RetrogeneDB ID: retro_rnor_436

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:58535187..58535686(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: 1110038F14Rik
• Ensembl ID: ENSRNOG00000034107
• Aliases: None
• Description: RIKEN cDNA 1110038F14 gene [Source:MGI Symbol;Acc:MGI:2152337]

Sequence

>retro_rnor_436
AGAACATGTCCCGTAGGGAACACAGTATCGATGAGGCAAAAGAAGAAGAAAACCCCGAACAGGGTCTCTGGGGCAAATGG
AAATGAAAAGCCCTCTGAGAAACCTACCCCCAGATGAAGCTCCCCCTGGTGCTGAGGCCCAGGCTGGGCAGCTGGCTCCG
GAGTTGGCCTAGTGTGTGGAACAGCTGGAGCTGGCCCTCAGGACGCAGAGACCCACCCCAAAGCACAAAGAGCAGACTGT
TGGGCCAATCCGAACGTTGCGCAGTGAAAAAGGCCCCTTGCCCGGGAAGAGAAAGCTGATGCGCTCCTTGTTTGGGGACT
ACAGGGCTCAGATGGATGCAGAGCGGCGGAGGCTACGGGCTCTAAAGGCTGCTACCCATTGGGCCCAGGTGGGTGAGGCC
GCCAGAAAGAAGAGTGGAAGTGTCTGCAGGTCTGGACCTGCAGGAAGAGGTGGAACCACGCCTGTCTTGACCAACTAAGA
GTTTCGGTTCAATTTCTTT

Alignment

ORF - retro_rnor_436 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.7 %
• Parental protein coverage: 76.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RTHPVGNTVSMKQKKKKTPNRVSGTNGKEKPSENPTP-DEAPPSAEAQAEQLARELAWCVEQLELGLRTQ
          RT.PVGNTVSM.QKKKKTPNRVSG.NG.EKPSE.PTP.DEAPP.AEAQA.QLA.ELA.CVEQLEL.LRTQ
Retrocopy RTCPVGNTVSMRQKKKKTPNRVSGANGNEKPSEKPTP>DEAPPGAEAQAGQLAPELA*CVEQLELALRTQ

Parental  RPTPKQKEQAVGAIRTLRSEKTPLPRKRQLMRSLFGDYRAQMDAEWREALRALKAATRSAQVQLVGEAAR
          RPTPK.KEQ.VG.IRTLRSEK.PLP.KR.LMRSLFGDYRAQMDAE.R..LRALKAAT..AQV...GEAAR
Retrocopy RPTPKHKEQTVGPIRTLRSEKGPLPGKRKLMRSLFGDYRAQMDAE-RRRLRALKAATHWAQV---GEAAR

Parental  KKSGRVCRPRPAGRAGTMSDLTNEEFRFNFF
          KKSG.VCR..PAGR.GT...LTN.EFRFNFF
Retrocopy KKSGSVCRSGPAGRGGTTPVLTN*EFRFNFF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	3.95 RPM
SRP017611_kidney	0.00 RPM	5.44 RPM
SRP017611_liver	0.00 RPM	2.89 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_436 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_436 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_436 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000015805	3 retrocopies	retro_dnov_1578, retro_dnov_406, retro_dnov_521,
Macaca mulatta	ENSMMUG00000016084	1 retrocopy	retro_mmul_1436,
Monodelphis domestica	ENSMODG00000028791	2 retrocopies	retro_mdom_1056, retro_mdom_388,
Mustela putorius furo	ENSMPUG00000005972	1 retrocopy	retro_mputfur_1096,
Rattus norvegicus	ENSRNOG00000034107	1 retrocopy	retro_rnor_436 ,