Gene loci information

Transcript annotation

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

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_2 g4867 g4867.t4 TTS g4867.t4 5569745 5569745
chr_2 g4867 g4867.t4 isoform g4867.t4 5570035 5571017
chr_2 g4867 g4867.t4 exon g4867.t4.exon1 5570035 5570535
chr_2 g4867 g4867.t4 cds g4867.t4.CDS1 5570035 5570472
chr_2 g4867 g4867.t4 exon g4867.t4.exon2 5570596 5570940
chr_2 g4867 g4867.t4 exon g4867.t4.exon3 5571005 5571017
chr_2 g4867 g4867.t4 TSS g4867.t4 5572019 5572019

Sequences

>g4867.t4 Gene=g4867 Length=859
TCTCGATTGGAATTGTGATGGAACATTCTTAGCAACAGGCTCATATGATGGTTATGCACG
TATTTGGACAACAGAAGGACGATTAGCAAATACGCTGGGACAACATAAAGGTCCGATATT
TGCTTTAAAATGGAACAAGAAAGGCAACTACATTCTCTCAGCTGGTGTCGATAAGACAAC
AATCATTTGGAATGCAGTAACAGGAGAATCGCATCAACAATTTTCATTTCATAATGCGCC
CGCTCTTGATGTTGATTGGCAAACTAACACATCTTTTGCCAGTTGCAGTACAGATCAACA
AATTCACGTTTGTAAATTAGGAGCTGACAAACCAATCAAAACATTTATTGGACACTTGAA
TGAAGTAAATGCAATTAAATGGGATCCACAAGGTCAATTGCTCGCTTCCTGTTCTGATGA
TATGACACTCAAAATTTGGTCAATGAATTTCGATACATATGTGCATGATCTACAAGCGCA
CTCAAAAGAAATATATACAATCAAATGGTCACCAACAGGTCCGGGCACCGCTAATCCAAA
TATGAATTTAATACTTGCAAGTGCAAGTTTCGATTCAACAGTTCGTCTATGGGACGTTGA
ACGTGGAACATCGATTCATACACTCACAAAACATACAGAACCAGTCTATTCGGTTGCATT
TAGTCCTGATGGTAAATTTTTAGCATCGGGAAGTTTCGATAAATGTGTTCACATTTGGAG
TACACAAACAGGACAATTGGTTCATAGCTATAGAGGAACTGGTGGTATTTTTGAAGTATG
TTGGAATTCAAAGGGATGCAAAGTTGGTGCAAGTGCTTCTGATGGTTCAGTTTTTGTTCT
TGACTTGAGAAAGCTCTAA

>g4867.t4 Gene=g4867 Length=145
MTLKIWSMNFDTYVHDLQAHSKEIYTIKWSPTGPGTANPNMNLILASASFDSTVRLWDVE
RGTSIHTLTKHTEPVYSVAFSPDGKFLASGSFDKCVHIWSTQTGQLVHSYRGTGGIFEVC
WNSKGCKVGASASDGSVFVLDLRKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g4867.t4 Gene3D G3DSA:2.130.10.10 - 1 144 5.4E-64
4 g4867.t4 PANTHER PTHR22846 WD40 REPEAT PROTEIN 1 140 2.5E-82
5 g4867.t4 PANTHER PTHR22846:SF60 F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1X 1 140 2.5E-82
7 g4867.t4 PRINTS PR00320 G protein beta WD-40 repeat signature 45 59 7.1E-5
8 g4867.t4 PRINTS PR00320 G protein beta WD-40 repeat signature 87 101 7.1E-5
6 g4867.t4 PRINTS PR00320 G protein beta WD-40 repeat signature 128 142 7.1E-5
3 g4867.t4 Pfam PF00400 WD domain, G-beta repeat 14 58 4.1E-5
1 g4867.t4 Pfam PF00400 WD domain, G-beta repeat 63 100 5.4E-10
2 g4867.t4 Pfam PF00400 WD domain, G-beta repeat 104 139 0.097
11 g4867.t4 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 45 59 -
15 g4867.t4 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 1 109 27.79
17 g4867.t4 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 17 67 12.714
16 g4867.t4 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 68 109 16.925
13 g4867.t4 SMART SM00320 WD40_4 10 58 1.6E-7
12 g4867.t4 SMART SM00320 WD40_4 61 100 3.7E-12
14 g4867.t4 SMART SM00320 WD40_4 103 141 0.33
9 g4867.t4 SUPERFAMILY SSF50978 WD40 repeat-like 2 144 1.05E-36

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.

Raw TPM values