General information for g4867.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as F-box-like/WD repeat-containing protein TBL1XR1-B.
Parent gene
- The parent gene g4867 is located on chr_2: 5571017..5571848 (- 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_2 | g4867 | g4867.t1 | TTS | g4867.t1 | 5569745 | 5569745 |
| chr_2 | g4867 | g4867.t1 | isoform | g4867.t1 | 5570035 | 5571848 |
| chr_2 | g4867 | g4867.t1 | exon | g4867.t1.exon1 | 5570035 | 5570535 |
| chr_2 | g4867 | g4867.t1 | cds | g4867.t1.CDS1 | 5570035 | 5570535 |
| chr_2 | g4867 | g4867.t1 | exon | g4867.t1.exon2 | 5570596 | 5570940 |
| chr_2 | g4867 | g4867.t1 | cds | g4867.t1.CDS2 | 5570596 | 5570940 |
| chr_2 | g4867 | g4867.t1 | exon | g4867.t1.exon3 | 5571005 | 5571447 |
| chr_2 | g4867 | g4867.t1 | cds | g4867.t1.CDS3 | 5571005 | 5571447 |
| chr_2 | g4867 | g4867.t1 | exon | g4867.t1.exon4 | 5571506 | 5571547 |
| chr_2 | g4867 | g4867.t1 | cds | g4867.t1.CDS4 | 5571506 | 5571547 |
| chr_2 | g4867 | g4867.t1 | exon | g4867.t1.exon5 | 5571614 | 5571721 |
| chr_2 | g4867 | g4867.t1 | cds | g4867.t1.CDS5 | 5571614 | 5571721 |
| chr_2 | g4867 | g4867.t1 | exon | g4867.t1.exon6 | 5571791 | 5571848 |
| chr_2 | g4867 | g4867.t1 | cds | g4867.t1.CDS6 | 5571791 | 5571848 |
| chr_2 | g4867 | g4867.t1 | TSS | g4867.t1 | 5572019 | 5572019 |
Sequences
>g4867.t1 Gene=g4867 Length=1497
ATGTCATTTTCATCAGACGAAGTGAACTTTCTTGTTTATAGATATCTTCAGGAATCGGGA
TTCTTGCATTCGGCGTATATGTTTGGTATTGAATCACACATTTCGCAGAGTAACATCAAT
GGAGCACTTGTTCCACCCGCAGCATTATTATCAATAATACAAAAAGGCTTGCAGTATACT
GAAGCAGAAATAAGTGTGGGAGAAGATGGCACAGAAACAAAGATAGTGGAAAAATTAAGC
CTAATCGATGCAGTGATGCCAGAAGTTGTTGCAAATCGTCAAAATCAATTGAATAAATCA
AAAGCGAATATGTCAGAACCAGCAGAAACAAATGGAGAGCAAACTGCAGAATCAACAAAT
GCAACAGAAAAAACAGAGGGTGCAATTAAAGATGATCCAGATTCAGATAATTTCATTGAA
ATCTCACAAAATAAAGCGACAATTTTGCGAGGACATGAAAGTGAAGTATTTATTTGTGCT
TGGAATCCAATGCGTGATTTGCTAGCGAGTGGATCTGGCGATTCGACTGCACGTATTTGG
GATATGTCAGATAATGTTGCAACCAGTAATCAACTTGTTTTGAGGCATTGTATCAAACAA
GGAGGAGCTGAAGTACCATCGAATAAAGATGTCACATCTCTCGATTGGAATTGTGATGGA
ACATTCTTAGCAACAGGCTCATATGATGGTTATGCACGTATTTGGACAACAGAAGGACGA
TTAGCAAATACGCTGGGACAACATAAAGGTCCGATATTTGCTTTAAAATGGAACAAGAAA
GGCAACTACATTCTCTCAGCTGGTGTCGATAAGACAACAATCATTTGGAATGCAGTAACA
GGAGAATCGCATCAACAATTTTCATTTCATAATGCGCCCGCTCTTGATGTTGATTGGCAA
ACTAACACATCTTTTGCCAGTTGCAGTACAGATCAACAAATTCACGTTTGTAAATTAGGA
GCTGACAAACCAATCAAAACATTTATTGGACACTTGAATGAAGTAAATGCAATTAAATGG
GATCCACAAGGTCAATTGCTCGCTTCCTGTTCTGATGATATGACACTCAAAATTTGGTCA
ATGAATTTCGATACATATGTGCATGATCTACAAGCGCACTCAAAAGAAATATATACAATC
AAATGGTCACCAACAGGTCCGGGCACCGCTAATCCAAATATGAATTTAATACTTGCAAGT
GCAAGTTTCGATTCAACAGTTCGTCTATGGGACGTTGAACGTGGAACATCGATTCATACA
CTCACAAAACATACAGAACCAGTCTATTCGGTTGCATTTAGTCCTGATGGTAAATTTTTA
GCATCGGGAAGTTTCGATAAATGTGTTCACATTTGGAGTACACAAACAGGACAATTGGTT
CATAGCTATAGAGGAACTGGTGGTATTTTTGAAGTATGTTGGAATTCAAAGGGATGCAAA
GTTGGTGCAAGTGCTTCTGATGGTTCAGTTTTTGTTCTTGACTTGAGAAAGCTCTAA
>g4867.t1 Gene=g4867 Length=498
MSFSSDEVNFLVYRYLQESGFLHSAYMFGIESHISQSNINGALVPPAALLSIIQKGLQYT
EAEISVGEDGTETKIVEKLSLIDAVMPEVVANRQNQLNKSKANMSEPAETNGEQTAESTN
ATEKTEGAIKDDPDSDNFIEISQNKATILRGHESEVFICAWNPMRDLLASGSGDSTARIW
DMSDNVATSNQLVLRHCIKQGGAEVPSNKDVTSLDWNCDGTFLATGSYDGYARIWTTEGR
LANTLGQHKGPIFALKWNKKGNYILSAGVDKTTIIWNAVTGESHQQFSFHNAPALDVDWQ
TNTSFASCSTDQQIHVCKLGADKPIKTFIGHLNEVNAIKWDPQGQLLASCSDDMTLKIWS
MNFDTYVHDLQAHSKEIYTIKWSPTGPGTANPNMNLILASASFDSTVRLWDVERGTSIHT
LTKHTEPVYSVAFSPDGKFLASGSFDKCVHIWSTQTGQLVHSYRGTGGIFEVCWNSKGCK
VGASASDGSVFVLDLRKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g4867.t1 | CDD | cd00200 | WD40 | 149 | 453 | 4.15277E-83 |
| 15 | g4867.t1 | Gene3D | G3DSA:1.20.960.30 | - | 1 | 88 | 1.5E-35 |
| 14 | g4867.t1 | Gene3D | G3DSA:2.130.10.10 | - | 137 | 497 | 1.6E-159 |
| 29 | g4867.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 98 | 123 | - |
| 30 | g4867.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 98 | 136 | - |
| 8 | g4867.t1 | PANTHER | PTHR22846 | WD40 REPEAT PROTEIN | 1 | 493 | 3.3E-263 |
| 9 | g4867.t1 | PANTHER | PTHR22846:SF40 | F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1XR1 | 1 | 493 | 3.3E-263 |
| 11 | g4867.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 168 | 182 | 1.2E-7 |
| 12 | g4867.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 347 | 361 | 1.2E-7 |
| 10 | g4867.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 398 | 412 | 1.2E-7 |
| 1 | g4867.t1 | Pfam | PF08513 | LisH | 6 | 32 | 5.2E-7 |
| 6 | g4867.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 147 | 181 | 3.0E-5 |
| 3 | g4867.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 209 | 235 | 1.5E-5 |
| 2 | g4867.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 243 | 277 | 0.0014 |
| 5 | g4867.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 323 | 360 | 1.1E-9 |
| 4 | g4867.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 367 | 411 | 3.3E-4 |
| 7 | g4867.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 416 | 453 | 3.5E-9 |
| 28 | g4867.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 168 | 182 | - |
| 26 | g4867.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 264 | 278 | - |
| 27 | g4867.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 398 | 412 | - |
| 38 | g4867.t1 | ProSiteProfiles | PS50896 | LIS1 homology (LisH) motif profile. | 4 | 36 | 10.199 |
| 31 | g4867.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 149 | 462 | 55.472 |
| 33 | g4867.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 149 | 190 | 14.953 |
| 35 | g4867.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 211 | 235 | 10.174 |
| 36 | g4867.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 245 | 286 | 12.313 |
| 34 | g4867.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 328 | 369 | 14.352 |
| 37 | g4867.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 370 | 420 | 12.714 |
| 32 | g4867.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 421 | 462 | 16.925 |
| 17 | g4867.t1 | SMART | SM00667 | Lish | 4 | 36 | 3.2E-5 |
| 21 | g4867.t1 | SMART | SM00320 | WD40_4 | 142 | 181 | 2.6E-8 |
| 22 | g4867.t1 | SMART | SM00320 | WD40_4 | 191 | 236 | 4.2E-4 |
| 20 | g4867.t1 | SMART | SM00320 | WD40_4 | 238 | 277 | 1.4E-6 |
| 18 | g4867.t1 | SMART | SM00320 | WD40_4 | 280 | 318 | 0.093 |
| 24 | g4867.t1 | SMART | SM00320 | WD40_4 | 321 | 360 | 1.9E-10 |
| 19 | g4867.t1 | SMART | SM00320 | WD40_4 | 363 | 411 | 1.6E-7 |
| 25 | g4867.t1 | SMART | SM00320 | WD40_4 | 414 | 453 | 3.7E-12 |
| 23 | g4867.t1 | SMART | SM00320 | WD40_4 | 456 | 494 | 0.33 |
| 13 | g4867.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 144 | 492 | 2.11E-73 |
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 transcript has been annotated with K04508 (transducin (beta)-like 1)
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.
