RetrogeneDB ID: retro_rnor_1066

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:80463803..80464165(-)
• Located in intron of: ENSRNOG00000007643

Retrocopy information

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

Parental gene information

• Parental gene symbol: 1810009A15Rik
• Ensembl ID: ENSRNOG00000019701
• Aliases: LOC690349, RGD1304652
• Description: RIKEN cDNA 1810009A15 gene [Source:MGI Symbol;Acc:MGI:1913526]

Sequence

>retro_rnor_1066
ATGGGACCTCCAGGAAGAAAGAAAATCAGTCATCCCCAGACGGAGCTGAAGAAGAACTTGATTAAGCGCGGGGTCCTAAG
CAGGGATCCAGAAGGAAGCGCCAGGTGGTCAGGGCTGTGACACAGAAGGGCTGACTCCGAGGCACCACCTCAAGAAGCAA
CGTCCAGTGCACGTACCAACATCACTCTATCTGAGGAGCCGCGCAGAAAATTCCTGCAGCAGATCCGACTTGCCCAGAAA
GAAAAAGCAGCCATGAAGTGGAAGCCCTCTCCAAGTCAACCAGGACTAGTCAGCCACGGGCCAAAAAACAAGAGAAAATA
AAAGCTCCCCAGGACGTAGCTATGGAAGGTCTGGGAGACAGG

Alignment

ORF - retro_rnor_1066 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.72 %
• Parental protein coverage: 99.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAPPGGK-INRPRTELKKKLFKRRRVLSRD-RRRKRLVVGAVID-EGLTTKHHLKKR-ASSARANITLSG
          M.PPG.K.I..P.TELKK.L.KR..VLSRD..RRKR.VV.AV...EGLT..HHLKK...SSAR.NITLS.
Retrocopy MGPPGRKKISHPQTELKKNLIKRG-VLSRD<SRRKRQVVRAVTQ<EGLTPRHHLKKQ<TSSARTNITLSE

Parental  KKRRKLLQQIRLAQKEKAAM-EVEVLSTSTGTSQPKPKRQKKTQAPQDVDMEDLEDK
          ..RRK.LQQIRLAQKEKAAM.EVE.LS.ST.TSQP..K.Q.K..APQDV.ME.L.D.
Retrocopy EPRRKFLQQIRLAQKEKAAM<EVEALSKSTRTSQPRAKKQEKIKAPQDVAMEGLGDR

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	5.25 RPM
SRP017611_kidney	0.00 RPM	10.26 RPM
SRP017611_liver	0.00 RPM	6.32 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1066 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1066 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1066 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_759

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006512	1 retrocopy	retro_amel_1386,
Bos taurus	ENSBTAG00000010465	2 retrocopies	retro_btau_1195, retro_btau_1799,
Canis familiaris	ENSCAFG00000015719	2 retrocopies	retro_cfam_1104, retro_cfam_757,
Felis catus	ENSFCAG00000025454	2 retrocopies	retro_fcat_1722, retro_fcat_773,
Macaca mulatta	ENSMMUG00000013949	4 retrocopies	retro_mmul_1186, retro_mmul_1541, retro_mmul_1785, retro_mmul_1981,
Mus musculus	ENSMUSG00000071653	2 retrocopies	retro_mmus_1809, retro_mmus_759,
Otolemur garnettii	ENSOGAG00000033103	1 retrocopy	retro_ogar_811,
Rattus norvegicus	ENSRNOG00000019701	4 retrocopies	retro_rnor_1066 , retro_rnor_1955, retro_rnor_851, retro_rnor_883,
Sus scrofa	ENSSSCG00000023323	2 retrocopies	retro_sscr_1162, retro_sscr_1163,