General information for g4867.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative F-box-like/WD repeat-containing protein ebi.
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.t6 | isoform | g4867.t6 | 5570933 | 5571848 |
| chr_2 | g4867 | g4867.t6 | exon | g4867.t6.exon1 | 5570933 | 5570940 |
| chr_2 | g4867 | g4867.t6 | cds | g4867.t6.CDS1 | 5570935 | 5570940 |
| chr_2 | g4867 | g4867.t6 | exon | g4867.t6.exon2 | 5571005 | 5571447 |
| chr_2 | g4867 | g4867.t6 | cds | g4867.t6.CDS2 | 5571005 | 5571400 |
| chr_2 | g4867 | g4867.t6 | exon | g4867.t6.exon3 | 5571595 | 5571721 |
| chr_2 | g4867 | g4867.t6 | exon | g4867.t6.exon4 | 5571791 | 5571848 |
| chr_2 | g4867 | g4867.t6 | TSS | g4867.t6 | 5572019 | 5572019 |
| chr_2 | g4867 | g4867.t6 | TTS | g4867.t6 | NA | NA |
Sequences
>g4867.t6 Gene=g4867 Length=636
ATGTCATTTTCATCAGACGAAGTGAACTTTCTTGTTTATAGATATCTTCAGGAATCGGGA
TTCTTGCATTCGGCGTATATGTTTGGTATTGAATCACACATTTCGCAGAGTAACATCAAT
GGAGCACTTGTTCCACCCGCAGCATTATTATCAATAATACAAAAAGGTATGCTGATATTA
TAAATGCACAGAAACAAAGATAGTGGAAAAATTAAGCCTAATCGATGCAGTGATGCCAGA
AGTTGTTGCAAATCGTCAAAATCAATTGAATAAATCAAAAGCGAATATGTCAGAACCAGC
AGAAACAAATGGAGAGCAAACTGCAGAATCAACAAATGCAACAGAAAAAACAGAGGGTGC
AATTAAAGATGATCCAGATTCAGATAATTTCATTGAAATCTCACAAAATAAAGCGACAAT
TTTGCGAGGACATGAAAGTGAAGTATTTATTTGTGCTTGGAATCCAATGCGTGATTTGCT
AGCGAGTGGATCTGGCGATTCGACTGCACGTATTTGGGATATGTCAGATAATGTTGCAAC
CAGTAATCAACTTGTTTTGAGGCATTGTATCAAACAAGGAGGAGCTGAAGTACCATCGAA
TAAAGATGTCACATCTCTCGATTGGAATTGTGATGG
>g4867.t6 Gene=g4867 Length=134
MPEVVANRQNQLNKSKANMSEPAETNGEQTAESTNATEKTEGAIKDDPDSDNFIEISQNK
ATILRGHESEVFICAWNPMRDLLASGSGDSTARIWDMSDNVATSNQLVLRHCIKQGGAEV
PSNKDVTSLDWNCD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g4867.t6 | Gene3D | G3DSA:2.130.10.10 | - | 51 | 134 | 6.7E-25 |
| 8 | g4867.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 50 | - |
| 9 | g4867.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 38 | - |
| 2 | g4867.t6 | PANTHER | PTHR22846 | WD40 REPEAT PROTEIN | 17 | 133 | 1.6E-38 |
| 3 | g4867.t6 | PANTHER | PTHR22846:SF40 | F-BOX-LIKE/WD REPEAT-CONTAINING PROTEIN TBL1XR1 | 17 | 133 | 1.6E-38 |
| 1 | g4867.t6 | Pfam | PF00400 | WD domain, G-beta repeat | 62 | 96 | 4.0E-6 |
| 6 | g4867.t6 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 83 | 97 | - |
| 10 | g4867.t6 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 64 | 105 | 13.659 |
| 11 | g4867.t6 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 64 | 105 | 14.953 |
| 7 | g4867.t6 | SMART | SM00320 | WD40_4 | 57 | 96 | 2.6E-8 |
| 4 | g4867.t6 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 62 | 101 | 3.14E-10 |
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. There were no conditions that were differentially expressed