Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative RNA exonuclease 5.

Parent gene

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_4 g16316 g16316.t1 TTS g16316.t1 9064470 9064470
chr_4 g16316 g16316.t1 isoform g16316.t1 9064529 9066437
chr_4 g16316 g16316.t1 exon g16316.t1.exon1 9064529 9066277
chr_4 g16316 g16316.t1 cds g16316.t1.CDS1 9064529 9066277
chr_4 g16316 g16316.t1 exon g16316.t1.exon2 9066333 9066437
chr_4 g16316 g16316.t1 cds g16316.t1.CDS2 9066333 9066437
chr_4 g16316 g16316.t1 TSS g16316.t1 9066534 9066534

Sequences

>g16316.t1 Gene=g16316 Length=1854
ATGAGAAAGCAAGAAAGATTAGAAAAGAAGAAACGAAAAACTGCAGCCTTAGTAAACATG
ATAAAAATTAACGAAATCGACAAAATTCATGAAAAAAATTCTGAAGAACCAGAAGCAAAA
AAATCAAAATTAAATCTCGATATTCAAATCTCAGATGATCAATACAAACTACTCAAAAAA
GAACTTGCAGAACGTCGCAATGCACTTCAAAATGCTCCGAAATTTCGTCTAAAATTCTTT
GGTGAAAAAGCAACTTTGTTGACAAATCCAACTAAAAGACAACCTTTGATGTTTGAAGAT
ATTCAATATTTGTTAATGACATCACTTCTTGGCAGCAGTTCACCATTTAAACCAGATCGT
TGGTGTGTTCTTGAGAAAGCAAATCGAATAACTCACACTGTTGTGTTGGTCATTGAAGGA
TTAACAAGTTACAATTTTACAGCAAATGAAAGTCAATTTATACGCACAAAAGGAATTTTT
GAACATCAACTTGAACTTGTGCTGCCGAAATATAAGAAAAATCGTTTAGTTGAGGAAATT
TCAAATGTTCCATTGACTCAATCACATAAGGAAAGTTTAATCAAGCAATATGGAAGTCTT
GAAGCTGCATTAAAGCTCAACAAAGATCCAAATACGATGTTTTCAAAAAGTTTATTTCCA
ATTGATATTGACACTGATTCAGAAGAGCAAAAAATTGAATTAAATGAAAATGAAACTTTT
CCTAGAACTCGCTTGCTGTTGTCACCATTACAAATGATGATTGAAGGCTATCCAATACCA
ATTAAAGGTGAATATGAAGAACGTTATCGTGGATATCGCTCAACAAAATCAATTTACAAA
CCAGTCACATCAAAATCACCAATGTTTGGTTTAGATTGTGAAATGTGTCGTACAATTAAA
TCAGAAAATGAACTTGCAAGAGTTTCAATTGTTGATGAAAATTTTAAAAGTATTTATGAA
ACTTTAGTGAGACCAGAAAATAAAATTGTCAATTATTTAACACCATGGTCAGGAATAACA
AAAGAAATGATGGAAAATGTCACAAAAACATTAAAAGAAGTTCAAGAGGAAGTTTCAAAT
TTATTACCAGCTGATGCAATTCTTGTTGGACAATCATTAAATTGTGATTTAAATGCAATG
AAATTGATGCATCCTTATGTCATTGATACAAGTGTAATTTATAATTTGAGTGGTGATAGA
AACAGAAAATCAAAGCTACAACATTTGACAAAACATTTTTTAAACGAAGAAATTCAAATT
GATAAACTTGGACATTCAAGTATTGAAGATTCAATTGCATGTCTTAAATTAACAAAATTG
AAACTTTCAAAAGACATTTATTTTGGTGATGTCGCTTTAGAAGCTAAAAAAAGCATCTTA
AAGAATGAAGAAGGTAAAATTGGAATTGTTAAAGACATTGAAAGTTCATCAAATGTAAAA
ACTCCAATTTTTAGTCATGCATTAAAGAGACAAAAGAAATCTGTAATTGTCAGCACTCAT
AATTGTGAAATTAATCTTAAAAAATCAATGTTAATGAGTGAAGGAAGTGAAGATCATGGA
ATTAAACATTTTAAAGAAAATTCAATTAAAAAAGTTGTAAAAAAGACAAAGGAAATTTTA
TTGGATCACGATTTTATTCTTTCACATATAAACATTTTTAATGATTTTGTTGATGAAGAA
AATGAAAAAGTTGATTGCAGCAGTGAAGAAAAAATTGCAGAAATTGTTCCAAAAATTGAC
AAATGGATTGAAAAAGTTTGGTCAAATGTTGCAACTAATGGAATTTTTGTAGTGATTTTT
GGTGGACGTGATTTGAATTCTAATGGAGTTTCAATGGTTCAAATTAAAAGTTAA

>g16316.t1 Gene=g16316 Length=617
MRKQERLEKKKRKTAALVNMIKINEIDKIHEKNSEEPEAKKSKLNLDIQISDDQYKLLKK
ELAERRNALQNAPKFRLKFFGEKATLLTNPTKRQPLMFEDIQYLLMTSLLGSSSPFKPDR
WCVLEKANRITHTVVLVIEGLTSYNFTANESQFIRTKGIFEHQLELVLPKYKKNRLVEEI
SNVPLTQSHKESLIKQYGSLEAALKLNKDPNTMFSKSLFPIDIDTDSEEQKIELNENETF
PRTRLLLSPLQMMIEGYPIPIKGEYEERYRGYRSTKSIYKPVTSKSPMFGLDCEMCRTIK
SENELARVSIVDENFKSIYETLVRPENKIVNYLTPWSGITKEMMENVTKTLKEVQEEVSN
LLPADAILVGQSLNCDLNAMKLMHPYVIDTSVIYNLSGDRNRKSKLQHLTKHFLNEEIQI
DKLGHSSIEDSIACLKLTKLKLSKDIYFGDVALEAKKSILKNEEGKIGIVKDIESSSNVK
TPIFSHALKRQKKSVIVSTHNCEINLKKSMLMSEGSEDHGIKHFKENSIKKVVKKTKEIL
LDHDFILSHINIFNDFVDEENEKVDCSSEEKIAEIVPKIDKWIEKVWSNVATNGIFVVIF
GGRDLNSNGVSMVQIKS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g16316.t1 CDD cd06145 REX1_like 289 434 0e+00
6 g16316.t1 Gene3D G3DSA:3.30.420.10 - 283 455 0e+00
2 g16316.t1 PANTHER PTHR12801:SF115 LD29573P 46 606 0e+00
3 g16316.t1 PANTHER PTHR12801 RNA EXONUCLEASE REXO1 / RECO3 FAMILY MEMBER-RELATED 46 606 0e+00
1 g16316.t1 Pfam PF00929 Exonuclease 291 437 1e-07
5 g16316.t1 SMART SM00479 exoiiiendus 287 447 0e+00
4 g16316.t1 SUPERFAMILY SSF53098 Ribonuclease H-like 289 443 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

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.

Raw TPM values