General information for g3608.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Exosome complex component RRP45.
Parent gene
- The parent gene g3608 is located on chr_3: 26732471..26734057 (+ 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_3 | g3608 | g3608.t4 | isoform | g3608.t4 | 26732471 | 26733730 |
| chr_3 | g3608 | g3608.t4 | exon | g3608.t4.exon1 | 26732471 | 26732621 |
| chr_3 | g3608 | g3608.t4 | cds | g3608.t4.CDS1 | 26732471 | 26732621 |
| chr_3 | g3608 | g3608.t4 | exon | g3608.t4.exon2 | 26732685 | 26732948 |
| chr_3 | g3608 | g3608.t4 | cds | g3608.t4.CDS2 | 26732685 | 26732948 |
| chr_3 | g3608 | g3608.t4 | exon | g3608.t4.exon3 | 26733003 | 26733233 |
| chr_3 | g3608 | g3608.t4 | cds | g3608.t4.CDS3 | 26733003 | 26733233 |
| chr_3 | g3608 | g3608.t4 | exon | g3608.t4.exon4 | 26733292 | 26733730 |
| chr_3 | g3608 | g3608.t4 | cds | g3608.t4.CDS4 | 26733292 | 26733350 |
| chr_3 | g3608 | g3608.t4 | TTS | g3608.t4 | 26733850 | 26733850 |
| chr_3 | g3608 | g3608.t4 | TSS | g3608.t4 | NA | NA |
Sequences
>g3608.t4 Gene=g3608 Length=1085
ATGAAAGAAACAATTTTATCAAATAATGAACGAGTGTTTGTTGAGAAGTCGATTGAAGAA
GTTTTAAGAATTGATAAACGTCAATTGACAGAATTTAGAAATTTAGGAATATTTTTTGGC
AAAAAATATGGAAGCGTGTTAGTTTCATTAGGTGATACACGAGTTTTCGCAAATGTTTCA
TGCGAAGTTAATATACCGAAAACCACTCGTCCAAATGAAGGAACAGTATTTATAAATGTT
GAAATGTCAAATGAAAAAATGAGTGAATCTTGCATTGTTACTACAAGAATTCTTGAAAGA
ACAATTCGTGATTCTAGATGTATTGATCTTGAATCATTATGTATAATTGCAGAAGAAAAA
GTTTGGAATCTAAGAGTTGATGTGTCTATTTTAAATAATGAAGGAAATGTTACAGATTGT
GCGTGTATTGCAGCTGTGAGTGCTTTAGCTCATTTTAAAAGACCCGATTGCACAACTTCA
GGAGATGGTGAATTTATAATTCATAAGTCTTCTGAAAAAGACTTGATTCCTACTGTTTTA
CACCACTATCCGATATGTATGACGTATGCTTTATTTAAAGGAAAAATTCCAATAGCAGAT
CCAACATTATTAGAAGAACGAGTAACAAATGCTGGTCTAACTTTAGTCCATTTCTCATCC
AAAAATGCTCGGAAATGGCTGCTGAACGAGCAAAACATGTTGTAGAATTTATTAAAAGTA
CACTTGAGCAAGATTCTATAGATCGCGAAAAATCTAATGTGAAAGGTTTTAAACAAAGTA
TCATTTTAACAAATGTTACTTCAAATTTTTGCGACGAGCAATCCATTGATAACAATGCAG
AAGAAATTTCAGAAGTCGCAAGTAATCATGATGAAATTATTGTTGTATCACAAGAGCAAA
AGTTCAAGAAAATTGATGAAAACACAATTTCAACAACAAAATGGAAGGACGAAAATGAAG
AAACGAGTAGTAGTGACAGTGAAATCATTACATTATCACAATCAAACCAAGAGAAATCTA
AAGTAGAAAGTATGCAAATCGATTCAAGTGATGATGAAGAGAAAGAAACTATTATATTAA
ATTAA
>g3608.t4 Gene=g3608 Length=234
MKETILSNNERVFVEKSIEEVLRIDKRQLTEFRNLGIFFGKKYGSVLVSLGDTRVFANVS
CEVNIPKTTRPNEGTVFINVEMSNEKMSESCIVTTRILERTIRDSRCIDLESLCIIAEEK
VWNLRVDVSILNNEGNVTDCACIAAVSALAHFKRPDCTTSGDGEFIIHKSSEKDLIPTVL
HHYPICMTYALFKGKIPIADPTLLEERVTNAGLTLVHFSSKNARKWLLNEQNML
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3608.t4 | CDD | cd11368 | RNase_PH_RRP45 | 6 | 216 | 0.0e+00 |
| 6 | g3608.t4 | Gene3D | G3DSA:3.30.230.70 | GHMP Kinase | 1 | 228 | 0.0e+00 |
| 2 | g3608.t4 | PANTHER | PTHR11097:SF14 | EXOSOME COMPLEX COMPONENT RRP45 | 3 | 216 | 0.0e+00 |
| 3 | g3608.t4 | PANTHER | PTHR11097 | EXOSOME COMPLEX EXONUCLEASE RIBOSOMAL RNA PROCESSING PROTEIN | 3 | 216 | 0.0e+00 |
| 1 | g3608.t4 | Pfam | PF01138 | 3’ exoribonuclease family, domain 1 | 31 | 155 | 0.0e+00 |
| 4 | g3608.t4 | SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 1 | 207 | 0.0e+00 |
| 5 | g3608.t4 | SUPERFAMILY | SSF55666 | Ribonuclease PH domain 2-like | 180 | 223 | 7.1e-06 |
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:0006396 | RNA processing | BP |
| GO:0000178 | exosome (RNase complex) | 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.
