General information for g2749.t1
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.t1 | TTS | g2749.t1 | 19968116 | 19968116 |
| chr_3 | g2749 | g2749.t1 | isoform | g2749.t1 | 19968483 | 19978275 |
| chr_3 | g2749 | g2749.t1 | exon | g2749.t1.exon1 | 19968483 | 19968592 |
| chr_3 | g2749 | g2749.t1 | cds | g2749.t1.CDS1 | 19968483 | 19968592 |
| chr_3 | g2749 | g2749.t1 | exon | g2749.t1.exon2 | 19968966 | 19969071 |
| chr_3 | g2749 | g2749.t1 | cds | g2749.t1.CDS2 | 19968966 | 19969071 |
| chr_3 | g2749 | g2749.t1 | exon | g2749.t1.exon3 | 19969161 | 19969331 |
| chr_3 | g2749 | g2749.t1 | cds | g2749.t1.CDS3 | 19969161 | 19969331 |
| chr_3 | g2749 | g2749.t1 | exon | g2749.t1.exon4 | 19969418 | 19969423 |
| chr_3 | g2749 | g2749.t1 | cds | g2749.t1.CDS4 | 19969418 | 19969423 |
| chr_3 | g2749 | g2749.t1 | exon | g2749.t1.exon5 | 19973377 | 19973484 |
| chr_3 | g2749 | g2749.t1 | cds | g2749.t1.CDS5 | 19973377 | 19973484 |
| chr_3 | g2749 | g2749.t1 | exon | g2749.t1.exon6 | 19973551 | 19973726 |
| chr_3 | g2749 | g2749.t1 | cds | g2749.t1.CDS6 | 19973551 | 19973726 |
| chr_3 | g2749 | g2749.t1 | exon | g2749.t1.exon7 | 19975278 | 19975909 |
| chr_3 | g2749 | g2749.t1 | cds | g2749.t1.CDS7 | 19975278 | 19975909 |
| chr_3 | g2749 | g2749.t1 | exon | g2749.t1.exon8 | 19977721 | 19977926 |
| chr_3 | g2749 | g2749.t1 | cds | g2749.t1.CDS8 | 19977721 | 19977926 |
| chr_3 | g2749 | g2749.t1 | exon | g2749.t1.exon9 | 19977988 | 19978275 |
| chr_3 | g2749 | g2749.t1 | cds | g2749.t1.CDS9 | 19977988 | 19978275 |
| chr_3 | g2749 | g2749.t1 | TSS | g2749.t1 | 19978741 | 19978741 |
Sequences
>g2749.t1 Gene=g2749 Length=1803
ATGCAAAACATCAAATTACAATCATCTGACAGTGAAATTTTCGAATGCGATTTAGCTGTT
GCTAAGTGCTCTGGAACAATTCGAACAATGCTGGAGGATTTAGGAATCGATGAATCCAGT
GAGGATGAAGTTGTTCCTCTTCCAAATGTTAATTCGGCTATTCTTCGTAAAGTGATTCAA
TTTTGCACTTATCATAAAGATGATCCAGTTCCATCGAGTACCGATGATGACGAAAATAAG
GAAAAGCGTACTGATGATATCACATCATGGGATGCAGATTTCTTAAAGGTCGATCAAGGA
ACATTATTTGAACTTATTCTCGCAGCAAATTATTTAGACATTCGAAGTCTTTTGGATGTT
ACATGCAAGACTGTTGCAAATATGATTAAAGGAAAGACACCAGATGAAATCCGCAAGACG
TTTAACATTAAGAATGACTTTTCACCAGCTGAAGAAGAACAAGTTCGTAAAGAAAACACC
TGGTGTGAAGAAAACATCATAAAAAATATTAAATACACCCCGTCGGATATCACAGTCAAG
TTGGATTTCAAACAAAATTGTGCGGCCGCTAGCGGCAATAGTGTTGTGAACAGCAGTAAC
ACATCATCGCTCGGTTTAGGCCCCATTTCGCCAACAGATTCTCAGCAGTTTAATATTTTC
CCTGCAATTTTTAGTCGGCAGTTAAATTTCTCTACCGGCAATTGTAATCAACAAAAATTC
ATGATTCATAATAGCATGGAAGAGCTACGTCCAAATCTTGTTGGTGGTCTTTTAGGCCTT
CAACAAGGTCTTATAGAGGATCATCATAATCAAATACCACATAATAATTCCGACACAAAG
TTTATGTCGCTTCAAGAAAATCACAATAGATACGAAAATCGTCTCTTGGGACTTTCACAA
GAAAGTAGAAATTCATCATTAGCATCCTTGGCTGGAAATACGACACTTAATTTACCAAAT
GGAAATGATACAAATAAAGCATCAAATCAACGAAAATGTAGTAGTACGCCAGAAGACTTT
AATTCATTATATGGATCAACACTCGATAACACACATCATCATACGCCTGCACATACGCCT
CCTAATCCGAATCGATTGAGCGATCATAATCATAGTGCAATAACAGCCGAAGGAGCGTTT
AAAAAATTAAAGCCTGAGCCAAATAGTGGAATTTCTTCAGTTTCCGGTAGTGGCATTTCA
TCGCCTGGAAGTGGGATTTCTTTACCTCATGCTGGACATACACCGACCACTGTTTCTTGT
CCAACACCAGCTAGACGCAGACATAGAACCACTTTTACTCAGGAACAACTGGCTGAATTA
GAAGCTGCATTTGCAAAATCACATTATCCCGATATTTATTGCAGAGAAGAATTAGCCAGA
ACGACAAAACTGAATGAAGCTAGAATACAGGTTTGGTTTCAAAACAGAAGGGCAAAATAT
CGAAAACAAGAAAAACAGCTTCAAAAAGCGTTAGCTCCATCGGTGATACCCTCGTGTAAT
GGAATGATGCGAAATATTCAGGGTTATAGTGTATCTCGGTCTTATCAACCATATCCACAT
CCAAATTCTATCAATCGCTATCCTCAAGATCTATTTCAAATGGGAGCATCATCTTATCCA
GGCATGACGCAGCCATTTTCAATGTCACATAGTTCAAACATGAGTTCCGTCGGTGTTCGT
CAGGATTCAATGAGTATGTCTGCAGCAGAGGATGAATGGTACAACAAGAGCCTTTCAGCT
TTGAGAATGAACAGTTCACATCACCCAAACTTGTCAGCACCGATGCTTCAATATCAAACA
TAA
>g2749.t1 Gene=g2749 Length=600
MQNIKLQSSDSEIFECDLAVAKCSGTIRTMLEDLGIDESSEDEVVPLPNVNSAILRKVIQ
FCTYHKDDPVPSSTDDDENKEKRTDDITSWDADFLKVDQGTLFELILAANYLDIRSLLDV
TCKTVANMIKGKTPDEIRKTFNIKNDFSPAEEEQVRKENTWCEENIIKNIKYTPSDITVK
LDFKQNCAAASGNSVVNSSNTSSLGLGPISPTDSQQFNIFPAIFSRQLNFSTGNCNQQKF
MIHNSMEELRPNLVGGLLGLQQGLIEDHHNQIPHNNSDTKFMSLQENHNRYENRLLGLSQ
ESRNSSLASLAGNTTLNLPNGNDTNKASNQRKCSSTPEDFNSLYGSTLDNTHHHTPAHTP
PNPNRLSDHNHSAITAEGAFKKLKPEPNSGISSVSGSGISSPGSGISLPHAGHTPTTVSC
PTPARRRHRTTFTQEQLAELEAAFAKSHYPDIYCREELARTTKLNEARIQVWFQNRRAKY
RKQEKQLQKALAPSVIPSCNGMMRNIQGYSVSRSYQPYPHPNSINRYPQDLFQMGASSYP
GMTQPFSMSHSSNMSSVGVRQDSMSMSAAEDEWYNKSLSALRMNSSHHPNLSAPMLQYQT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g2749.t1 | CDD | cd18322 | BTB_POZ_SKP1 | 3 | 129 | 1.51241E-69 |
| 13 | g2749.t1 | CDD | cd00086 | homeodomain | 426 | 484 | 8.7715E-23 |
| 11 | g2749.t1 | Coils | Coil | Coil | 281 | 301 | - |
| 10 | g2749.t1 | Gene3D | G3DSA:3.30.710.10 | Potassium Channel Kv1.1; Chain A | 1 | 165 | 3.6E-73 |
| 9 | g2749.t1 | Gene3D | G3DSA:1.10.10.60 | - | 416 | 487 | 9.3E-28 |
| 17 | g2749.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 312 | 337 | - |
| 19 | g2749.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 406 | 426 | - |
| 18 | g2749.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 410 | 426 | - |
| 4 | g2749.t1 | PANTHER | PTHR24329 | HOMEOBOX PROTEIN ARISTALESS | 188 | 600 | 1.2E-174 |
| 5 | g2749.t1 | PANTHER | PTHR24329:SF520 | ALX HOMEOBOX PROTEIN 1-LIKE PROTEIN | 188 | 600 | 1.2E-174 |
| 1 | g2749.t1 | Pfam | PF03931 | Skp1 family, tetramerisation domain | 3 | 67 | 2.0E-22 |
| 3 | g2749.t1 | Pfam | PF01466 | Skp1 family, dimerisation domain | 116 | 162 | 1.2E-26 |
| 2 | g2749.t1 | Pfam | PF00046 | Homeodomain | 426 | 482 | 5.0E-22 |
| 16 | g2749.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 458 | 481 | - |
| 20 | g2749.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 423 | 483 | 20.504 |
| 14 | g2749.t1 | SMART | SM00512 | skp1_3 | 1 | 114 | 1.9E-49 |
| 15 | g2749.t1 | SMART | SM00389 | HOX_1 | 425 | 487 | 4.0E-25 |
| 7 | g2749.t1 | SUPERFAMILY | SSF54695 | POZ domain | 3 | 70 | 2.88E-20 |
| 6 | g2749.t1 | SUPERFAMILY | SSF81382 | Skp1 dimerisation domain-like | 87 | 162 | 6.8E-30 |
| 8 | g2749.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 404 | 485 | 1.63E-25 |
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:0003677 | DNA binding | MF |
| GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific | MF |
| GO:0006511 | ubiquitin-dependent protein catabolic process | BP |
| GO:0006355 | regulation of transcription, DNA-templated | 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.
