General information for g4803.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative RNA exonuclease 1.
Parent gene
- The parent gene g4803 is located on chr_2: 5050251..5052117 (- 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 | g4803 | g4803.t2 | isoform | g4803.t2 | 5050251 | 5052117 |
| chr_2 | g4803 | g4803.t2 | exon | g4803.t2.exon1 | 5050251 | 5050927 |
| chr_2 | g4803 | g4803.t2 | cds | g4803.t2.CDS1 | 5050251 | 5050927 |
| chr_2 | g4803 | g4803.t2 | exon | g4803.t2.exon2 | 5050983 | 5052117 |
| chr_2 | g4803 | g4803.t2 | cds | g4803.t2.CDS2 | 5050983 | 5052117 |
| chr_2 | g4803 | g4803.t2 | TSS | g4803.t2 | 5052094 | 5052094 |
| chr_2 | g4803 | g4803.t2 | TTS | g4803.t2 | NA | NA |
Sequences
>g4803.t2 Gene=g4803 Length=1812
ATGAAAATTAACCATGATGAGTTAAGCGAAAAAAAAATTTCAACGAATGAAGATTTAGTA
AGCAATAATTTATTTTTTCATCGTAATTTGAGCATATTTAAATGGATTTTGTATCGTTTT
CAGATAGACGAGCCAATAATAAAGAAAGTTAAGATGGAAGACGAAGAATTGTGCAGTGAA
TTCTTGTCAACTAGTCAATTTAAAATTATTAAGAAAAGTCTTGTTGAGCGACGAAATCAG
TTGCTTTCTACACCGAAATTTCGCTTCTACAACCGTGCTGAATTGGCTCGAATTTCTCAA
GATATATGCACACGCAAACCAATATTCCTAGAAGACATCCAGAATATTCTATTGAGTGCC
GTTCTCAAGAGTAATTTTCTACTAAATCCTCACAAATGGTGCGTTCTTGAAAAAACAAAT
AAAATCACTCAAACAGTGATAATTCTGCTCAATGGACCAACGTCATACAATTTTGTGGCC
AACGAGAGTTTATTCATAAAAACTGGTAAGATATTTGAGCATCAATACGAAGTTACATTA
GCAAACGATATTTTGTTGGAAGAGCTTCTCATCATACCTTGGATTTATTCAAATAAAAAG
AAAGTCGTTCAAAAATATGGAAGTTTAGAAGCAGCTTTCATGTTTCATAAAAATCTCAAT
GCACTTTCCAAATTCTTCTCTATTGAAGATACTTGTATCAATGAAAAGGAAGATCAGAAG
AAGGAAATTGATAATCAAGAAGAGCATGATGCTTTTCCGCGTACCCGTTTATTGCTTTCA
CCGTTACAAATGATAGCAGAAAACTATCCATTACCATTTGAGAATAACGAACTTTATAAG
GATTACCGTTTAACAAAGGACAAATATAAGCCAGTTACTCCTAATAGTCGAATGTTTGGT
CTCGATTGTGAAATGGTTCGCTCAGTTAAAGCATATAATGAACTTGCTCGAGTTTCAATT
GTTGATGAGGATTATAATAGCGTTTATGAAACATTAGTTCGACCAGATTGTAAAATCGTT
AATTATCTCACTCGATGGTCTGGAATAACAAAAGAAATGATGATTGATGCTACAAAGAGT
CTTAAAGAAGTTCAAGATGATGTATGCAACTTACTTCCTGCTGATGCTATCTTAGTTGGA
CAATCATTGAACTGTGATTTGAATGCCATGAAATTGATGCATCCTTATGTGATTGATACA
AGCGTTATTTACAATTTGAGTGGCAACAGAAATGTTAAAACAAAGCTTCAAACTCTTGCT
CGACACTTTTTAGATATAGATATTCAAAATGATGAAATGGGACATTCTAGTGTTGAAGAT
TCAATTACATGTTTGAAATTAGCAAAATTGAAATTATCTAAGGATATTTGTTTTGGTGAT
GCTGTTTTGCAGAAGAAGAGTAAATTCTATACTGCTAAGAAGGAAGAAGAACCAAACGTT
GAAGTTGATGCTAATATTATTAAAACGGTTTTGGTTACATCACAAAACCCCGATCTTAAT
TTCAAAGAGATGTTCAATAAAAACTATGAGCATCATAATGAAACATCGGCAGAGAAAGCA
ATTGAAACTACTTGCAAAGTTGTAAAGAACAATGACTATTGTGTAACATATATTAATGTA
ATGGATGCTTTTCAAGGCAATGATTCTAATAACGATCCTGATGAAAAGATTTCCAAATGT
GTGCTTTCTATTGATAAGTACATAAATGAAGTTTGGGAGAATATGATGAAGAATGGACTT
TTGATTGTGATTTTCGGAGGTCGACAGGAAAGTAATGATAATGCTTTGACTATGATGCAG
ATTAAAAAATGA
>g4803.t2 Gene=g4803 Length=603
MKINHDELSEKKISTNEDLVSNNLFFHRNLSIFKWILYRFQIDEPIIKKVKMEDEELCSE
FLSTSQFKIIKKSLVERRNQLLSTPKFRFYNRAELARISQDICTRKPIFLEDIQNILLSA
VLKSNFLLNPHKWCVLEKTNKITQTVIILLNGPTSYNFVANESLFIKTGKIFEHQYEVTL
ANDILLEELLIIPWIYSNKKKVVQKYGSLEAAFMFHKNLNALSKFFSIEDTCINEKEDQK
KEIDNQEEHDAFPRTRLLLSPLQMIAENYPLPFENNELYKDYRLTKDKYKPVTPNSRMFG
LDCEMVRSVKAYNELARVSIVDEDYNSVYETLVRPDCKIVNYLTRWSGITKEMMIDATKS
LKEVQDDVCNLLPADAILVGQSLNCDLNAMKLMHPYVIDTSVIYNLSGNRNVKTKLQTLA
RHFLDIDIQNDEMGHSSVEDSITCLKLAKLKLSKDICFGDAVLQKKSKFYTAKKEEEPNV
EVDANIIKTVLVTSQNPDLNFKEMFNKNYEHHNETSAEKAIETTCKVVKNNDYCVTYINV
MDAFQGNDSNNDPDEKISKCVLSIDKYINEVWENMMKNGLLIVIFGGRQESNDNALTMMQ
IKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4803.t2 | CDD | cd06145 | REX1_like | 299 | 444 | 0e+00 |
| 6 | g4803.t2 | Gene3D | G3DSA:3.30.420.10 | - | 294 | 468 | 0e+00 |
| 2 | g4803.t2 | PANTHER | PTHR12801:SF115 | LD29573P | 99 | 590 | 0e+00 |
| 3 | g4803.t2 | PANTHER | PTHR12801 | RNA EXONUCLEASE REXO1 / RECO3 FAMILY MEMBER-RELATED | 99 | 590 | 0e+00 |
| 1 | g4803.t2 | Pfam | PF00929 | Exonuclease | 301 | 447 | 1e-07 |
| 5 | g4803.t2 | SMART | SM00479 | exoiiiendus | 297 | 457 | 0e+00 |
| 4 | g4803.t2 | SUPERFAMILY | SSF53098 | Ribonuclease H-like | 299 | 452 | 0e+00 |
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 transcript has been annotated with K14570 (RNA exonuclease [EC:3.1.-.-])
Pathway
- This transcript belongs to the following pathways
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.
