General information for g7848.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Pre-mRNA-processing-splicing factor 8.
Parent gene
- The parent gene g7848 is located on chr_2: 26404153..26404494 (- 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 | g7848 | g7848.t1 | isoform | g7848.t1 | 26404153 | 26404494 |
| chr_2 | g7848 | g7848.t1 | exon | g7848.t1.exon1 | 26404153 | 26404494 |
| chr_2 | g7848 | g7848.t1 | cds | g7848.t1.CDS1 | 26404153 | 26404494 |
| chr_2 | g7848 | g7848.t1 | TSS | g7848.t1 | NA | NA |
| chr_2 | g7848 | g7848.t1 | TTS | g7848.t1 | NA | NA |
Sequences
>g7848.t1 Gene=g7848 Length=342
ATGGTTCTATTTAACTTGTACGACGACTGGTTGAAAACAATTCTCTTCATTACTGCATTT
TCTCGTCTTATTCTTATTCTTCGTGCTCTTCATGTTAATACGGAGAGAACAAAAGTTATT
TTGAAACCAGATAAGACTACAATCACTGAAGCTCATCATATTTGGCCAACATTGAGTGAT
GAAGGATGGATTAAGGTTGAGGTACAATTGAAAGACTTAATTTTGGCTGATTATGGCAAG
AAGAATAATGTAAATGTAGCCATCATAACACAATCAGAAATTCGTGATATTATTTTGGGT
ATGGAATTTCAGCACTTCGGCACAGCGTCAACAAATTGCTGA
>g7848.t1 Gene=g7848 Length=113
MVLFNLYDDWLKTILFITAFSRLILILRALHVNTERTKVILKPDKTTITEAHHIWPTLSD
EGWIKVEVQLKDLILADYGKKNNVNVAIITQSEIRDIILGMEFQHFGTASTNC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g7848.t1 | Gene3D | G3DSA:1.20.80.40 | - | 9 | 106 | 1.8E-46 |
| 2 | g7848.t1 | PANTHER | PTHR11140:SF0 | PRE-MRNA-PROCESSING-SPLICING FACTOR 8 | 1 | 104 | 6.1E-49 |
| 3 | g7848.t1 | PANTHER | PTHR11140 | PRE-MRNA SPLICING FACTOR PRP8 | 1 | 104 | 6.1E-49 |
| 1 | g7848.t1 | Pfam | PF12134 | PRP8 domain IV core | 1 | 76 | 3.3E-32 |
| 8 | g7848.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 11 | - |
| 9 | g7848.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 30 | - |
| 7 | g7848.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 31 | 113 | - |
| 5 | g7848.t1 | SUPERFAMILY | SSF53098 | Ribonuclease H-like | 1 | 102 | 4.93E-41 |
| 4 | g7848.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 10 | 32 | - |
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:0005681 | spliceosomal complex | CC |
| GO:0000398 | mRNA splicing, via spliceosome | BP |
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