General information for g11473.t5
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.t5 | isoform | g11473.t5 | 16434579 | 16435599 |
| chr_1 | g11473 | g11473.t5 | exon | g11473.t5.exon1 | 16434579 | 16434589 |
| chr_1 | g11473 | g11473.t5 | cds | g11473.t5.CDS1 | 16434579 | 16434589 |
| chr_1 | g11473 | g11473.t5 | exon | g11473.t5.exon2 | 16434654 | 16434846 |
| chr_1 | g11473 | g11473.t5 | cds | g11473.t5.CDS2 | 16434654 | 16434846 |
| chr_1 | g11473 | g11473.t5 | exon | g11473.t5.exon3 | 16434917 | 16435369 |
| chr_1 | g11473 | g11473.t5 | cds | g11473.t5.CDS3 | 16434917 | 16435369 |
| chr_1 | g11473 | g11473.t5 | exon | g11473.t5.exon4 | 16435425 | 16435599 |
| chr_1 | g11473 | g11473.t5 | cds | g11473.t5.CDS4 | 16435425 | 16435505 |
| chr_1 | g11473 | g11473.t5 | TSS | g11473.t5 | NA | NA |
| chr_1 | g11473 | g11473.t5 | TTS | g11473.t5 | NA | NA |
Sequences
>g11473.t5 Gene=g11473 Length=832
GGGATCAGTACTTTGCTTGCAGTATGACGATAAAGTTATTATTAGTGGTTCCAGTGATTC
AACCGTTCGTGTTTGGGATGTAAAATCTGGAGAAATGACAAATACATTAATACATCATTG
TGAAGCAGTTTTGCATTTAAGATTTAATAATGGAATGATGGTTACATGTTCAAAAGATCG
ATCAATTGCGGTTTGGGATATGACTTCGCCTAAAGAAATAACTTTGCGTAGAGTGCTTGT
TGGGCATAGAGCTGCTGTTAATGTTGTAGACTTTGACGAAAAATATATTGTATCAGCATC
TGGAGACAGAACCATTAAAGTTTGGAGCACTTCTTCATGTGAATTTATTAGGACATTAAA
TGGTCATAAACGAGGAATAGCTTGTCTTCAATATCGTGACAGATTGGTTGTTAGTGGAAG
TTCTGATAATTCAATTCGTTTATGGGATATTGAATGTGGTGCATGTCTACGCGTTTTAGA
AGGACACGAAGAGCTAGTTCGTTGCATTCGATTTGATTCAAAGAGGATAGTGTCTGGAGC
CTATGATGGTAAGATTAAAGTTTGGGATTTAGTTGCTGCATTAGATCCTCGGGCTCAACC
ATCATCATTATGTATTAAAACACTAAATGAACACACAGGACGAGTTTTTAGACTTCAATT
TGACGAATTCCAAATCGTAAGCAGCTCTCATGATGATACGATTTTAATATGGGATTTCCT
AAATTATTCACAAGAAAATAATGCCGATCCTGGGCCAAATCGCAACAATAACACCTTAAC
GATGACGACTGCAAATAATGAAAGTGGAAGAAGTCCATCCCCTATGGAATAA
>g11473.t5 Gene=g11473 Length=245
MTNTLIHHCEAVLHLRFNNGMMVTCSKDRSIAVWDMTSPKEITLRRVLVGHRAAVNVVDF
DEKYIVSASGDRTIKVWSTSSCEFIRTLNGHKRGIACLQYRDRLVVSGSSDNSIRLWDIE
CGACLRVLEGHEELVRCIRFDSKRIVSGAYDGKIKVWDLVAALDPRAQPSSLCIKTLNEH
TGRVFRLQFDEFQIVSSSHDDTILIWDFLNYSQENNADPGPNRNNNTLTMTTANNESGRS
PSPME
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g11473.t5 | CDD | cd00200 | WD40 | 1 | 207 | 2.83637E-54 |
| 11 | g11473.t5 | Gene3D | G3DSA:2.130.10.10 | - | 1 | 206 | 3.2E-75 |
| 22 | g11473.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 217 | 245 | - |
| 5 | g11473.t5 | PANTHER | PTHR22847:SF664 | BETA-TRANSDUCIN REPEAT CONTAINING E3 UBIQUITIN PROTEIN LIGASE | 1 | 215 | 4.6E-132 |
| 6 | g11473.t5 | PANTHER | PTHR22847 | WD40 REPEAT PROTEIN | 1 | 215 | 4.6E-132 |
| 9 | g11473.t5 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 65 | 79 | 1.0E-9 |
| 8 | g11473.t5 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 105 | 119 | 1.0E-9 |
| 7 | g11473.t5 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 145 | 159 | 1.0E-9 |
| 2 | g11473.t5 | Pfam | PF00400 | WD domain, G-beta repeat | 45 | 78 | 7.4E-4 |
| 4 | g11473.t5 | Pfam | PF00400 | WD domain, G-beta repeat | 84 | 118 | 4.4E-5 |
| 3 | g11473.t5 | Pfam | PF00400 | WD domain, G-beta repeat | 122 | 158 | 1.8E-6 |
| 1 | g11473.t5 | Pfam | PF00400 | WD domain, G-beta repeat | 173 | 207 | 0.021 |
| 21 | g11473.t5 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 22 | 36 | - |
| 19 | g11473.t5 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 105 | 119 | - |
| 18 | g11473.t5 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 145 | 159 | - |
| 20 | g11473.t5 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 194 | 208 | - |
| 23 | g11473.t5 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 5 | 216 | 42.079 |
| 26 | g11473.t5 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 5 | 44 | 10.241 |
| 25 | g11473.t5 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 48 | 87 | 13.148 |
| 27 | g11473.t5 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 88 | 127 | 13.717 |
| 28 | g11473.t5 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 128 | 159 | 13.115 |
| 24 | g11473.t5 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 177 | 207 | 10.174 |
| 15 | g11473.t5 | SMART | SM00320 | WD40_4 | 2 | 35 | 0.041 |
| 13 | g11473.t5 | SMART | SM00320 | WD40_4 | 41 | 78 | 3.4E-6 |
| 14 | g11473.t5 | SMART | SM00320 | WD40_4 | 81 | 118 | 3.0E-6 |
| 16 | g11473.t5 | SMART | SM00320 | WD40_4 | 121 | 158 | 1.1E-6 |
| 17 | g11473.t5 | SMART | SM00320 | WD40_4 | 170 | 207 | 7.0E-5 |
| 10 | g11473.t5 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 3 | 213 | 1.07E-55 |
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 |
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.
