General information for g2749.t20
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as S-phase kinase-associated protein 1.
Parent gene
- The parent gene g2749 is located on chr_3: 19977989..19981630 (- 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_3 | g2749 | g2749.t20 | isoform | g2749.t20 | 19977490 | 19978465 |
| chr_3 | g2749 | g2749.t20 | exon | g2749.t20.exon1 | 19977490 | 19977926 |
| chr_3 | g2749 | g2749.t20 | TTS | g2749.t20 | 19977502 | 19977502 |
| chr_3 | g2749 | g2749.t20 | cds | g2749.t20.CDS1 | 19977717 | 19977926 |
| chr_3 | g2749 | g2749.t20 | exon | g2749.t20.exon2 | 19977988 | 19978336 |
| chr_3 | g2749 | g2749.t20 | cds | g2749.t20.CDS2 | 19977988 | 19978275 |
| chr_3 | g2749 | g2749.t20 | exon | g2749.t20.exon3 | 19978450 | 19978465 |
| chr_3 | g2749 | g2749.t20 | TSS | g2749.t20 | 19978741 | 19978741 |
Sequences
>g2749.t20 Gene=g2749 Length=802
TCTGTGAATTCTCATTTGTGTGTACTTCAAAACTTCACTTTTTACATAGAGCTATTTTAA
AAATAAACTCCTAAAAAATGCAAAACATCAAATTACAATCATCTGACAGTGAAATTTTCG
AATGCGATTTAGCTGTTGCTAAGTGCTCTGGAACAATTCGAACAATGCTGGAGGATTTAG
GAATCGATGAATCCAGTGAGGATGAAGTTGTTCCTCTTCCAAATGTTAATTCGGCTATTC
TTCGTAAAGTGATTCAATTTTGCACTTATCATAAAGATGATCCAGTTCCATCGAGTACCG
ATGATGACGAAAATAAGGAAAAGCGTACTGATGATATCACATCATGGGATGCAGATTTCT
TAAAGGTCGATCAAGGAACATTATTTGAACTTATTCTCGCAGCAAATTATTTAGACATTC
GAAGTCTTTTGGATGTTACATGCAAGACTGTTGCAAATATGATTAAAGGAAAGACACCAG
ATGAAATCCGCAAGACGTTTAACATTAAGAATGACTTTTCACCAGCTGAAGAAGAACAAG
TTCGTAAAGAAAACACCTGGTGTGAAGAAAAGTAAATTGGGTTTTTTATTTAACTTCTTC
ATAAATTTTTCGTCAACTTATGTGTTTATTTTTTAAAATTACTTCTGAGCCATTAAAAAT
TCAGATAAAAATAAATTTGTTTATGTCCTATTTTCATCAAATCAAATTTTTCTGTTAATA
TTATAGCATGATTTCGAACAGTATATTATGAAAAATCTAAAACCAAGGAAAAATAAAAAA
ATTTTAAACGAACATTTTAAAT
>g2749.t20 Gene=g2749 Length=165
MQNIKLQSSDSEIFECDLAVAKCSGTIRTMLEDLGIDESSEDEVVPLPNVNSAILRKVIQ
FCTYHKDDPVPSSTDDDENKEKRTDDITSWDADFLKVDQGTLFELILAANYLDIRSLLDV
TCKTVANMIKGKTPDEIRKTFNIKNDFSPAEEEQVRKENTWCEEK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g2749.t20 | CDD | cd18322 | BTB_POZ_SKP1 | 3 | 129 | 0 |
| 8 | g2749.t20 | Gene3D | G3DSA:3.30.710.10 | Potassium Channel Kv1.1; Chain A | 1 | 165 | 0 |
| 3 | g2749.t20 | PANTHER | PTHR11165:SF120 | S-PHASE KINASE-ASSOCIATED PROTEIN 1 | 1 | 165 | 0 |
| 4 | g2749.t20 | PANTHER | PTHR11165 | SKP1 | 1 | 165 | 0 |
| 9 | g2749.t20 | PIRSF | PIRSF028729 | SCF_Skp | 1 | 165 | 0 |
| 1 | g2749.t20 | Pfam | PF03931 | Skp1 family, tetramerisation domain | 3 | 67 | 0 |
| 2 | g2749.t20 | Pfam | PF01466 | Skp1 family, dimerisation domain | 116 | 162 | 0 |
| 7 | g2749.t20 | SMART | SM00512 | skp1_3 | 1 | 114 | 0 |
| 6 | g2749.t20 | SUPERFAMILY | SSF54695 | POZ domain | 3 | 70 | 0 |
| 5 | g2749.t20 | SUPERFAMILY | SSF81382 | Skp1 dimerisation domain-like | 87 | 162 | 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 transcript has been annotated with K03094 (S-phase kinase-associated protein 1)
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.
