General information for g11473.t9
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as F-box/WD repeat-containing protein 1A.
Parent gene
- The parent gene g11473 is located on chr_1: 16436603..16437311 (- 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 | g11473 | g11473.t9 | isoform | g11473.t9 | 16435443 | 16436918 |
| chr_1 | g11473 | g11473.t9 | exon | g11473.t9.exon1 | 16435443 | 16435616 |
| chr_1 | g11473 | g11473.t9 | cds | g11473.t9.CDS1 | 16435443 | 16435616 |
| chr_1 | g11473 | g11473.t9 | exon | g11473.t9.exon2 | 16435697 | 16435876 |
| chr_1 | g11473 | g11473.t9 | cds | g11473.t9.CDS2 | 16435697 | 16435876 |
| chr_1 | g11473 | g11473.t9 | exon | g11473.t9.exon3 | 16435931 | 16436291 |
| chr_1 | g11473 | g11473.t9 | cds | g11473.t9.CDS3 | 16435931 | 16436291 |
| chr_1 | g11473 | g11473.t9 | exon | g11473.t9.exon4 | 16436351 | 16436481 |
| chr_1 | g11473 | g11473.t9 | cds | g11473.t9.CDS4 | 16436351 | 16436481 |
| chr_1 | g11473 | g11473.t9 | exon | g11473.t9.exon5 | 16436883 | 16436918 |
| chr_1 | g11473 | g11473.t9 | cds | g11473.t9.CDS5 | 16436883 | 16436918 |
| chr_1 | g11473 | g11473.t9 | TSS | g11473.t9 | NA | NA |
| chr_1 | g11473 | g11473.t9 | TTS | g11473.t9 | NA | NA |
Sequences
>g11473.t9 Gene=g11473 Length=882
ATGGAGACTGACAAAATAGAAGATCCAAAATCACAGTTTCCAACGACTATACTCTATGAT
CCTGCACGTAAAAAGGAACCTTCTTCACAATATATAAAAGAAAGAGACAAATGTCTTTCG
ATGTTTTGCAACTGGAACGATGACGAACAAGTTGATTTTGTCGAACAATTACTTTCACGA
ATGTGTCATTATCAACACGGAAATATAAATGCATTCTTAAAGCCAATGCTTCAAAGAGAT
TTCATCTCTCTACTGCCGAAAAAAGGTCTCGATCATGTTGCTGATAATATACTTTCATTT
TTGGATGCTGAGTCACTTTGTGCTGCAGAGCTAGTGTCAAAAGAATGGAATCGTGTAATT
TCTGAGGGAATGTTATGGAAGAAACTAATTGAAAGAAAAGTTCGAAGTGATTCATTATGG
CGTGGGTTAGCGGAACGTAAAAAATGGATCAAGTATTTATTTGTACCAAGACAAGGAGAA
TATCGTAACCACTCATTTTATAGACAACTTTATCCTGTCATCATGAAGGACATTGAAACG
ATCGAAAATAATTGGCGTTCTGGAAATCACAATTTGCAACGAATAAATTGTAGATCTGAA
AATTCAAAAGGAGTCTATTGTCTTCAATATGATGATAACAAAATTGTCTCTGGTTTGCGT
GATAATACCATTAAAATTTGGAGTAGGTCTACTTTACAATGCGAAAAGATTTTGACGGGT
CATACGGGATCAGTACTTTGCTTGCAGTATGACGATAAAGTTATTATTAGTGGTTCCAGT
GATTCAACCGTTCGTGTTTGGGATGTAAAATCTGGAGAAATGACAAATACATTAATACAT
CATTGTGAAGCAGTTTTGCATTTAAGATTTAATAATGGAATG
>g11473.t9 Gene=g11473 Length=294
METDKIEDPKSQFPTTILYDPARKKEPSSQYIKERDKCLSMFCNWNDDEQVDFVEQLLSR
MCHYQHGNINAFLKPMLQRDFISLLPKKGLDHVADNILSFLDAESLCAAELVSKEWNRVI
SEGMLWKKLIERKVRSDSLWRGLAERKKWIKYLFVPRQGEYRNHSFYRQLYPVIMKDIET
IENNWRSGNHNLQRINCRSENSKGVYCLQYDDNKIVSGLRDNTIKIWSRSTLQCEKILTG
HTGSVLCLQYDDKVIISGSSDSTVRVWDVKSGEMTNTLIHHCEAVLHLRFNNGM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g11473.t9 | Gene3D | G3DSA:1.20.1280.50 | - | 79 | 184 | 6.5E-44 |
| 14 | g11473.t9 | Gene3D | G3DSA:2.130.10.10 | - | 185 | 294 | 1.6E-33 |
| 5 | g11473.t9 | PANTHER | PTHR44156 | - | 24 | 294 | 9.5E-145 |
| 6 | g11473.t9 | PANTHER | PTHR44156:SF2 | F-BOX/WD REPEAT-CONTAINING PROTEIN 1A | 24 | 294 | 9.5E-145 |
| 2 | g11473.t9 | Pfam | PF12125 | D domain of beta-TrCP | 40 | 78 | 4.8E-24 |
| 1 | g11473.t9 | Pfam | PF12937 | F-box-like | 96 | 129 | 3.7E-7 |
| 3 | g11473.t9 | Pfam | PF00400 | WD domain, G-beta repeat | 203 | 228 | 0.029 |
| 4 | g11473.t9 | Pfam | PF00400 | WD domain, G-beta repeat | 233 | 268 | 7.0E-7 |
| 13 | g11473.t9 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 255 | 269 | - |
| 18 | g11473.t9 | ProSiteProfiles | PS50181 | F-box domain profile. | 91 | 129 | 8.835 |
| 16 | g11473.t9 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 198 | 294 | 21.305 |
| 17 | g11473.t9 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 238 | 277 | 16.022 |
| 11 | g11473.t9 | SMART | SM01028 | Beta-TrCP_D_2 | 39 | 78 | 1.0E-21 |
| 12 | g11473.t9 | SMART | SM00256 | fbox_2 | 90 | 129 | 1.1E-4 |
| 9 | g11473.t9 | SMART | SM00320 | WD40_4 | 191 | 228 | 0.072 |
| 10 | g11473.t9 | SMART | SM00320 | WD40_4 | 231 | 268 | 9.0E-9 |
| 8 | g11473.t9 | SUPERFAMILY | SSF81383 | F-box domain | 74 | 186 | 9.55E-25 |
| 7 | g11473.t9 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 195 | 292 | 2.01E-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:0005515 | protein binding | MF |
| GO:0046983 | protein dimerization activity | MF |
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.
