General information for g7840.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Pre-mRNA-processing-splicing factor 8.
Parent gene
- The parent gene g7840 is located on chr_2: 26386900..26394988 (+ 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 | g7840 | g7840.t3 | TSS | g7840.t3 | 26386507 | 26386507 |
| chr_2 | g7840 | g7840.t3 | isoform | g7840.t3 | 26386508 | 26389027 |
| chr_2 | g7840 | g7840.t3 | exon | g7840.t3.exon1 | 26386508 | 26386610 |
| chr_2 | g7840 | g7840.t3 | exon | g7840.t3.exon2 | 26386878 | 26388020 |
| chr_2 | g7840 | g7840.t3 | cds | g7840.t3.CDS1 | 26386900 | 26388020 |
| chr_2 | g7840 | g7840.t3 | exon | g7840.t3.exon3 | 26388393 | 26389027 |
| chr_2 | g7840 | g7840.t3 | cds | g7840.t3.CDS2 | 26388393 | 26389026 |
| chr_2 | g7840 | g7840.t3 | TTS | g7840.t3 | 26388995 | 26388995 |
Sequences
>g7840.t3 Gene=g7840 Length=1881
AGAAGAAAAATCAACAAACGCCGAAAAAAGAATTTAGATCTTATTATTTTTACTTTTTAT
CGGATTAATATTACTAATTTCATTACAAAAACTATTGAAAAGTAAGGATCAAAACTAACA
AATAAATGAATCCATATATTTTGCCCGGAATGGGTGGGCCACCTGGTGGGCCTCAAAATC
CTTGGGCAGCACAATTAATGGCTCAACAAGCAATGATGGCACAACAAATGCATGCTCAAC
AGCTTGCAGCAACACAAATTCAAATACCACCAACAGGAGGAATGGACTGGAACTTTAGTA
ATGCACCTACACCACAAAAACCAGAGACAATCAGTGAAGAAAAACTTCAAGAAAAGTCAT
TGAAATGGCAGCAACTTCAATCGAAAAGATTTGCAGAGAAGAGAAAATTTGGTTTTGTTG
ATGCACAAAAAGCAGATATGCCAGCAGAGCATGTAAGAAAAATTATCAGAGATCATGGTG
ATATGACAAGCAGAAAATATCGTCACGATAAGCGAGTGTATTTGGGCGCATTAAAATATA
TGCCACATGCTGTAATGAAACTACTTGAAAATATGCCTATGCCATGGGAACAAATAAGAG
ATGTTTCAGTTCTCTATCATATTACTGGCGCTATCACATTTGTAAATGAAATTCCTTGGG
TAATTGAGCCAGTTTATATAGCTCAATGGGGAACAATGTGGATTATGATGAGAAGAGAAA
AGAGAGATCGTCGACATTTCAAAAGAATGCGATTCCCGCCATTTGATGATGAAGAACCGC
CATTAGATTATGCTGACAATGTTCTCGATGTTGAACCTTTAGAAGCAATTCAGATTGATT
TGGATCCAGATGAAGATGCAAGTGTATGTGAATGGCTTTATGATCATAAACCTCTTGTTG
GTACACCTTATGTAAATGGATCAACTTTTAGACGATGGAATTTGACATTACCTCAAATGG
CAACATTATATCGTTTAGCCAATCAACTTTTGACTGATTTAGTTGATACAAACTTCTTCT
ATTTGTTTGATCCAAAAAGTTTCTTTACTGCAAAAGCTCTTAATATGGCAATTCCTGGTG
GACCGAAATTTGAACCACTCATTAAAGATCATAATTTGGGTGATGAAGACTGGAATGAAT
TCAATGATATCAATAAAATCATTATTCGTCAACCCATCAGAACTGAATATCGTATTGCTT
TTCCATATCTTTACAATAACATGCCTCTTTTTGTACATCTCTCTTGGTATCACACACCAA
ATGTTGTTTACATCAAAACTGAAGATCCAGATTTGCCTGCATTCTACTTTGATCCATTAA
TTAATCCAATTGCTCATCGACATGGTGTTAAATCATCAGACCCTTTGCCAGAAGATGACG
AAGAATTTTCATTGCCTGATGAAGTTCAACCATTTTTGCAAGATACACCTTTATACACGG
ACAACACAGCAAACGGTATTGCATTATTGTGGGCTCCTAGACCATTCAATATGAGATCAG
GTCGTTGTCGTCGTGCAATTGATGTACCTTTAGTTAAAAGCTGGTACAAAGAACATTGTC
CTCCTGGTAATCCAGTAAAAGTCAGAGTCAGTTATCAAAAATTACTCAAGTATTATGTCT
TGAATGCGCTCAAACATCGACGTCCTAAACCACAAAAGAAGCGCTACTTGTTTAGATCAT
TTAAAGCTACTAAATTCTTCCAAACTACAACATTGGATTGGGTAGAAGCTGGTTTACAAG
TTTGCAGACAAGGATATAATATGCTAAACTTGTTGATTCATCGCAAAAATCTTAATTATC
TTCATCTCGACTATAACTTTAATTTGAAACCAGTTAAGACACTTACAACAAAAGAAAGAA
AGAAATCACGATTCGGAAATG
>g7840.t3 Gene=g7840 Length=585
MNPYILPGMGGPPGGPQNPWAAQLMAQQAMMAQQMHAQQLAATQIQIPPTGGMDWNFSNA
PTPQKPETISEEKLQEKSLKWQQLQSKRFAEKRKFGFVDAQKADMPAEHVRKIIRDHGDM
TSRKYRHDKRVYLGALKYMPHAVMKLLENMPMPWEQIRDVSVLYHITGAITFVNEIPWVI
EPVYIAQWGTMWIMMRREKRDRRHFKRMRFPPFDDEEPPLDYADNVLDVEPLEAIQIDLD
PDEDASVCEWLYDHKPLVGTPYVNGSTFRRWNLTLPQMATLYRLANQLLTDLVDTNFFYL
FDPKSFFTAKALNMAIPGGPKFEPLIKDHNLGDEDWNEFNDINKIIIRQPIRTEYRIAFP
YLYNNMPLFVHLSWYHTPNVVYIKTEDPDLPAFYFDPLINPIAHRHGVKSSDPLPEDDEE
FSLPDEVQPFLQDTPLYTDNTANGIALLWAPRPFNMRSGRCRRAIDVPLVKSWYKEHCPP
GNPVKVRVSYQKLLKYYVLNALKHRRPKPQKKRYLFRSFKATKFFQTTTLDWVEAGLQVC
RQGYNMLNLLIHRKNLNYLHLDYNFNLKPVKTLTTKERKKSRFGN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g7840.t3 | PANTHER | PTHR11140 | PRE-MRNA SPLICING FACTOR PRP8 | 52 | 585 | 0 |
| 4 | g7840.t3 | PANTHER | PTHR11140:SF2 | PRE-MRNA-PROCESSING-SPLICING FACTOR 8A-RELATED | 52 | 585 | 0 |
| 1 | g7840.t3 | Pfam | PF08082 | PRO8NT (NUC069), PrP8 N-terminal domain | 102 | 253 | 0 |
| 2 | g7840.t3 | Pfam | PF08083 | PROCN (NUC071) domain | 439 | 585 | 0 |
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.
