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.t4 isoform g11473.t4 16434579 16435368
chr_1 g11473 g11473.t4 exon g11473.t4.exon1 16434579 16434589
chr_1 g11473 g11473.t4 cds g11473.t4.CDS1 16434579 16434589
chr_1 g11473 g11473.t4 exon g11473.t4.exon2 16434654 16434846
chr_1 g11473 g11473.t4 cds g11473.t4.CDS2 16434654 16434846
chr_1 g11473 g11473.t4 exon g11473.t4.exon3 16434917 16435368
chr_1 g11473 g11473.t4 cds g11473.t4.CDS3 16434917 16435345
chr_1 g11473 g11473.t4 TSS g11473.t4 NA NA
chr_1 g11473 g11473.t4 TTS g11473.t4 NA NA

Sequences

>g11473.t4 Gene=g11473 Length=656
ATCGATCAATTGCGGTTTGGGATATGACTTCGCCTAAAGAAATAACTTTGCGTAGAGTGC
TTGTTGGGCATAGAGCTGCTGTTAATGTTGTAGACTTTGACGAAAAATATATTGTATCAG
CATCTGGAGACAGAACCATTAAAGTTTGGAGCACTTCTTCATGTGAATTTATTAGGACAT
TAAATGGTCATAAACGAGGAATAGCTTGTCTTCAATATCGTGACAGATTGGTTGTTAGTG
GAAGTTCTGATAATTCAATTCGTTTATGGGATATTGAATGTGGTGCATGTCTACGCGTTT
TAGAAGGACACGAAGAGCTAGTTCGTTGCATTCGATTTGATTCAAAGAGGATAGTGTCTG
GAGCCTATGATGGTAAGATTAAAGTTTGGGATTTAGTTGCTGCATTAGATCCTCGGGCTC
AACCATCATCATTATGTATTAAAACACTAAATGAACACACAGGACGAGTTTTTAGACTTC
AATTTGACGAATTCCAAATCGTAAGCAGCTCTCATGATGATACGATTTTAATATGGGATT
TCCTAAATTATTCACAAGAAAATAATGCCGATCCTGGGCCAAATCGCAACAATAACACCT
TAACGATGACGACTGCAAATAATGAAAGTGGAAGAAGTCCATCCCCTATGGAATAA

>g11473.t4 Gene=g11473 Length=210
MTSPKEITLRRVLVGHRAAVNVVDFDEKYIVSASGDRTIKVWSTSSCEFIRTLNGHKRGI
ACLQYRDRLVVSGSSDNSIRLWDIECGACLRVLEGHEELVRCIRFDSKRIVSGAYDGKIK
VWDLVAALDPRAQPSSLCIKTLNEHTGRVFRLQFDEFQIVSSSHDDTILIWDFLNYSQEN
NADPGPNRNNNTLTMTTANNESGRSPSPME

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g11473.t4 CDD cd00200 WD40 9 173 6.89425E-46
11 g11473.t4 Gene3D G3DSA:2.130.10.10 - 1 171 2.1E-61
20 g11473.t4 MobiDBLite mobidb-lite consensus disorder prediction 182 210 -
5 g11473.t4 PANTHER PTHR19865:SF9 F-BOX AND WD REPEAT DOMAIN-CONTAINING 11A 9 185 6.1E-117
6 g11473.t4 PANTHER PTHR19865 U3 SMALL NUCLEOLAR RNA INTERACTING PROTEIN 2 9 185 6.1E-117
8 g11473.t4 PRINTS PR00320 G protein beta WD-40 repeat signature 30 44 7.1E-10
9 g11473.t4 PRINTS PR00320 G protein beta WD-40 repeat signature 70 84 7.1E-10
7 g11473.t4 PRINTS PR00320 G protein beta WD-40 repeat signature 110 124 7.1E-10
4 g11473.t4 Pfam PF00400 WD domain, G-beta repeat 10 43 5.8E-4
3 g11473.t4 Pfam PF00400 WD domain, G-beta repeat 49 83 3.5E-5
1 g11473.t4 Pfam PF00400 WD domain, G-beta repeat 87 123 1.4E-6
2 g11473.t4 Pfam PF00400 WD domain, G-beta repeat 138 172 0.017
19 g11473.t4 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 70 84 -
17 g11473.t4 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 110 124 -
18 g11473.t4 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 159 173 -
21 g11473.t4 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 13 181 35.989
25 g11473.t4 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 13 52 13.148
24 g11473.t4 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 53 92 13.717
22 g11473.t4 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 93 124 13.115
23 g11473.t4 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 142 172 10.174
14 g11473.t4 SMART SM00320 WD40_4 6 43 3.4E-6
16 g11473.t4 SMART SM00320 WD40_4 46 83 3.0E-6
15 g11473.t4 SMART SM00320 WD40_4 86 123 1.1E-6
13 g11473.t4 SMART SM00320 WD40_4 135 172 7.0E-5
10 g11473.t4 SUPERFAMILY SSF50978 WD40 repeat-like 7 178 6.64E-49

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:0034511 U3 snoRNA binding MF
GO:0005515 protein binding MF
GO:0006364 rRNA processing 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.

Raw TPM values