General information for g8068.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Chondroitin sulfate N-acetylgalactosaminyltransferase 2.
Parent gene
- The parent gene g8068 is located on chr_2: 28401901..28404536 (+ 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 | g8068 | g8068.t1 | isoform | g8068.t1 | 28401901 | 28404536 |
| chr_2 | g8068 | g8068.t1 | exon | g8068.t1.exon1 | 28401901 | 28402018 |
| chr_2 | g8068 | g8068.t1 | cds | g8068.t1.CDS1 | 28401901 | 28402018 |
| chr_2 | g8068 | g8068.t1 | exon | g8068.t1.exon2 | 28402093 | 28402239 |
| chr_2 | g8068 | g8068.t1 | cds | g8068.t1.CDS2 | 28402093 | 28402239 |
| chr_2 | g8068 | g8068.t1 | exon | g8068.t1.exon3 | 28402311 | 28402699 |
| chr_2 | g8068 | g8068.t1 | cds | g8068.t1.CDS3 | 28402311 | 28402699 |
| chr_2 | g8068 | g8068.t1 | exon | g8068.t1.exon4 | 28402758 | 28403181 |
| chr_2 | g8068 | g8068.t1 | cds | g8068.t1.CDS4 | 28402758 | 28403181 |
| chr_2 | g8068 | g8068.t1 | exon | g8068.t1.exon5 | 28403351 | 28403508 |
| chr_2 | g8068 | g8068.t1 | cds | g8068.t1.CDS5 | 28403351 | 28403508 |
| chr_2 | g8068 | g8068.t1 | exon | g8068.t1.exon6 | 28403755 | 28403951 |
| chr_2 | g8068 | g8068.t1 | cds | g8068.t1.CDS6 | 28403755 | 28403951 |
| chr_2 | g8068 | g8068.t1 | exon | g8068.t1.exon7 | 28404024 | 28404126 |
| chr_2 | g8068 | g8068.t1 | cds | g8068.t1.CDS7 | 28404024 | 28404126 |
| chr_2 | g8068 | g8068.t1 | exon | g8068.t1.exon8 | 28404195 | 28404536 |
| chr_2 | g8068 | g8068.t1 | cds | g8068.t1.CDS8 | 28404195 | 28404536 |
| chr_2 | g8068 | g8068.t1 | TSS | g8068.t1 | NA | NA |
| chr_2 | g8068 | g8068.t1 | TTS | g8068.t1 | NA | NA |
Sequences
>g8068.t1 Gene=g8068 Length=1878
ATGGGTATCACGATACTAGCCAGAATGCTGCTCTTAATTTCCTCAGTGACTTTAATCTCG
CTATTGGCATTATCAAAATGTGGCCTCAGTGGTGCGCTCGATAACGGCATCGATGACGGA
ATTGCGCATCCAATAAAATCAGCGCTGCGTAACGATGAACAACACGCACTCTTAATGGAA
CAGCGTGAAGAAGAGAATCAACAGGAAATTGCAAAACTTAAAGCTGAAATCAAGAACCTT
AAACTAGAACTTTTTCAATTGAGAAATAATCCGATTTTATCAGACCAAATATTGTCATTG
AATCAAAATGCTTCCACATCATCAATGATGATTCAGCAGCAACAGTCTGCAGCTGCATCG
TATCAATTAGACTGTACAAATTATATTCGTCGACAAGTTGGTCAGGCCGAAATACTTCAT
GGAATGCCAATGAATAATGAATATGAAATTATTCCGTTCAATCATTTCACATTCAGTCGT
GTCTATCCAATCGAGTTAGGTTTAGGCAAACGAGTTGTTGAGAAACCTATAGGCTATAAA
CGCAAAGATCTGCTTGATGCACTCAATAGGGGCTTAGATTCATTAAATAAAAATGCCACA
CTACTAAATCAGCGATATACATTAGATGATTTTATTGAAGGCATTTATCGCAATGATCCA
ACTACAGGAACACAGTATGAGCTGTATTTTCGAACAAAGGAAATATGCAATAAAACTAGT
AATCCCTCACCATCGTCATCATCACATCACAATGATCATGGCACTACAAAAATTATTGTT
ATGCGACCCTTTGCACCGTTACAGACTGTTCAAATTGAGAAATTTCCAAAAACAGCAGAA
AAGGAAATCATTCATATAATTTTGCCATTATCAGGCCGTATCTCTACTTTTCAAGGATTT
ATGGACAAATTTGTTAAAATTGCTCTCAAAAATGACCGACGTGTGCAACTCACTGTTGTT
TATTTTGGCGAGGAAGGTCTCTCTGAGGCGAGACAAATCATGAAACGCATTGTTGCTCAG
AAAAGTTCTTATTCATCCAATTTAAAATTATTAGCCTTAAATGAAACATTTTCTAGAGCT
AAAGGACTTCGTGTTGGCGCCGAACAGATATGGAATGAGGATAAAAGTCGAGGGAAGAAT
AATAAGGACGTGCTACTTTTTATGTGTGATGTGGATATTGTATTTAGTGCAAAGTTCTTA
GATCGATGTCGATGGAATACGAAACCTAATCGTAAAGTTTATTATCCAGTAGTATTTAGT
CTATATAATCCACATGTCGTTTATACGCTGCAAGGTAAAGAAATGCCATCGGAAACAGAT
CAGCTTGTGATATCACGAGATACAGGATTCTGGCGTGACTTTGGTTATGGTATGACATGC
CAATTTCGATCTGACTTCCTTAAAGTACGTGGTTTTGATGAGGAGAGTGTAGGATGGGGA
TATGAAGATGTTATGTTATATCGAAAATACGTTAGATCTAATATAAAAGTAATAAGAGCT
AGTGATCCTGGAATTTTCCATTTATACCATTCTAAGGTTTGTTCCGGCTCACAAAATGGA
CAAAAGATGTCTGCCGATCAATATAGAGCGTGTATACGTTCAAGAGCTCTCAATGAAGCC
TCACATCCACAACTTGGCTTTCTCGCCTTTCATGATGAGCTAATCTTAAACAATAATCAG
ACTGAATTGAATCAGAATTCCAATAATAATACGAACAATAATAATAAAAATAGTAATAGT
AGTAGTAATAGCGTTTATGAGCTAAGAAGTACAAGGAAGCACATATCTAATAAACAGCAG
CAGCAGAAACAGCATACGACAAAAAATACTCGTGTCAAAGTCCCATCATCAACAACAACC
ACGAAAAAAGCTACATGA
>g8068.t1 Gene=g8068 Length=625
MGITILARMLLLISSVTLISLLALSKCGLSGALDNGIDDGIAHPIKSALRNDEQHALLME
QREEENQQEIAKLKAEIKNLKLELFQLRNNPILSDQILSLNQNASTSSMMIQQQQSAAAS
YQLDCTNYIRRQVGQAEILHGMPMNNEYEIIPFNHFTFSRVYPIELGLGKRVVEKPIGYK
RKDLLDALNRGLDSLNKNATLLNQRYTLDDFIEGIYRNDPTTGTQYELYFRTKEICNKTS
NPSPSSSSHHNDHGTTKIIVMRPFAPLQTVQIEKFPKTAEKEIIHIILPLSGRISTFQGF
MDKFVKIALKNDRRVQLTVVYFGEEGLSEARQIMKRIVAQKSSYSSNLKLLALNETFSRA
KGLRVGAEQIWNEDKSRGKNNKDVLLFMCDVDIVFSAKFLDRCRWNTKPNRKVYYPVVFS
LYNPHVVYTLQGKEMPSETDQLVISRDTGFWRDFGYGMTCQFRSDFLKVRGFDEESVGWG
YEDVMLYRKYVRSNIKVIRASDPGIFHLYHSKVCSGSQNGQKMSADQYRACIRSRALNEA
SHPQLGFLAFHDELILNNNQTELNQNSNNNTNNNNKNSNSSSNSVYELRSTRKHISNKQQ
QQKQHTTKNTRVKVPSSTTTTKKAT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g8068.t1 | Coils | Coil | Coil | 56 | 90 | - |
| 9 | g8068.t1 | Coils | Coil | Coil | 185 | 205 | - |
| 7 | g8068.t1 | Gene3D | G3DSA:3.90.550.10 | Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A | 231 | 541 | 4.0E-23 |
| 15 | g8068.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 567 | 625 | - |
| 2 | g8068.t1 | PANTHER | PTHR12369:SF45 | HEXOSYLTRANSFERASE | 2 | 560 | 4.2E-239 |
| 3 | g8068.t1 | PANTHER | PTHR12369 | CHONDROITIN SYNTHASE | 2 | 560 | 4.2E-239 |
| 1 | g8068.t1 | Pfam | PF05679 | Chondroitin N-acetylgalactosaminyltransferase | 42 | 545 | 2.4E-83 |
| 11 | g8068.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 25 | - |
| 12 | g8068.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 9 | - |
| 13 | g8068.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 10 | 21 | - |
| 14 | g8068.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 22 | 25 | - |
| 10 | g8068.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 26 | 625 | - |
| 4 | g8068.t1 | SUPERFAMILY | SSF53448 | Nucleotide-diphospho-sugar transferases | 283 | 523 | 1.74E-21 |
| 6 | g8068.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 32 | - |
| 5 | g8068.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 32 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0032580 | Golgi cisterna membrane | CC |
| GO:0008376 | acetylgalactosaminyltransferase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00746 (chondroitin sulfate N-acetylgalactosaminyltransferase 1/2)
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. There were no conditions that were differentially expressed