General information for g11473.t1
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.t1 | isoform | g11473.t1 | 16434579 | 16436918 |
| chr_1 | g11473 | g11473.t1 | exon | g11473.t1.exon1 | 16434579 | 16434589 |
| chr_1 | g11473 | g11473.t1 | cds | g11473.t1.CDS1 | 16434579 | 16434589 |
| chr_1 | g11473 | g11473.t1 | exon | g11473.t1.exon2 | 16434654 | 16434846 |
| chr_1 | g11473 | g11473.t1 | cds | g11473.t1.CDS2 | 16434654 | 16434846 |
| chr_1 | g11473 | g11473.t1 | exon | g11473.t1.exon3 | 16434917 | 16435369 |
| chr_1 | g11473 | g11473.t1 | cds | g11473.t1.CDS3 | 16434917 | 16435369 |
| chr_1 | g11473 | g11473.t1 | exon | g11473.t1.exon4 | 16435425 | 16435616 |
| chr_1 | g11473 | g11473.t1 | cds | g11473.t1.CDS4 | 16435425 | 16435616 |
| chr_1 | g11473 | g11473.t1 | exon | g11473.t1.exon5 | 16435697 | 16435876 |
| chr_1 | g11473 | g11473.t1 | cds | g11473.t1.CDS5 | 16435697 | 16435876 |
| chr_1 | g11473 | g11473.t1 | exon | g11473.t1.exon6 | 16435931 | 16436291 |
| chr_1 | g11473 | g11473.t1 | cds | g11473.t1.CDS6 | 16435931 | 16436291 |
| chr_1 | g11473 | g11473.t1 | exon | g11473.t1.exon7 | 16436351 | 16436481 |
| chr_1 | g11473 | g11473.t1 | cds | g11473.t1.CDS7 | 16436351 | 16436481 |
| chr_1 | g11473 | g11473.t1 | exon | g11473.t1.exon8 | 16436883 | 16436918 |
| chr_1 | g11473 | g11473.t1 | cds | g11473.t1.CDS8 | 16436883 | 16436918 |
| chr_1 | g11473 | g11473.t1 | TSS | g11473.t1 | NA | NA |
| chr_1 | g11473 | g11473.t1 | TTS | g11473.t1 | NA | NA |
Sequences
>g11473.t1 Gene=g11473 Length=1557
ATGGAGACTGACAAAATAGAAGATCCAAAATCACAGTTTCCAACGACTATACTCTATGAT
CCTGCACGTAAAAAGGAACCTTCTTCACAATATATAAAAGAAAGAGACAAATGTCTTTCG
ATGTTTTGCAACTGGAACGATGACGAACAAGTTGATTTTGTCGAACAATTACTTTCACGA
ATGTGTCATTATCAACACGGAAATATAAATGCATTCTTAAAGCCAATGCTTCAAAGAGAT
TTCATCTCTCTACTGCCGAAAAAAGGTCTCGATCATGTTGCTGATAATATACTTTCATTT
TTGGATGCTGAGTCACTTTGTGCTGCAGAGCTAGTGTCAAAAGAATGGAATCGTGTAATT
TCTGAGGGAATGTTATGGAAGAAACTAATTGAAAGAAAAGTTCGAAGTGATTCATTATGG
CGTGGGTTAGCGGAACGTAAAAAATGGATCAAGTATTTATTTGTACCAAGACAAGGAGAA
TATCGTAACCACTCATTTTATAGACAACTTTATCCTGTCATCATGAAGGACATTGAAACG
ATCGAAAATAATTGGCGTTCTGGAAATCACAATTTGCAACGAATAAATTGTAGATCTGAA
AATTCAAAAGGAGTCTATTGTCTTCAATATGATGATAACAAAATTGTCTCTGGTTTGCGT
GATAATACCATTAAAATTTGGAGTAGGTCTACTTTACAATGCGAAAAGATTTTGACGGGT
CATACGGGATCAGTACTTTGCTTGCAGTATGACGATAAAGTTATTATTAGTGGTTCCAGT
GATTCAACCGTTCGTGTTTGGGATGTAAAATCTGGAGAAATGACAAATACATTAATACAT
CATTGTGAAGCAGTTTTGCATTTAAGATTTAATAATGGAATGATGGTTACATGTTCAAAA
GATCGATCAATTGCGGTTTGGGATATGACTTCGCCTAAAGAAATAACTTTGCGTAGAGTG
CTTGTTGGGCATAGAGCTGCTGTTAATGTTGTAGACTTTGACGAAAAATATATTGTATCA
GCATCTGGAGACAGAACCATTAAAGTTTGGAGCACTTCTTCATGTGAATTTATTAGGACA
TTAAATGGTCATAAACGAGGAATAGCTTGTCTTCAATATCGTGACAGATTGGTTGTTAGT
GGAAGTTCTGATAATTCAATTCGTTTATGGGATATTGAATGTGGTGCATGTCTACGCGTT
TTAGAAGGACACGAAGAGCTAGTTCGTTGCATTCGATTTGATTCAAAGAGGATAGTGTCT
GGAGCCTATGATGGTAAGATTAAAGTTTGGGATTTAGTTGCTGCATTAGATCCTCGGGCT
CAACCATCATCATTATGTATTAAAACACTAAATGAACACACAGGACGAGTTTTTAGACTT
CAATTTGACGAATTCCAAATCGTAAGCAGCTCTCATGATGATACGATTTTAATATGGGAT
TTCCTAAATTATTCACAAGAAAATAATGCCGATCCTGGGCCAAATCGCAACAATAACACC
TTAACGATGACGACTGCAAATAATGAAAGTGGAAGAAGTCCATCCCCTATGGAATAA
>g11473.t1 Gene=g11473 Length=518
METDKIEDPKSQFPTTILYDPARKKEPSSQYIKERDKCLSMFCNWNDDEQVDFVEQLLSR
MCHYQHGNINAFLKPMLQRDFISLLPKKGLDHVADNILSFLDAESLCAAELVSKEWNRVI
SEGMLWKKLIERKVRSDSLWRGLAERKKWIKYLFVPRQGEYRNHSFYRQLYPVIMKDIET
IENNWRSGNHNLQRINCRSENSKGVYCLQYDDNKIVSGLRDNTIKIWSRSTLQCEKILTG
HTGSVLCLQYDDKVIISGSSDSTVRVWDVKSGEMTNTLIHHCEAVLHLRFNNGMMVTCSK
DRSIAVWDMTSPKEITLRRVLVGHRAAVNVVDFDEKYIVSASGDRTIKVWSTSSCEFIRT
LNGHKRGIACLQYRDRLVVSGSSDNSIRLWDIECGACLRVLEGHEELVRCIRFDSKRIVS
GAYDGKIKVWDLVAALDPRAQPSSLCIKTLNEHTGRVFRLQFDEFQIVSSSHDDTILIWD
FLNYSQENNADPGPNRNNNTLTMTTANNESGRSPSPME
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g11473.t1 | CDD | cd00200 | WD40 | 202 | 480 | 5.12221E-81 |
| 17 | g11473.t1 | Gene3D | G3DSA:1.20.1280.50 | - | 79 | 184 | 1.9E-43 |
| 16 | g11473.t1 | Gene3D | G3DSA:2.130.10.10 | - | 185 | 479 | 1.4E-107 |
| 33 | g11473.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 490 | 518 | - |
| 9 | g11473.t1 | PANTHER | PTHR44129 | - | 23 | 487 | 2.6E-270 |
| 10 | g11473.t1 | PANTHER | PTHR44129:SF4 | F-BOX/WD REPEAT-CONTAINING PROTEIN 11 | 23 | 487 | 2.6E-270 |
| 11 | g11473.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 255 | 269 | 6.2E-10 |
| 12 | g11473.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 378 | 392 | 6.2E-10 |
| 13 | g11473.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 418 | 432 | 6.2E-10 |
| 2 | g11473.t1 | Pfam | PF12125 | D domain of beta-TrCP | 40 | 78 | 1.0E-23 |
| 1 | g11473.t1 | Pfam | PF12937 | F-box-like | 96 | 129 | 8.0E-7 |
| 7 | g11473.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 203 | 228 | 0.06 |
| 8 | g11473.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 233 | 268 | 1.5E-6 |
| 4 | g11473.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 318 | 351 | 0.002 |
| 6 | g11473.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 357 | 391 | 1.2E-4 |
| 3 | g11473.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 395 | 431 | 5.1E-6 |
| 5 | g11473.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 446 | 480 | 0.06 |
| 29 | g11473.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 255 | 269 | - |
| 32 | g11473.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 295 | 309 | - |
| 30 | g11473.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 378 | 392 | - |
| 31 | g11473.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 418 | 432 | - |
| 28 | g11473.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 467 | 481 | - |
| 41 | g11473.t1 | ProSiteProfiles | PS50181 | F-box domain profile. | 91 | 129 | 8.835 |
| 34 | g11473.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 198 | 489 | 59.532 |
| 38 | g11473.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 238 | 277 | 16.022 |
| 37 | g11473.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 278 | 317 | 10.241 |
| 39 | g11473.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 321 | 360 | 13.148 |
| 40 | g11473.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 361 | 400 | 13.717 |
| 36 | g11473.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 401 | 432 | 13.115 |
| 35 | g11473.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 450 | 480 | 10.174 |
| 26 | g11473.t1 | SMART | SM01028 | Beta-TrCP_D_2 | 39 | 78 | 1.0E-21 |
| 27 | g11473.t1 | SMART | SM00256 | fbox_2 | 90 | 129 | 1.1E-4 |
| 20 | g11473.t1 | SMART | SM00320 | WD40_4 | 191 | 228 | 0.072 |
| 22 | g11473.t1 | SMART | SM00320 | WD40_4 | 231 | 268 | 9.0E-9 |
| 24 | g11473.t1 | SMART | SM00320 | WD40_4 | 271 | 308 | 5.4E-4 |
| 21 | g11473.t1 | SMART | SM00320 | WD40_4 | 314 | 351 | 3.4E-6 |
| 19 | g11473.t1 | SMART | SM00320 | WD40_4 | 354 | 391 | 3.0E-6 |
| 25 | g11473.t1 | SMART | SM00320 | WD40_4 | 394 | 431 | 1.1E-6 |
| 23 | g11473.t1 | SMART | SM00320 | WD40_4 | 443 | 480 | 7.0E-5 |
| 15 | g11473.t1 | SUPERFAMILY | SSF81383 | F-box domain | 74 | 186 | 2.88E-24 |
| 14 | g11473.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 189 | 480 | 5.86E-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.
