General information for g9579.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative RNA exonuclease 1-like protein.
Parent gene
- The parent gene g9579 is located on chr_1: 4131869..4133101 (+ 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_1 | g9579 | g9579.t1 | TSS | g9579.t1 | 4131313 | 4131313 |
| chr_1 | g9579 | g9579.t1 | isoform | g9579.t1 | 4131869 | 4133101 |
| chr_1 | g9579 | g9579.t1 | exon | g9579.t1.exon1 | 4131869 | 4131962 |
| chr_1 | g9579 | g9579.t1 | cds | g9579.t1.CDS1 | 4131869 | 4131962 |
| chr_1 | g9579 | g9579.t1 | exon | g9579.t1.exon2 | 4132015 | 4132122 |
| chr_1 | g9579 | g9579.t1 | cds | g9579.t1.CDS2 | 4132015 | 4132122 |
| chr_1 | g9579 | g9579.t1 | exon | g9579.t1.exon3 | 4132186 | 4132288 |
| chr_1 | g9579 | g9579.t1 | cds | g9579.t1.CDS3 | 4132186 | 4132288 |
| chr_1 | g9579 | g9579.t1 | exon | g9579.t1.exon4 | 4132383 | 4133034 |
| chr_1 | g9579 | g9579.t1 | cds | g9579.t1.CDS4 | 4132383 | 4133034 |
| chr_1 | g9579 | g9579.t1 | exon | g9579.t1.exon5 | 4133093 | 4133101 |
| chr_1 | g9579 | g9579.t1 | cds | g9579.t1.CDS5 | 4133093 | 4133101 |
| chr_1 | g9579 | g9579.t1 | TTS | g9579.t1 | NA | NA |
Sequences
>g9579.t1 Gene=g9579 Length=966
ATGTCATTTAGCGAGGAATTCTCATTGAAAAATGAAGTTTCTAGTGAAACAATCAAATCT
ATAGCAGAAGAAGATTACAATAAAAAAAATGAAGATGTCTTCGAAGTATATTTGAGCGAA
TATTATGATGAAAAGGATCAGCCATTAGTTCGATCTATTTTAAAAGAAATGGGATATGAA
TTCCTCTGCTTCTTATTTGAAAAGGAAAAGATTGATCTTGAAAATTTTCAAAATCTCAAC
ACAAACTTTATCATGACATTACTGAATCAATATCCCATTGGATTTATAGTAAAGTTTAAC
CAGGCTATCCATTTTTCTTTGTTACTCGCTGGTGCTGCTGGATCAAAAGTTTCTTGGTCA
ATGAATAATAAGCAAAAAGTGGCAAATTCAGACTCTTCATTGTTAACAATTGACAATTGT
TCTAGTTCTCAAGCTTATGATCTCGTTGCTGATTGTCTTCTTACTGAACAACAATTAAGA
GAAAATGGATTTCCACGACAAACTGAAATAAAAGGAAGAGCTCAGTTTTTTACTCCAAAG
AAAGCGAAGCCGCAAAATGGGCGCGATGATGATTATTATTGTGCGCGATGCAATAAGGTC
TTTAACGTTGAAATTTATGATGAAGTTCAGCGAGATTTATGTAATTATCACCCTAAAAGA
TCAGGATATAGACGAGGTCATGCAGATAATTATTATTACTGTTGTCAATCAATAGCCGAA
AGTACAGGATGTTGTTACGCTGACTATCACGTATTTGATTATATCGATTATAATAATCTC
GTTGGATATGTCAAAACAATCGATAAAGATGAAAATTATGTGTGCACAAAAAAAGATATT
TTTGCATTAGATTGTGAAATGTGCTATACAGTATGTGGTTTTGAATTGACACGTTTGACA
ATTGTCGATTATGATGAGAAAGTTGTTTATGATAAATTCGTCCGACCACAAAATCGTATG
CGTTAA
>g9579.t1 Gene=g9579 Length=321
MSFSEEFSLKNEVSSETIKSIAEEDYNKKNEDVFEVYLSEYYDEKDQPLVRSILKEMGYE
FLCFLFEKEKIDLENFQNLNTNFIMTLLNQYPIGFIVKFNQAIHFSLLLAGAAGSKVSWS
MNNKQKVANSDSSLLTIDNCSSSQAYDLVADCLLTEQQLRENGFPRQTEIKGRAQFFTPK
KAKPQNGRDDDYYCARCNKVFNVEIYDEVQRDLCNYHPKRSGYRRGHADNYYYCCQSIAE
STGCCYADYHVFDYIDYNNLVGYVKTIDKDENYVCTKKDIFALDCEMCYTVCGFELTRLT
IVDYDEKVVYDKFVRPQNRMR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g9579.t1 | Gene3D | G3DSA:3.30.420.10 | - | 274 | 321 | 0 |
| 2 | g9579.t1 | PANTHER | PTHR12801:SF138 | FI18136P1-RELATED | 100 | 319 | 0 |
| 3 | g9579.t1 | PANTHER | PTHR12801 | RNA EXONUCLEASE REXO1 / RECO3 FAMILY MEMBER-RELATED | 100 | 319 | 0 |
| 1 | g9579.t1 | Pfam | PF15870 | ElonginA binding-protein 1 | 102 | 180 | 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:0003676 | nucleic acid 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.
