RetrogeneDB ID: retro_rnor_2670

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:26332343..26332638(+)
• Located in intron of: ENSRNOG00000033402

Retrocopy information

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

Parental gene information

• Parental gene symbol: Erh
• Ensembl ID: ENSRNOG00000004883
• Aliases: None
• Description: enhancer of rudimentary homolog [Source:RefSeq peptide;Acc:NP_001102912]

Sequence

>retro_rnor_2670
TTGCTGAAACAGCCTACCAAGATGCCGGATAGCAAGTCTTAGGCTGACTAAGAGTCTGTGAATGGGTTCACAGAAAGTGT
TTGTAAAGTGTATGAAGAATCTCTGAAGGGAATGAATCCCAACTGCCCCTCCACACACAGTATATCAATCAGTTGTTTGA
TTTTATTGACAACCTGGCAGATCTTAGCTGTCTTCTTTACTAAGTTGACATGGAGACATACCAGTCTCATAGCAGAGACC
AGAGCAAAGACAGTATCTATGTGTTCTCCATAGGCAGGCCCAACAGACTGGGAAG

Alignment

ORF - retro_rnor_2670 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.39 %
• Parental protein coverage: 81.15 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLVQPTKRPEGRTYADYESVNECMEGVCKMYEEHLKRMNPNSPSI-TYDISQLFDFIDDLADLSCLVYRA
          LL.QPTK.P.....AD.ESVN...E.VCK.YEE.LK.MNPN.PS..T..I.QLFDFID.LADLSCL.Y..
Retrocopy LLKQPTKMPDSKS*AD*ESVNGFTESVCKVYEESLKGMNPNCPST<TQYINQLFDFIDNLADLSCLLY*V

Parental  DTQTYQPYNKDWIKEKIYV-LLRRQAQQAGK
          D..TYQ....D..K..IYV..L.RQAQQ.GK
Retrocopy DMETYQSHSRDQSKDSIYV<VLHRQAQQTGK

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	0.07 RPM	27.39 RPM
SRP017611_kidney	0.28 RPM	23.17 RPM
SRP017611_liver	0.34 RPM	10.29 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2670 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2670 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2670 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014529	1 retrocopy	retro_amel_1906,
Callithrix jacchus	ENSCJAG00000014940	2 retrocopies	retro_cjac_209, retro_cjac_846,
Dipodomys ordii	ENSDORG00000006912	3 retrocopies	retro_dord_250, retro_dord_406, retro_dord_562,
Equus caballus	ENSECAG00000019178	1 retrocopy	retro_ecab_45,
Macropus eugenii	ENSMEUG00000014602	3 retrocopies	retro_meug_1469, retro_meug_498, retro_meug_64,
Myotis lucifugus	ENSMLUG00000011879	1 retrocopy	retro_mluc_142,
Macaca mulatta	ENSMMUG00000021571	1 retrocopy	retro_mmul_1649,
Oryctolagus cuniculus	ENSOCUG00000004636	1 retrocopy	retro_ocun_42,
Otolemur garnettii	ENSOGAG00000029388	5 retrocopies	retro_ogar_1170, retro_ogar_1537, retro_ogar_2710, retro_ogar_625, retro_ogar_854,
Rattus norvegicus	ENSRNOG00000004883	3 retrocopies	retro_rnor_1721, retro_rnor_2670 , retro_rnor_308,