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.t6 isoform g9085.t6 35197187 35197619
chr_2 g9085 g9085.t6 exon g9085.t6.exon1 35197187 35197384
chr_2 g9085 g9085.t6 cds g9085.t6.CDS1 35197324 35197384
chr_2 g9085 g9085.t6 exon g9085.t6.exon2 35197444 35197619
chr_2 g9085 g9085.t6 cds g9085.t6.CDS2 35197444 35197619
chr_2 g9085 g9085.t6 TTS g9085.t6 35197707 35197707
chr_2 g9085 g9085.t6 TSS g9085.t6 NA NA

Sequences

>g9085.t6 Gene=g9085 Length=374
GTGGTACAAACGATAACAGTAGAAAAACAGGTTTTGAATATCCAGATAAGAAACCAGATT
ACGAAATTGATCCAACACATCGTGTTCCTGTCTCACCAACTGATTCAAGCAGTGGTAGCT
CCGATAATGTGTTGATAATGAACACATCTAATGAGGATCGCACGACGAGCTTTTTCGCTC
AACCAGGTATTTTGGCAGCTGTCATTGGTGGAGCAGTGGTTGGATTATTGTTTGCTATTT
TAATAGTCATGTTTTGTGTTTATCGACTTCGAAAGAAGGATGAAGGATCATATGCACTCG
ATGAGCCACAGAAACGATCACCACAAGCCAACTCATATACTAAAAATCATAATAATCGGG
AATTTTATGCCTGA

>g9085.t6 Gene=g9085 Length=78
MNTSNEDRTTSFFAQPGILAAVIGGAVVGLLFAILIVMFCVYRLRKKDEGSYALDEPQKR
SPQANSYTKNHNNREFYA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g9085.t6 MobiDBLite mobidb-lite consensus disorder prediction 51 78 -
5 g9085.t6 MobiDBLite mobidb-lite consensus disorder prediction 58 78 -
2 g9085.t6 PANTHER PTHR10915:SF1 SYNDECAN 1 78 1.6E-43
3 g9085.t6 PANTHER PTHR10915 SYNDECAN 1 78 1.6E-43
1 g9085.t6 Pfam PF01034 Syndecan domain 11 76 9.1E-29
8 g9085.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 17 -
9 g9085.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 18 42 -
7 g9085.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 43 78 -
4 g9085.t6 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