RetrogeneDB ID: retro_rnor_2778

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:22986483..22987130(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dnaja2
• Ensembl ID: ENSRNOG00000016251
• Aliases: Dnaja2, Cpr3, Dj3, DjA2, Dnj3, Hirip4, Rdj2
• Description: dnaJ homolog subfamily A member 2 [Source:RefSeq peptide;Acc:NP_114468]

Sequence

>retro_rnor_2778
ATGGCTATCTTGCCCTACATGAAGTTTTAAAACATCTTGGCCATCCTTCCTGGCAGCGCCAGGAAGAATGACCTGAAGAA
AGCATACAAAAAGTTAGCCAAATAATACTATCCTAATAAGAATCTCAATGTTGAAGATAAATTTAAAGAAACAAGTTTTG
CATATGAAGTATTGTCAAATCCAGAGTACCAGGAGCTATATGACAGATATGGAGAACAATGTCTACATGAATGCAGCGGC
AGAGGTGATAGCATGGATGATATTTTATTACATATTTTTGGTGGAGGATTGTTTAGCTTCATGGATAATTAGAGTAGGAG
TTGAAATGTCAAAAGACAAAAGGACATGATGCATCCACTGAAAGTATTTTTAGAAGACCTGTATTATGGCAAGACAACCA
AACTACTACTAAGCAAGAATGTGCTCTGTACTGCATGCATTGACCATGGTAGAAATTATGGATCTTTTCAGAAATATACT
GCTTGTCAGGGTCGTAGTGTGCGCACCTTGATCAAGTAGTTGAAAACAGGAATGGTGTGGCAGATGCAGTTTTTATGCTC
TGATTGCAATGGAGAAGGGGAGGTCATCAATGAAACGGACTTATGTGAAAATGTGAAGGAAAGAAGTTGATTAGAGAACT
CAAGATT

Alignment

ORF - retro_rnor_2778 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.06 %
• Parental protein coverage: 52.43 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MANVADTKLYDILGVPPG-ASENELKKAYRKLAKEYHPDKNPNAGDKFKEISFAYEVLSNPEKRELYDRY
          MA.....K...IL...PG.A..N.LKKAY.KLAK.Y.P.KN.N..DKFKE.SFAYEVLSNPE..ELYDRY
Retrocopy MAILPYMKF*NILAILPGSARKNDLKKAYKKLAK*YYPNKNLNVEDKFKETSFAYEVLSNPEYQELYDRY

Parental  GEQGLREGSGGGGGMDDIFSHIFGGGLFGFMGNQSRSRNGRRRGEDMMHPLKVSLEDLYNGKTTKLQLSK
          GEQ.L.E.SG.G..MDDI..HIFGGGLF.FM.N.SRS.N..R...DMMHPLKV.LEDLY.GKTTKL.LSK
Retrocopy GEQCLHECSGRGDSMDDILLHIFGGGLFSFMDN*SRS*NVKRQ-KDMMHPLKVFLEDLYYGKTTKLLLSK

Parental  NVLCSACSGQGGKSGAVQKCSACRGRGVRIMIRQLAPGMVQQMQSVCSDCNGEGEVINEKDRCK-KCEGK
          NVLC.AC...G...G..QK..AC.GR.VR..I..L..GMV.QMQ..CSDCNGEGEVINE.D.C..KCEGK
Retrocopy NVLCTACIDHGRNYGSFQKYTACQGRSVRTLIK*LKTGMVWQMQFLCSDCNGEGEVINETDLCE<KCEGK

Parental  KVIKEVKI
          K.I.E.KI
Retrocopy KLIRELKI

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	122.01 RPM
SRP017611_kidney	0.00 RPM	100.07 RPM
SRP017611_liver	0.00 RPM	44.31 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2778 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2778 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2778 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003757	3 retrocopies	retro_btau_1215, retro_btau_1625, retro_btau_798,
Cavia porcellus	ENSCPOG00000006955	1 retrocopy	retro_cpor_1466,
Dasypus novemcinctus	ENSDNOG00000013794	1 retrocopy	retro_dnov_40,
Macaca mulatta	ENSMMUG00000002247	1 retrocopy	retro_mmul_36,
Oryctolagus cuniculus	ENSOCUG00000004839	1 retrocopy	retro_ocun_1126,
Rattus norvegicus	ENSRNOG00000007029	2 retrocopies	retro_rnor_2208, retro_rnor_608,
Rattus norvegicus	ENSRNOG00000016251	1 retrocopy	retro_rnor_2778 ,