Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Syndecan.

Parent gene

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 g9085 g9085.t5 isoform g9085.t5 35195638 35198306
chr_2 g9085 g9085.t5 exon g9085.t5.exon1 35195638 35195950
chr_2 g9085 g9085.t5 exon g9085.t5.exon2 35197187 35197384
chr_2 g9085 g9085.t5 cds g9085.t5.CDS1 35197324 35197384
chr_2 g9085 g9085.t5 exon g9085.t5.exon3 35197444 35198306
chr_2 g9085 g9085.t5 cds g9085.t5.CDS2 35197444 35197619
chr_2 g9085 g9085.t5 TTS g9085.t5 35197707 35197707
chr_2 g9085 g9085.t5 TSS g9085.t5 NA NA

Sequences

>g9085.t5 Gene=g9085 Length=1374
GATGCATTAGAGAATGAGAATGATGACGTTGATGGATCAGGCTCTGGAGATGGATTTCCT
GGTGATGATGAAGACGGTTTCAAACCAAAAGATAAGAACATAAAACCGGACTATAATACA
AATCAACCTCATCATTCAGGTGATGGTTCAGACCACGGTGTTGATAATGATGATGATGAA
GAAGAAGAAATTAACAGAAAGAAAATTATTGAGGATCAAAAACCACCTTCACCCACTGAA
AAATCCGATGATATTTTCTTTGAGACTTCAACAGAAACTGACACTTATCCATCACAAACA
GACGACGAAGATAGTGGTACAAACGATAACAGTAGAAAAACAGGTTTTGAATATCCAGAT
AAGAAACCAGATTACGAAATTGATCCAACACATCGTGTTCCTGTCTCACCAACTGATTCA
AGCAGTGGTAGCTCCGATAATGTGTTGATAATGAACACATCTAATGAGGATCGCACGACG
AGCTTTTTCGCTCAACCAGGTATTTTGGCAGCTGTCATTGGTGGAGCAGTGGTTGGATTA
TTGTTTGCTATTTTAATAGTCATGTTTTGTGTTTATCGACTTCGAAAGAAGGATGAAGGA
TCATATGCACTCGATGAGCCACAGAAACGATCACCACAAGCCAACTCATATACTAAAAAT
CATAATAATCGGGAATTTTATGCCTGAAACGATAATTCCCGATATTAAACTTAACAAAGA
GAACGATTAAGAGTGAATTAAATTAATAATTAAATTTTGAAGAGAAATCACGCCGAATAG
AAAAGAAGGATATTAAGAAAAGCAAAATAAAAACATACACACACATAAACTGGTATAAAA
AATTTATAAATGTTAAAAATTAATATTTACAAAAGAAAAGGATAGAAATATGCCTAGCTG
TTGTATTCAGGACACGAAGAATTATTAGATGAAAACCCTTTTTTGAATATAAAAAATTGA
AAACTTTTGCTGGCTTTTCCAAACTAAATTCATAAAAAAAGAAAAGCGCGTAGAGTAAAG
GTAAAAAATTCTTTTGAGAATGATAATTATAAATTCTCGAGAGTTTTCTTTTTGCTCTGC
AAGAGAATTAATTAATTAATGAAAGTGGAGAAATGCAAGATGATAAGAAGAGTCTTTTTT
GCGGTCTATTTTCGTACCGCACTAGCTGTTTTATCTAAAAACGTGGTAATGAACCATAGA
AAATTCTATCTAATGATAATCAATTTAAAAATAATGAATGAATATCTTTAAAGAAAAATG
TCATAATAGATTTTTAAGCTGTATTGTTTTAAATTGGGATAATTTTCTACTAGTTACAAC
GTATAATGTAAGACTATTATATATTATATACATAATAATGACTTCACTATGCAT

>g9085.t5 Gene=g9085 Length=78
MNTSNEDRTTSFFAQPGILAAVIGGAVVGLLFAILIVMFCVYRLRKKDEGSYALDEPQKR
SPQANSYTKNHNNREFYA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g9085.t5 MobiDBLite mobidb-lite consensus disorder prediction 51 78 -
5 g9085.t5 MobiDBLite mobidb-lite consensus disorder prediction 58 78 -
2 g9085.t5 PANTHER PTHR10915:SF1 SYNDECAN 1 78 1.6E-43
3 g9085.t5 PANTHER PTHR10915 SYNDECAN 1 78 1.6E-43
1 g9085.t5 Pfam PF01034 Syndecan domain 11 76 9.1E-29
8 g9085.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 17 -
9 g9085.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 18 42 -
7 g9085.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 43 78 -
4 g9085.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 20 42 -

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:0016020 membrane CC
GO:0007411 axon guidance BP

KEGG

Orthology

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.

Raw TPM values