53448 | Nucleotide-diphospho-sugar transferases | 139 | 464 | 6.0E-56 |
| 5 | g4335.t1 | SUPERFAMILY | SSF50370 | Ricin B-like lectins | 473 | 609 | 1.54E-18 |
| 14 | g4335.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 25 | 47 | - |
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.
