General information for g2749.t29
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.t29 | TTS | g2749.t29 | 19977502 | 19977502 |
| chr_3 | g2749 | g2749.t29 | isoform | g2749.t29 | 19977510 | 19979210 |
| chr_3 | g2749 | g2749.t29 | exon | g2749.t29.exon1 | 19977510 | 19977926 |
| chr_3 | g2749 | g2749.t29 | cds | g2749.t29.CDS1 | 19977717 | 19977926 |
| chr_3 | g2749 | g2749.t29 | exon | g2749.t29.exon2 | 19977988 | 19978220 |
| chr_3 | g2749 | g2749.t29 | cds | g2749.t29.CDS2 | 19977988 | 19978188 |
| chr_3 | g2749 | g2749.t29 | exon | g2749.t29.exon3 | 19978926 | 19979210 |
| chr_3 | g2749 | g2749.t29 | TSS | g2749.t29 | NA | NA |
Sequences
>g2749.t29 Gene=g2749 Length=935
TTTTTTGCTTTTCTAAAAAAGAGAAATTTTTCTGTACTATTTTTATGTTTCGATTGATTG
TTTTGAACTAAAATGATTTATCAATCGCAATTAACTTTCTTAATGATTAACAACTTGCTT
ACCTGAGAATAAGAGAGTTTTTAATGTTTTTATTTACATTTAGGTAGGATTTTTAGAAGA
ATTATTGAAAGTCTTAATCTTATTACTGTTTTTAGCACATTTTTATAATAAAATGAGATT
TTGTTTACGTTTTGTCCACTTTCTTGTTTTCACTTGAAATTTTTCCTGTTGCTAAGTGCT
CTGGAACAATTCGAACAATGCTGGAGGATTTAGGAATCGATGAATCCAGTGAGGATGAAG
TTGTTCCTCTTCCAAATGTTAATTCGGCTATTCTTCGTAAAGTGATTCAATTTTGCACTT
ATCATAAAGATGATCCAGTTCCATCGAGTACCGATGATGACGAAAATAAGGAAAAGCGTA
CTGATGATATCACATCATGGGATGCAGATTTCTTAAAGGTCGATCAAGGAACATTATTTG
AACTTATTCTCGCAGCAAATTATTTAGACATTCGAAGTCTTTTGGATGTTACATGCAAGA
CTGTTGCAAATATGATTAAAGGAAAGACACCAGATGAAATCCGCAAGACGTTTAACATTA
AGAATGACTTTTCACCAGCTGAAGAAGAACAAGTTCGTAAAGAAAACACCTGGTGTGAAG
AAAAGTAAATTGGGTTTTTTATTTAACTTCTTCATAAATTTTTCGTCAACTTATGTGTTT
ATTTTTTAAAATTACTTCTGAGCCATTAAAAATTCAGATAAAAATAAATTTGTTTATGTC
CTATTTTCATCAAATCAAATTTTTCTGTTAATATTATAGCATGATTTCGAACAGTATATT
ATGAAAAATCTAAAACCAAGGAAAAATAAAAAAAT
>g2749.t29 Gene=g2749 Length=136
MLEDLGIDESSEDEVVPLPNVNSAILRKVIQFCTYHKDDPVPSSTDDDENKEKRTDDITS
WDADFLKVDQGTLFELILAANYLDIRSLLDVTCKTVANMIKGKTPDEIRKTFNIKNDFSP
AEEEQVRKENTWCEEK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g2749.t29 | CDD | cd18322 | BTB_POZ_SKP1 | 1 | 100 | 0 |
| 8 | g2749.t29 | Gene3D | G3DSA:3.30.710.10 | Potassium Channel Kv1.1; Chain A | 1 | 136 | 0 |
| 3 | g2749.t29 | PANTHER | PTHR11165:SF120 | S-PHASE KINASE-ASSOCIATED PROTEIN 1 | 1 | 136 | 0 |
| 4 | g2749.t29 | PANTHER | PTHR11165 | SKP1 | 1 | 136 | 0 |
| 9 | g2749.t29 | PIRSF | PIRSF028729 | SCF_Skp | 1 | 136 | 0 |
| 1 | g2749.t29 | Pfam | PF03931 | Skp1 family, tetramerisation domain | 1 | 38 | 0 |
| 2 | g2749.t29 | Pfam | PF01466 | Skp1 family, dimerisation domain | 87 | 133 | 0 |
| 7 | g2749.t29 | SMART | SM00512 | skp1_3 | 1 | 85 | 0 |
| 6 | g2749.t29 | SUPERFAMILY | SSF54695 | POZ domain | 1 | 41 | 0 |
| 5 | g2749.t29 | SUPERFAMILY | SSF81382 | Skp1 dimerisation domain-like | 58 | 133 | 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.
