General information for g8769.t121
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Pre-mRNA-processing factor 17.
Parent gene
- The parent gene g8769 is located on chr_2: 33054625..33056469 (+ 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 | g8769 | g8769.t121 | isoform | g8769.t121 | 33054100 | 33054625 |
| chr_2 | g8769 | g8769.t121 | exon | g8769.t121.exon1 | 33054100 | 33054625 |
| chr_2 | g8769 | g8769.t121 | cds | g8769.t121.CDS1 | 33054209 | 33054625 |
| chr_2 | g8769 | g8769.t121 | TTS | g8769.t121 | 33054692 | 33054692 |
| chr_2 | g8769 | g8769.t121 | TSS | g8769.t121 | NA | NA |
Sequences
>g8769.t121 Gene=g8769 Length=526
ACGAAGTGGAGAAATTGTTCAAGAATATGATAGACATTTAGGAGCAGTTAATACAATTAC
ATTTGTTGACGATAACCGAAGATTTGTGACAACATCTGATGACAAAAGCATGAGAGTTTG
GGAGTGGGACATTCCTGTCGATATGAAATATATAGCGGATCCATCAATGCACAGTATGCC
TTCAGTAACACTTTCGCCAAATGGAAAATGGCTAGCATGTCAAAGTTTGGACAATAAGAT
TGTAATATTTTCTGCAATGAATCGTTTTAAAATGAATAGAAAGAAAACATTTGAAGGACA
TATGGTTTCTGGATATGCTTGCGGTCTCGATTTCTCGCCAGATATGTCATATCTTGTATC
AGGTGATGGTGATGGAAAATGTTATATATGGGATTGGAAAACAACAAAATTATATAAAAA
ATGGCAAGCACATGATGGTGTCTGTATTAGTACTATATGGAATCCTCACGAATCAAGCAA
AGTGTTTACTGCTGGTTGGGATGGTTTAATAAAACTATGGGACTAA
>g8769.t121 Gene=g8769 Length=138
MRVWEWDIPVDMKYIADPSMHSMPSVTLSPNGKWLACQSLDNKIVIFSAMNRFKMNRKKT
FEGHMVSGYACGLDFSPDMSYLVSGDGDGKCYIWDWKTTKLYKKWQAHDGVCISTIWNPH
ESSKVFTAGWDGLIKLWD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g8769.t121 | Gene3D | G3DSA:2.130.10.10 | - | 1 | 138 | 0.0000000 |
| 3 | g8769.t121 | PANTHER | PTHR43979 | PRE-MRNA-PROCESSING FACTOR 17 | 1 | 138 | 0.0000000 |
| 2 | g8769.t121 | Pfam | PF00400 | WD domain, G-beta repeat | 58 | 95 | 0.0000009 |
| 1 | g8769.t121 | Pfam | PF00400 | WD domain, G-beta repeat | 104 | 138 | 0.0085000 |
| 9 | g8769.t121 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 1 | 138 | 18.0880000 |
| 10 | g8769.t121 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 73 | 104 | 9.9400000 |
| 11 | g8769.t121 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 105 | 138 | 10.6420000 |
| 7 | g8769.t121 | SMART | SM00320 | WD40_4 | 11 | 48 | 14.0000000 |
| 5 | g8769.t121 | SMART | SM00320 | WD40_4 | 54 | 95 | 0.0000096 |
| 6 | g8769.t121 | SMART | SM00320 | WD40_4 | 98 | 138 | 0.0000220 |
| 4 | g8769.t121 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 18 | 138 | 0.0000000 |
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 |
| GO:0000398 | mRNA splicing, via spliceosome | BP |
| GO:0071013 | catalytic step 2 spliceosome | CC |
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.
