Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative STIP1 homology and U box-containing protein 1.

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 g4652 g4652.t2 TTS g4652.t2 3954904 3954904
chr_2 g4652 g4652.t2 isoform g4652.t2 3955073 3955723
chr_2 g4652 g4652.t2 exon g4652.t2.exon1 3955073 3955241
chr_2 g4652 g4652.t2 cds g4652.t2.CDS1 3955073 3955241
chr_2 g4652 g4652.t2 exon g4652.t2.exon2 3955297 3955427
chr_2 g4652 g4652.t2 cds g4652.t2.CDS2 3955297 3955427
chr_2 g4652 g4652.t2 exon g4652.t2.exon3 3955486 3955723
chr_2 g4652 g4652.t2 cds g4652.t2.CDS3 3955486 3955575
chr_2 g4652 g4652.t2 TSS g4652.t2 3956712 3956712

Sequences

>g4652.t2 Gene=g4652 Length=538
TGGTAAAGAGCAAAAATTAAATTTTGGAGATGATATTGCTTCACAATTGCGTTTAGCAAG
AAAGAAACGATGGAATTTATTGGAAGAAAAAAGAATTCAACAAGAAATTGAATTGCAATC
TTATCTTACTCGCTTAATTCGTGAAGATATGGAAAATCGAATAGCAAAATTGAAACTTGA
AGATAATATGACTGAAGAAGAAAAGAAAGATGCAGCATCTGATGTTGAACAACAATGTGA
AAATTATACAAACGAACTGAATGGACTTTTTGCAAAGGTTGATGATAGACGACAAAAGCG
TGAAGTTCCTGATTATCTCTGTGGCAAAATTTCCTTTGAAATTTTGCAAGAACCTGTTAT
TACTCCAAGTGGCATCACATATGAACGGAAGGACATCGAAGAACATCTACAGCGCGTTGG
TCACTTTGATCCAGTGACTCGTGTTCCATTGACTGTCGATCAACTAATTCCTAACTTTTC
AATGAAAGAAGTTGTCGATTCGTTTATTCAGGAAAATGAATGGGCTCTTGAGTACTAA

>g4652.t2 Gene=g4652 Length=129
MENRIAKLKLEDNMTEEEKKDAASDVEQQCENYTNELNGLFAKVDDRRQKREVPDYLCGK
ISFEILQEPVITPSGITYERKDIEEHLQRVGHFDPVTRVPLTVDQLIPNFSMKEVVDSFI
QENEWALEY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g4652.t2 CDD cd16654 RING-Ubox_CHIP 53 119 7.82013E-47
7 g4652.t2 Coils Coil Coil 16 43 -
6 g4652.t2 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 50 129 9.1E-25
10 g4652.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 25 -
3 g4652.t2 PANTHER PTHR46803 E3 UBIQUITIN-PROTEIN LIGASE CHIP 3 127 2.2E-47
4 g4652.t2 PANTHER PTHR46803:SF2 E3 UBIQUITIN-PROTEIN LIGASE CHIP 3 127 2.2E-47
2 g4652.t2 Pfam PF18391 CHIP N-terminal tetratricopeptide repeat domain 2 51 1.6E-8
1 g4652.t2 Pfam PF04564 U-box domain 53 125 2.9E-29
11 g4652.t2 ProSiteProfiles PS51698 U-box domain profile. 52 126 30.944
9 g4652.t2 SMART SM00504 Ubox_2 56 119 7.0E-23
5 g4652.t2 SUPERFAMILY SSF57850 RING/U-box 47 126 3.53E-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:0016567 protein ubiquitination BP
GO:0004842 ubiquitin-protein transferase activity MF

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