General information for g11384.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Chondroitin sulfate synthase 1.
Parent gene
- The parent gene g11384 is located on chr_1: 15889093..15890377 (+ 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 | g11384 | g11384.t1 | TSS | g11384.t1 | 15884879 | 15884879 |
| chr_1 | g11384 | g11384.t1 | isoform | g11384.t1 | 15885206 | 15889093 |
| chr_1 | g11384 | g11384.t1 | exon | g11384.t1.exon1 | 15885206 | 15885347 |
| chr_1 | g11384 | g11384.t1 | cds | g11384.t1.CDS1 | 15885206 | 15885347 |
| chr_1 | g11384 | g11384.t1 | exon | g11384.t1.exon2 | 15886028 | 15886216 |
| chr_1 | g11384 | g11384.t1 | cds | g11384.t1.CDS2 | 15886028 | 15886216 |
| chr_1 | g11384 | g11384.t1 | exon | g11384.t1.exon3 | 15886453 | 15886653 |
| chr_1 | g11384 | g11384.t1 | cds | g11384.t1.CDS3 | 15886453 | 15886653 |
| chr_1 | g11384 | g11384.t1 | exon | g11384.t1.exon4 | 15886726 | 15886839 |
| chr_1 | g11384 | g11384.t1 | cds | g11384.t1.CDS4 | 15886726 | 15886839 |
| chr_1 | g11384 | g11384.t1 | exon | g11384.t1.exon5 | 15886904 | 15887016 |
| chr_1 | g11384 | g11384.t1 | cds | g11384.t1.CDS5 | 15886904 | 15887016 |
| chr_1 | g11384 | g11384.t1 | exon | g11384.t1.exon6 | 15887077 | 15887383 |
| chr_1 | g11384 | g11384.t1 | cds | g11384.t1.CDS6 | 15887077 | 15887383 |
| chr_1 | g11384 | g11384.t1 | exon | g11384.t1.exon7 | 15887565 | 15887882 |
| chr_1 | g11384 | g11384.t1 | cds | g11384.t1.CDS7 | 15887565 | 15887882 |
| chr_1 | g11384 | g11384.t1 | exon | g11384.t1.exon8 | 15887940 | 15888139 |
| chr_1 | g11384 | g11384.t1 | cds | g11384.t1.CDS8 | 15887940 | 15888139 |
| chr_1 | g11384 | g11384.t1 | exon | g11384.t1.exon9 | 15888197 | 15889093 |
| chr_1 | g11384 | g11384.t1 | cds | g11384.t1.CDS9 | 15888197 | 15889093 |
| chr_1 | g11384 | g11384.t1 | TTS | g11384.t1 | 15889309 | 15889309 |
Sequences
>g11384.t1 Gene=g11384 Length=2481
ATGACACAACACTTAAAACTTTTTTATGGTCTTTTGGGAGCTGTGATAGGATTATGTATT
GGGACTTTTCTCAAAAGTTTCAATACTATGGAGACAATTACACAGTGCGACCTGTTGTCT
GCCGCAAGTGTTCAATTGAAATCACCATTACAATTAATTAATTTAACGGATGAAGAGACC
CCAGTAAACAGTCAACGAACATTGGTTTTTGTCGGCGTAATGACATCCAAAGACTTCTTA
GAATCGCGTGCAAAGTCTGTGTATAATACATGGGGTAAATCAGTTCCTGGAAGGATTGCT
TTCTTTAGTTCTGAAGGCTCAGCTATGGATGATCTTCCAGTTATTGCGCTTAATGGTGTT
GACGATCGTTATCCGCCACAACGTAAATCATTTACGATGCTACACTACATGTATGAACAT
TATATTGACAAATTCGAATGGTTTCTTCGTGCTGATGATGATGTTTTTATTAAGACGGAT
AAACTCGAAAAGTTTTTAAGACGTATCGACTCAACAAAGGCACAATTTATTGGGCAAGCA
GGGCGTGGAAATAATGAAGAATTTGGTCTTCTTTCTCTTGAGTATGACGAAAATTTTTGT
ATGGGAGGACCAGGCATAATTTTAAGTCGTCAAACTCTTAAACAAGTTGCTCCACACATT
CCTACTTGTCTAAAAAATCTCTATAGCACACATGAAGATGTTGAAGTAGGAAGATGCGTT
CAAAAATTTGCTGGAACTGCATGCACTTGGAACTATGAAATGCAATCAATTTTTCATCAT
AATTCAACTGGCAATCGAGCGTTTTCGGGTAGTCTTAAGAAAAAAGAAGTCCATAGTGCG
ATCACATTACATCCTATAAAACGTTCACCTCTCATGCATAGAATGTATGCGTACAATCTA
GGACTTATTGCCACTGATCTACGGCAACAATCTCTTTATTTACATAGAGATATTGCACAA
ATGATTAGTCTATTACAAATTCCAAAGACAAATATGCTTGCGCGAGGTGTATCATTATTC
TCGGAAAAAGATAATTATAATTTTTTATATGATCATGATATTTTAGCGTCCAATGCAAAT
CCTAAGCGAAAATTTGAGGCATCTATAAAAGAAGGTCTTGAAGATGTGATTAGAGAAATT
ATGGAAAACATAAATGTGTATTCGCGTCAACGTGGACGTGTAATTGAATATAGAGAAATT
CTCTACGGATACTCACGTGTCAATTCAATACATGGGCATGATTTAATTTTAGATTTACTG
TTAGTTTATAAAAAATATAGAGGAAAGAAAATGACCGTGCCTGTTCGGAAGCATCTTTAT
ATTCAACGTTCATTTACTGAAACGAGATTTAGAGAAATAACTAATGACATTAATAATGAC
GTTGAAACGCAATACAATTCAAGTGGTTTAAAATTTACTGATAAAATGAAATCATTATTT
AATGAGAAACTCAATAAAATTAGTGATTTATATGCTCCTGAAACAAGAAGATTACCATCA
TCTGATGCAGATAAAATTGTATTTATTCTGCCTCTCTCAGGCCGATATGAAATTTTTTTG
CGATTTTTAAGTAATTTTGAGGATGTTATTCTCAAGCCTTCAGAGAATGTTGATCTCATA
GTATCATTATTCATCAATAATAGCACCGATCCAAACATATCCTCTATTTTACAACTGATT
GATTATCTTAACAACAAATATCACCGACAATCAATAGTTTCTATAAAACTTTATGGTGAA
TTTTCTAGAGGTGTAGCCATCAACACAGCAATTCAATCGTCAAAAATTTCCAATAACGAC
ATAATTTTTCTCATTGATGTTGATATAATTTTTACATCACTCACAATTAGACGAATAAGA
CAAAATACAATAAGGAATAAACAAATTTACTTGCCAATTGTATTTAGTGAATATAATCCA
GATATAGTTTCTTTAAATCGACCACCAATGCCAAAATTAAATGGTGGAAATAATTTTTTG
TCAAATTATCGTATAATGTCAAAATATTACATGTTTTATGCTAATCAAACAGCAGACTTT
GTAAACAATGAAAGTGGTTATTTCCGTGAATTCGGTTATGGTTTAGTTTCAATCTACAAA
TGTGATATTATGAATAGTAAAATAAATGGCTTTGTAACTGATGTTAAGGGATGGGGACTT
GAGGATGTAAAATTCTTAGAAAGAATTCTCACTGCAAGCTATCAAGTTCAGAATCAGTAT
ATTTTATCAGTTGCCGAAGGCAATGAGATGAAAAACATTTCTAGCCATAATTTAGACATT
TTTCGATCACCCGACTCATCGCTGTGGCACATTTTCCATAATATTGCATGTGATAGCAAT
TTAGAAAAGAATCAATATAAAATGTGTCTTGGTACATCTGCAAGTACACTAGGCAATTTC
CGTTTATTGAAAGAAAAGTACATTCTTCAAAATGATTTTATGGAGTTTATGAGTAGAATT
AAAGAAATAGTTGCAAATTAA
>g11384.t1 Gene=g11384 Length=826
MTQHLKLFYGLLGAVIGLCIGTFLKSFNTMETITQCDLLSAASVQLKSPLQLINLTDEET
PVNSQRTLVFVGVMTSKDFLESRAKSVYNTWGKSVPGRIAFFSSEGSAMDDLPVIALNGV
DDRYPPQRKSFTMLHYMYEHYIDKFEWFLRADDDVFIKTDKLEKFLRRIDSTKAQFIGQA
GRGNNEEFGLLSLEYDENFCMGGPGIILSRQTLKQVAPHIPTCLKNLYSTHEDVEVGRCV
QKFAGTACTWNYEMQSIFHHNSTGNRAFSGSLKKKEVHSAITLHPIKRSPLMHRMYAYNL
GLIATDLRQQSLYLHRDIAQMISLLQIPKTNMLARGVSLFSEKDNYNFLYDHDILASNAN
PKRKFEASIKEGLEDVIREIMENINVYSRQRGRVIEYREILYGYSRVNSIHGHDLILDLL
LVYKKYRGKKMTVPVRKHLYIQRSFTETRFREITNDINNDVETQYNSSGLKFTDKMKSLF
NEKLNKISDLYAPETRRLPSSDADKIVFILPLSGRYEIFLRFLSNFEDVILKPSENVDLI
VSLFINNSTDPNISSILQLIDYLNNKYHRQSIVSIKLYGEFSRGVAINTAIQSSKISNND
IIFLIDVDIIFTSLTIRRIRQNTIRNKQIYLPIVFSEYNPDIVSLNRPPMPKLNGGNNFL
SNYRIMSKYYMFYANQTADFVNNESGYFREFGYGLVSIYKCDIMNSKINGFVTDVKGWGL
EDVKFLERILTASYQVQNQYILSVAEGNEMKNISSHNLDIFRSPDSSLWHIFHNIACDSN
LEKNQYKMCLGTSASTLGNFRLLKEKYILQNDFMEFMSRIKEIVAN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g11384.t1 | Coils | Coil | Coil | 370 | 390 | - |
| 6 | g11384.t1 | Gene3D | G3DSA:3.90.550.50 | - | 56 | 286 | 4.4E-21 |
| 2 | g11384.t1 | PANTHER | PTHR12369 | CHONDROITIN SYNTHASE | 3 | 812 | 1.4E-251 |
| 3 | g11384.t1 | PANTHER | PTHR12369:SF11 | HEXOSYLTRANSFERASE | 3 | 812 | 1.4E-251 |
| 1 | g11384.t1 | Pfam | PF05679 | Chondroitin N-acetylgalactosaminyltransferase | 219 | 802 | 1.9E-158 |
| 8 | g11384.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 6 | - |
| 10 | g11384.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 27 | - |
| 9 | g11384.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 28 | 826 | - |
| 5 | g11384.t1 | SUPERFAMILY | SSF53448 | Nucleotide-diphospho-sugar transferases | 483 | 793 | 1.69E-15 |
| 4 | g11384.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 24 | - |
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 K13499 (chondroitin sulfate synthase)
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.
