Gene loci information

Transcript annotation

  • This transcript has been annotated as F-box-like/WD repeat-containing protein TBL1XR1-B.

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.t5 TTS g4867.t5 5569745 5569745
chr_2 g4867 g4867.t5 isoform g4867.t5 5570600 5571848
chr_2 g4867 g4867.t5 exon g4867.t5.exon1 5570600 5570940
chr_2 g4867 g4867.t5 cds g4867.t5.CDS1 5570602 5570940
chr_2 g4867 g4867.t5 exon g4867.t5.exon2 5571005 5571447
chr_2 g4867 g4867.t5 cds g4867.t5.CDS2 5571005 5571447
chr_2 g4867 g4867.t5 exon g4867.t5.exon3 5571506 5571547
chr_2 g4867 g4867.t5 cds g4867.t5.CDS3 5571506 5571547
chr_2 g4867 g4867.t5 exon g4867.t5.exon4 5571614 5571721
chr_2 g4867 g4867.t5 cds g4867.t5.CDS4 5571614 5571721
chr_2 g4867 g4867.t5 exon g4867.t5.exon5 5571791 5571848
chr_2 g4867 g4867.t5 cds g4867.t5.CDS5 5571791 5571848
chr_2 g4867 g4867.t5 TSS g4867.t5 5572019 5572019

Sequences

>g4867.t5 Gene=g4867 Length=992
ATGTCATTTTCATCAGACGAAGTGAACTTTCTTGTTTATAGATATCTTCAGGAATCGGGA
TTCTTGCATTCGGCGTATATGTTTGGTATTGAATCACACATTTCGCAGAGTAACATCAAT
GGAGCACTTGTTCCACCCGCAGCATTATTATCAATAATACAAAAAGGCTTGCAGTATACT
GAAGCAGAAATAAGTGTGGGAGAAGATGGCACAGAAACAAAGATAGTGGAAAAATTAAGC
CTAATCGATGCAGTGATGCCAGAAGTTGTTGCAAATCGTCAAAATCAATTGAATAAATCA
AAAGCGAATATGTCAGAACCAGCAGAAACAAATGGAGAGCAAACTGCAGAATCAACAAAT
GCAACAGAAAAAACAGAGGGTGCAATTAAAGATGATCCAGATTCAGATAATTTCATTGAA
ATCTCACAAAATAAAGCGACAATTTTGCGAGGACATGAAAGTGAAGTATTTATTTGTGCT
TGGAATCCAATGCGTGATTTGCTAGCGAGTGGATCTGGCGATTCGACTGCACGTATTTGG
GATATGTCAGATAATGTTGCAACCAGTAATCAACTTGTTTTGAGGCATTGTATCAAACAA
GGAGGAGCTGAAGTACCATCGAATAAAGATGTCACATCTCTCGATTGGAATTGTGATGGA
ACATTCTTAGCAACAGGCTCATATGATGGTTATGCACGTATTTGGACAACAGAAGGACGA
TTAGCAAATACGCTGGGACAACATAAAGGTCCGATATTTGCTTTAAAATGGAACAAGAAA
GGCAACTACATTCTCTCAGCTGGTGTCGATAAGACAACAATCATTTGGAATGCAGTAACA
GGAGAATCGCATCAACAATTTTCATTTCATAATGCGCCCGCTCTTGATGTTGATTGGCAA
ACTAACACATCTTTTGCCAGTTGCAGTACAGATCAACAAATTCACGTTTGTAAATTAGGA
GCTGACAAACCAATCAAAACATTTATTGGACA

>g4867.t5 Gene=g4867 Length=330
MSFSSDEVNFLVYRYLQESGFLHSAYMFGIESHISQSNINGALVPPAALLSIIQKGLQYT
EAEISVGEDGTETKIVEKLSLIDAVMPEVVANRQNQLNKSKANMSEPAETNGEQTAESTN
ATEKTEGAIKDDPDSDNFIEISQNKATILRGHESEVFICAWNPMRDLLASGSGDSTARIW
DMSDNVATSNQLVLRHCIKQGGAEVPSNKDVTSLDWNCDGTFLATGSYDGYARIWTTEGR
LANTLGQHKGPIFALKWNKKGNYILSAGVDKTTIIWNAVTGESHQQFSFHNAPALDVDWQ
TNTSFASCSTDQQIHVCKLGADKPIKTFIG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g4867.t5 Gene3D G3DSA:1.20.960.30 - 1 88 7.4E-36
11 g4867.t5 Gene3D G3DSA:2.130.10.10 - 136 330 3.8E-76
20 g4867.t5 MobiDBLite mobidb-lite consensus disorder prediction 98 123 -
21 g4867.t5 MobiDBLite mobidb-lite consensus disorder prediction 98 136 -
5 g4867.t5 PANTHER PTHR22846 WD40 REPEAT PROTEIN 1 330 1.6E-155
6 g4867.t5 PANTHER PTHR22846:SF40 F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1XR1 1 330 1.6E-155
9 g4867.t5 PRINTS PR00320 G protein beta WD-40 repeat signature 168 182 1.8E-5
8 g4867.t5 PRINTS PR00320 G protein beta WD-40 repeat signature 223 237 1.8E-5
7 g4867.t5 PRINTS PR00320 G protein beta WD-40 repeat signature 264 278 1.8E-5
1 g4867.t5 Pfam PF08513 LisH 6 32 3.1E-7
4 g4867.t5 Pfam PF00400 WD domain, G-beta repeat 147 181 1.7E-5
3 g4867.t5 Pfam PF00400 WD domain, G-beta repeat 209 235 8.9E-6
2 g4867.t5 Pfam PF00400 WD domain, G-beta repeat 243 277 8.0E-4
14 g4867.t5 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 168 182 -
13 g4867.t5 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 264 278 -
26 g4867.t5 ProSiteProfiles PS50896 LIS1 homology (LisH) motif profile. 4 36 10.199
22 g4867.t5 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 149 330 23.466
23 g4867.t5 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 149 190 14.953
24 g4867.t5 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 211 235 10.174
25 g4867.t5 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 245 286 12.313
15 g4867.t5 SMART SM00667 Lish 4 36 3.2E-5
18 g4867.t5 SMART SM00320 WD40_4 142 181 2.6E-8
17 g4867.t5 SMART SM00320 WD40_4 191 236 4.2E-4
19 g4867.t5 SMART SM00320 WD40_4 238 277 1.4E-6
16 g4867.t5 SMART SM00320 WD40_4 280 318 0.093
10 g4867.t5 SUPERFAMILY SSF50978 WD40 repeat-like 143 328 1.55E-38

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