General information for g11473.t6
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.t6 | isoform | g11473.t6 | 16434579 | 16436291 |
| chr_1 | g11473 | g11473.t6 | exon | g11473.t6.exon1 | 16434579 | 16434589 |
| chr_1 | g11473 | g11473.t6 | cds | g11473.t6.CDS1 | 16434579 | 16434589 |
| chr_1 | g11473 | g11473.t6 | exon | g11473.t6.exon2 | 16434654 | 16434846 |
| chr_1 | g11473 | g11473.t6 | cds | g11473.t6.CDS2 | 16434654 | 16434846 |
| chr_1 | g11473 | g11473.t6 | exon | g11473.t6.exon3 | 16434917 | 16435369 |
| chr_1 | g11473 | g11473.t6 | cds | g11473.t6.CDS3 | 16434917 | 16435369 |
| chr_1 | g11473 | g11473.t6 | exon | g11473.t6.exon4 | 16435425 | 16435616 |
| chr_1 | g11473 | g11473.t6 | cds | g11473.t6.CDS4 | 16435425 | 16435616 |
| chr_1 | g11473 | g11473.t6 | exon | g11473.t6.exon5 | 16435697 | 16435876 |
| chr_1 | g11473 | g11473.t6 | cds | g11473.t6.CDS5 | 16435697 | 16435876 |
| chr_1 | g11473 | g11473.t6 | exon | g11473.t6.exon6 | 16435931 | 16436291 |
| chr_1 | g11473 | g11473.t6 | cds | g11473.t6.CDS6 | 16435931 | 16436278 |
| chr_1 | g11473 | g11473.t6 | TSS | g11473.t6 | NA | NA |
| chr_1 | g11473 | g11473.t6 | TTS | g11473.t6 | NA | NA |
Sequences
>g11473.t6 Gene=g11473 Length=1390
ATTACTTTCACGAATGTGTCATTATCAACACGGAAATATAAATGCATTCTTAAAGCCAAT
GCTTCAAAGAGATTTCATCTCTCTACTGCCGAAAAAAGGTCTCGATCATGTTGCTGATAA
TATACTTTCATTTTTGGATGCTGAGTCACTTTGTGCTGCAGAGCTAGTGTCAAAAGAATG
GAATCGTGTAATTTCTGAGGGAATGTTATGGAAGAAACTAATTGAAAGAAAAGTTCGAAG
TGATTCATTATGGCGTGGGTTAGCGGAACGTAAAAAATGGATCAAGTATTTATTTGTACC
AAGACAAGGAGAATATCGTAACCACTCATTTTATAGACAACTTTATCCTGTCATCATGAA
GGACATTGAAACGATCGAAAATAATTGGCGTTCTGGAAATCACAATTTGCAACGAATAAA
TTGTAGATCTGAAAATTCAAAAGGAGTCTATTGTCTTCAATATGATGATAACAAAATTGT
CTCTGGTTTGCGTGATAATACCATTAAAATTTGGAGTAGGTCTACTTTACAATGCGAAAA
GATTTTGACGGGTCATACGGGATCAGTACTTTGCTTGCAGTATGACGATAAAGTTATTAT
TAGTGGTTCCAGTGATTCAACCGTTCGTGTTTGGGATGTAAAATCTGGAGAAATGACAAA
TACATTAATACATCATTGTGAAGCAGTTTTGCATTTAAGATTTAATAATGGAATGATGGT
TACATGTTCAAAAGATCGATCAATTGCGGTTTGGGATATGACTTCGCCTAAAGAAATAAC
TTTGCGTAGAGTGCTTGTTGGGCATAGAGCTGCTGTTAATGTTGTAGACTTTGACGAAAA
ATATATTGTATCAGCATCTGGAGACAGAACCATTAAAGTTTGGAGCACTTCTTCATGTGA
ATTTATTAGGACATTAAATGGTCATAAACGAGGAATAGCTTGTCTTCAATATCGTGACAG
ATTGGTTGTTAGTGGAAGTTCTGATAATTCAATTCGTTTATGGGATATTGAATGTGGTGC
ATGTCTACGCGTTTTAGAAGGACACGAAGAGCTAGTTCGTTGCATTCGATTTGATTCAAA
GAGGATAGTGTCTGGAGCCTATGATGGTAAGATTAAAGTTTGGGATTTAGTTGCTGCATT
AGATCCTCGGGCTCAACCATCATCATTATGTATTAAAACACTAAATGAACACACAGGACG
AGTTTTTAGACTTCAATTTGACGAATTCCAAATCGTAAGCAGCTCTCATGATGATACGAT
TTTAATATGGGATTTCCTAAATTATTCACAAGAAAATAATGCCGATCCTGGGCCAAATCG
CAACAATAACACCTTAACGATGACGACTGCAAATAATGAAAGTGGAAGAAGTCCATCCCC
TATGGAATAA
>g11473.t6 Gene=g11473 Length=458
MCHYQHGNINAFLKPMLQRDFISLLPKKGLDHVADNILSFLDAESLCAAELVSKEWNRVI
SEGMLWKKLIERKVRSDSLWRGLAERKKWIKYLFVPRQGEYRNHSFYRQLYPVIMKDIET
IENNWRSGNHNLQRINCRSENSKGVYCLQYDDNKIVSGLRDNTIKIWSRSTLQCEKILTG
HTGSVLCLQYDDKVIISGSSDSTVRVWDVKSGEMTNTLIHHCEAVLHLRFNNGMMVTCSK
DRSIAVWDMTSPKEITLRRVLVGHRAAVNVVDFDEKYIVSASGDRTIKVWSTSSCEFIRT
LNGHKRGIACLQYRDRLVVSGSSDNSIRLWDIECGACLRVLEGHEELVRCIRFDSKRIVS
GAYDGKIKVWDLVAALDPRAQPSSLCIKTLNEHTGRVFRLQFDEFQIVSSSHDDTILIWD
FLNYSQENNADPGPNRNNNTLTMTTANNESGRSPSPME
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g11473.t6 | CDD | cd00200 | WD40 | 142 | 420 | 1.79784E-80 |
| 17 | g11473.t6 | Gene3D | G3DSA:1.20.1280.50 | - | 19 | 124 | 1.5E-43 |
| 16 | g11473.t6 | Gene3D | G3DSA:2.130.10.10 | - | 125 | 419 | 9.9E-108 |
| 32 | g11473.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 430 | 458 | - |
| 9 | g11473.t6 | PANTHER | PTHR44129 | - | 1 | 428 | 9.2E-257 |
| 10 | g11473.t6 | PANTHER | PTHR44129:SF4 | F-BOX/WD REPEAT-CONTAINING PROTEIN 11 | 1 | 428 | 9.2E-257 |
| 13 | g11473.t6 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 195 | 209 | 4.5E-10 |
| 12 | g11473.t6 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 318 | 332 | 4.5E-10 |
| 11 | g11473.t6 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 358 | 372 | 4.5E-10 |
| 2 | g11473.t6 | Pfam | PF12125 | D domain of beta-TrCP | 1 | 18 | 3.0E-9 |
| 1 | g11473.t6 | Pfam | PF12937 | F-box-like | 36 | 69 | 6.8E-7 |
| 8 | g11473.t6 | Pfam | PF00400 | WD domain, G-beta repeat | 143 | 168 | 0.052 |
| 6 | g11473.t6 | Pfam | PF00400 | WD domain, G-beta repeat | 173 | 208 | 1.3E-6 |
| 5 | g11473.t6 | Pfam | PF00400 | WD domain, G-beta repeat | 258 | 291 | 0.0017 |
| 7 | g11473.t6 | Pfam | PF00400 | WD domain, G-beta repeat | 297 | 331 | 1.0E-4 |
| 3 | g11473.t6 | Pfam | PF00400 | WD domain, G-beta repeat | 335 | 371 | 4.3E-6 |
| 4 | g11473.t6 | Pfam | PF00400 | WD domain, G-beta repeat | 386 | 420 | 0.051 |
| 31 | g11473.t6 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 195 | 209 | - |
| 28 | g11473.t6 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 235 | 249 | - |
| 30 | g11473.t6 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 318 | 332 | - |
| 29 | g11473.t6 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 358 | 372 | - |
| 27 | g11473.t6 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 407 | 421 | - |
| 40 | g11473.t6 | ProSiteProfiles | PS50181 | F-box domain profile. | 31 | 69 | 8.835 |
| 33 | g11473.t6 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 138 | 429 | 59.532 |
| 35 | g11473.t6 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 178 | 217 | 16.022 |
| 39 | g11473.t6 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 218 | 257 | 10.241 |
| 38 | g11473.t6 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 261 | 300 | 13.148 |
| 37 | g11473.t6 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 301 | 340 | 13.717 |
| 36 | g11473.t6 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 341 | 372 | 13.115 |
| 34 | g11473.t6 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 390 | 420 | 10.174 |
| 26 | g11473.t6 | SMART | SM00256 | fbox_2 | 30 | 69 | 1.1E-4 |
| 23 | g11473.t6 | SMART | SM00320 | WD40_4 | 131 | 168 | 0.072 |
| 25 | g11473.t6 | SMART | SM00320 | WD40_4 | 171 | 208 | 9.0E-9 |
| 19 | g11473.t6 | SMART | SM00320 | WD40_4 | 211 | 248 | 5.4E-4 |
| 22 | g11473.t6 | SMART | SM00320 | WD40_4 | 254 | 291 | 3.4E-6 |
| 21 | g11473.t6 | SMART | SM00320 | WD40_4 | 294 | 331 | 3.0E-6 |
| 20 | g11473.t6 | SMART | SM00320 | WD40_4 | 334 | 371 | 1.1E-6 |
| 24 | g11473.t6 | SMART | SM00320 | WD40_4 | 383 | 420 | 7.0E-5 |
| 15 | g11473.t6 | SUPERFAMILY | SSF81383 | F-box domain | 14 | 126 | 2.35E-24 |
| 14 | g11473.t6 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 129 | 420 | 4.58E-75 |
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 transcript has been annotated with K03362 (F-box and WD-40 domain protein 1/11)
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.
