General information for g14006.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative SCF ubiquitin ligase complex protein SKP1b.
Parent gene
- The parent gene g14006 is located on chr_1: 33967422..33967931 (+ 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 | g14006 | g14006.t1 | TSS | g14006.t1 | 33967369 | 33967369 |
| chr_1 | g14006 | g14006.t1 | isoform | g14006.t1 | 33967422 | 33967931 |
| chr_1 | g14006 | g14006.t1 | exon | g14006.t1.exon1 | 33967422 | 33967931 |
| chr_1 | g14006 | g14006.t1 | cds | g14006.t1.CDS1 | 33967422 | 33967931 |
| chr_1 | g14006 | g14006.t1 | TTS | g14006.t1 | 33968007 | 33968007 |
Sequences
>g14006.t1 Gene=g14006 Length=510
ATGGATATCGATAGACCAAGTGATCCTCAAGTTTCTGTTGTATCATCAGATGGCACGATG
TTTCATACAACATTAAAAAGTATTTTATTGAGTGGCACGATTAAAGATATGATCGAACAT
ATTGGAGAAGGAGGAGTAGAAAATATGGGAGCAATTCCTTTACAAAATGTTGATTCAAAA
ACTCTAGAAATAGTTATTAAATGGATAGAACATCACAAAGATAATATACAACCAACAAGT
GAAGAAATCAAAGATAAAACTGCAGATTTTATCGATCCTTGGGATGAAAATTTTTTGGAG
ATGGATTTAGATAAACTTTATAATTTGATTACTGCTGCCAATTATTTAAATATTCCTCAA
CTATTATGGCTATCAACACGTAAAATCGCTATGTTAATCAAAAACAGGACACCTCAGGAA
ATACGGTCGCTGTTTAATATCGAAGATGACTGGACACCGCAAGAAATAGAAGCTGTACAG
AAAGAAAACCAATGGTGTGAAGAGAAATAA
>g14006.t1 Gene=g14006 Length=169
MDIDRPSDPQVSVVSSDGTMFHTTLKSILLSGTIKDMIEHIGEGGVENMGAIPLQNVDSK
TLEIVIKWIEHHKDNIQPTSEEIKDKTADFIDPWDENFLEMDLDKLYNLITAANYLNIPQ
LLWLSTRKIAMLIKNRTPQEIRSLFNIEDDWTPQEIEAVQKENQWCEEK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g14006.t1 | CDD | cd18322 | BTB_POZ_SKP1 | 11 | 133 | 0 |
| 8 | g14006.t1 | Gene3D | G3DSA:3.30.710.10 | Potassium Channel Kv1.1; Chain A | 5 | 169 | 0 |
| 3 | g14006.t1 | PANTHER | PTHR11165 | SKP1 | 11 | 167 | 0 |
| 4 | g14006.t1 | PANTHER | PTHR11165:SF24 | S-PHASE KINASE-ASSOCIATED PROTEIN 1 | 11 | 167 | 0 |
| 9 | g14006.t1 | PIRSF | PIRSF028729 | SCF_Skp | 3 | 169 | 0 |
| 1 | g14006.t1 | Pfam | PF03931 | Skp1 family, tetramerisation domain | 11 | 74 | 0 |
| 2 | g14006.t1 | Pfam | PF01466 | Skp1 family, dimerisation domain | 120 | 166 | 0 |
| 7 | g14006.t1 | SMART | SM00512 | skp1_3 | 8 | 118 | 0 |
| 6 | g14006.t1 | SUPERFAMILY | SSF54695 | POZ domain | 11 | 75 | 0 |
| 5 | g14006.t1 | SUPERFAMILY | SSF81382 | Skp1 dimerisation domain-like | 91 | 166 | 0 |
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:0006511 | ubiquitin-dependent protein catabolic process | BP |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
