Gene loci information

Transcript annotation

  • This transcript has been annotated as F-box/WD repeat-containing protein 1A.

Parent gene

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.t7 isoform g11473.t7 16434579 16436918
chr_1 g11473 g11473.t7 exon g11473.t7.exon1 16434579 16434589
chr_1 g11473 g11473.t7 cds g11473.t7.CDS1 16434579 16434589
chr_1 g11473 g11473.t7 exon g11473.t7.exon2 16434654 16434846
chr_1 g11473 g11473.t7 cds g11473.t7.CDS2 16434654 16434846
chr_1 g11473 g11473.t7 exon g11473.t7.exon3 16434917 16435369
chr_1 g11473 g11473.t7 cds g11473.t7.CDS3 16434917 16435369
chr_1 g11473 g11473.t7 exon g11473.t7.exon4 16435425 16435616
chr_1 g11473 g11473.t7 cds g11473.t7.CDS4 16435425 16435616
chr_1 g11473 g11473.t7 exon g11473.t7.exon5 16435697 16435876
chr_1 g11473 g11473.t7 cds g11473.t7.CDS5 16435697 16435876
chr_1 g11473 g11473.t7 exon g11473.t7.exon6 16435931 16436291
chr_1 g11473 g11473.t7 cds g11473.t7.CDS6 16435931 16436291
chr_1 g11473 g11473.t7 exon g11473.t7.exon7 16436351 16436918
chr_1 g11473 g11473.t7 cds g11473.t7.CDS7 16436351 16436397
chr_1 g11473 g11473.t7 TSS g11473.t7 NA NA
chr_1 g11473 g11473.t7 TTS g11473.t7 NA NA

Sequences

>g11473.t7 Gene=g11473 Length=1958
ATGGAGACTGACAAAATAGAAGATCCAAAATCACAGGTATAAAACATATAAAATGTTTAA
AAGTATAAGAAATTTAGAAAAATTAGAAACTTAGCTGCATTCGTAAAAAATCATAATGGC
GAACTTTCAATTTTTTCGAGGACGATGATACGAAAATGAGAAGAAAATGACGTATGCATT
TGTTTTTCTGCTAGTAATCTATGCCAATATTGCACTATTATTGATTTCTCTATAAAAAAC
ATAAATTTTTATGAAAAACTTTTCGATTTTAAAAATTTATAATAATAAATTAATTTTTAT
ATGTATCATACCTTCCTCCATACATTCAATTAACTTTTAATAATTATAAAAACTCTATAT
GGTGTGTAAAAATTGTTAATTCTAGAATATAAATGATGTAATAAATAATTGTTATCGCTT
AAATAATCATTCTACAGTTTCCAACGACTATACTCTATGATCCTGCACGTAAAAAGGAAC
CTTCTTCACAATATATAAAAGAAAGAGACAAATGTCTTTCGATGTTTTGCAACTGGAACG
ATGACGAACAAGTTGATTTTGTCGAACAATTACTTTCACGAATGTGTCATTATCAACACG
GAAATATAAATGCATTCTTAAAGCCAATGCTTCAAAGAGATTTCATCTCTCTACTGCCGA
AAAAAGGTCTCGATCATGTTGCTGATAATATACTTTCATTTTTGGATGCTGAGTCACTTT
GTGCTGCAGAGCTAGTGTCAAAAGAATGGAATCGTGTAATTTCTGAGGGAATGTTATGGA
AGAAACTAATTGAAAGAAAAGTTCGAAGTGATTCATTATGGCGTGGGTTAGCGGAACGTA
AAAAATGGATCAAGTATTTATTTGTACCAAGACAAGGAGAATATCGTAACCACTCATTTT
ATAGACAACTTTATCCTGTCATCATGAAGGACATTGAAACGATCGAAAATAATTGGCGTT
CTGGAAATCACAATTTGCAACGAATAAATTGTAGATCTGAAAATTCAAAAGGAGTCTATT
GTCTTCAATATGATGATAACAAAATTGTCTCTGGTTTGCGTGATAATACCATTAAAATTT
GGAGTAGGTCTACTTTACAATGCGAAAAGATTTTGACGGGTCATACGGGATCAGTACTTT
GCTTGCAGTATGACGATAAAGTTATTATTAGTGGTTCCAGTGATTCAACCGTTCGTGTTT
GGGATGTAAAATCTGGAGAAATGACAAATACATTAATACATCATTGTGAAGCAGTTTTGC
ATTTAAGATTTAATAATGGAATGATGGTTACATGTTCAAAAGATCGATCAATTGCGGTTT
GGGATATGACTTCGCCTAAAGAAATAACTTTGCGTAGAGTGCTTGTTGGGCATAGAGCTG
CTGTTAATGTTGTAGACTTTGACGAAAAATATATTGTATCAGCATCTGGAGACAGAACCA
TTAAAGTTTGGAGCACTTCTTCATGTGAATTTATTAGGACATTAAATGGTCATAAACGAG
GAATAGCTTGTCTTCAATATCGTGACAGATTGGTTGTTAGTGGAAGTTCTGATAATTCAA
TTCGTTTATGGGATATTGAATGTGGTGCATGTCTACGCGTTTTAGAAGGACACGAAGAGC
TAGTTCGTTGCATTCGATTTGATTCAAAGAGGATAGTGTCTGGAGCCTATGATGGTAAGA
TTAAAGTTTGGGATTTAGTTGCTGCATTAGATCCTCGGGCTCAACCATCATCATTATGTA
TTAAAACACTAAATGAACACACAGGACGAGTTTTTAGACTTCAATTTGACGAATTCCAAA
TCGTAAGCAGCTCTCATGATGATACGATTTTAATATGGGATTTCCTAAATTATTCACAAG
AAAATAATGCCGATCCTGGGCCAAATCGCAACAATAACACCTTAACGATGACGACTGCAA
ATAATGAAAGTGGAAGAAGTCCATCCCCTATGGAATAA

>g11473.t7 Gene=g11473 Length=478
MFCNWNDDEQVDFVEQLLSRMCHYQHGNINAFLKPMLQRDFISLLPKKGLDHVADNILSF
LDAESLCAAELVSKEWNRVISEGMLWKKLIERKVRSDSLWRGLAERKKWIKYLFVPRQGE
YRNHSFYRQLYPVIMKDIETIENNWRSGNHNLQRINCRSENSKGVYCLQYDDNKIVSGLR
DNTIKIWSRSTLQCEKILTGHTGSVLCLQYDDKVIISGSSDSTVRVWDVKSGEMTNTLIH
HCEAVLHLRFNNGMMVTCSKDRSIAVWDMTSPKEITLRRVLVGHRAAVNVVDFDEKYIVS
ASGDRTIKVWSTSSCEFIRTLNGHKRGIACLQYRDRLVVSGSSDNSIRLWDIECGACLRV
LEGHEELVRCIRFDSKRIVSGAYDGKIKVWDLVAALDPRAQPSSLCIKTLNEHTGRVFRL
QFDEFQIVSSSHDDTILIWDFLNYSQENNADPGPNRNNNTLTMTTANNESGRSPSPME

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g11473.t7 CDD cd00200 WD40 162 440 2.62484E-80
17 g11473.t7 Gene3D G3DSA:1.20.1280.50 - 39 144 1.6E-43
16 g11473.t7 Gene3D G3DSA:2.130.10.10 - 145 439 1.1E-107
33 g11473.t7 MobiDBLite mobidb-lite consensus disorder prediction 450 478 -
9 g11473.t7 PANTHER PTHR44129 - 2 447 7.2E-265
10 g11473.t7 PANTHER PTHR44129:SF4 F-BOX/WD REPEAT-CONTAINING PROTEIN 11 2 447 7.2E-265
11 g11473.t7 PRINTS PR00320 G protein beta WD-40 repeat signature 215 229 5.0E-10
13 g11473.t7 PRINTS PR00320 G protein beta WD-40 repeat signature 338 352 5.0E-10
12 g11473.t7 PRINTS PR00320 G protein beta WD-40 repeat signature 378 392 5.0E-10
2 g11473.t7 Pfam PF12125 D domain of beta-TrCP 1 38 2.4E-23
1 g11473.t7 Pfam PF12937 F-box-like 56 89 7.2E-7
4 g11473.t7 Pfam PF00400 WD domain, G-beta repeat 163 188 0.054
8 g11473.t7 Pfam PF00400 WD domain, G-beta repeat 193 228 1.3E-6
5 g11473.t7 Pfam PF00400 WD domain, G-beta repeat 278 311 0.0018
3 g11473.t7 Pfam PF00400 WD domain, G-beta repeat 317 351 1.1E-4
6 g11473.t7 Pfam PF00400 WD domain, G-beta repeat 355 391 4.6E-6
7 g11473.t7 Pfam PF00400 WD domain, G-beta repeat 406 440 0.054
28 g11473.t7 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 215 229 -
29 g11473.t7 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 255 269 -
32 g11473.t7 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 338 352 -
30 g11473.t7 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 378 392 -
31 g11473.t7 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 427 441 -
41 g11473.t7 ProSiteProfiles PS50181 F-box domain profile. 51 89 8.835
34 g11473.t7 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 158 449 59.532
40 g11473.t7 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 198 237 16.022
36 g11473.t7 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 238 277 10.241
39 g11473.t7 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 281 320 13.148
37 g11473.t7 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 321 360 13.717
38 g11473.t7 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 361 392 13.115
35 g11473.t7 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 410 440 10.174
26 g11473.t7 SMART SM01028 Beta-TrCP_D_2 1 38 3.9E-20
27 g11473.t7 SMART SM00256 fbox_2 50 89 1.1E-4
23 g11473.t7 SMART SM00320 WD40_4 151 188 0.072
20 g11473.t7 SMART SM00320 WD40_4 191 228 9.0E-9
22 g11473.t7 SMART SM00320 WD40_4 231 268 5.4E-4
25 g11473.t7 SMART SM00320 WD40_4 274 311 3.4E-6
21 g11473.t7 SMART SM00320 WD40_4 314 351 3.0E-6
19 g11473.t7 SMART SM00320 WD40_4 354 391 1.1E-6
24 g11473.t7 SMART SM00320 WD40_4 403 440 7.0E-5
15 g11473.t7 SUPERFAMILY SSF81383 F-box domain 34 146 2.49E-24
14 g11473.t7 SUPERFAMILY SSF50978 WD40 repeat-like 149 440 7.32E-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

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.

Raw TPM values