RetrogeneDB ID: retro_rnor_2515

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:27096546..27096885(-)
• Located in intron of: ENSRNOG00000009088

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nsmce4a
• Ensembl ID: ENSRNOG00000020452
• Aliases: Nsmce4a, RGD1309025
• Description: non-structural maintenance of chromosomes element 4 homolog A [Source:RefSeq peptide;Acc:NP_001099771]

Sequence

>retro_rnor_2515
ATGCACCCAGACCTCCTGGAGCTGGCGGTGGACCGAGAGAAGTGCCGCAGCATCCGCAGGCAGTACCGGCAGCTCATCTA
CACCGTGCAGCAGAACCGCGAGGACATCGTGAACACGGCCAGCGACTCGCTGACGGAGGCCCTGGAGGAAGCCAATGTGC
TGTTTGACGGGGTGAGCCGAACCAGAGAGGCAGCCCTCGACGCCCAGTTTCTGGTTTTGGCTTCTGATCTGGGTAAAGAA
AAAGCAAAGCAGCTAAACTCGGATATGAGCTTTTTTAATCACGTGGCCTTCTGTGAGTTGCTGTTGGTGTTTGTGGGCCT
CAACTGGATGGAGGAGGAG

Alignment

ORF - retro_rnor_2515 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.72 %
• Parental protein coverage: 52.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDPACLEAEYDQGLCRQIRHQYRALINSVQQNREDILN-AGDKLTEVLEEANTLFNEVSRAREAVLDAQF
          M.P..LE...D...CR.IR.QYR.LI..VQQNREDI.N.A.D.LTE.LEEAN.LF..VSR.REA.LDAQF
Retrocopy MHPDLLELAVDREKCRSIRRQYRQLIYTVQQNREDIVNTASDSLTEALEEANVLFDGVSRTREAALDAQF

Parental  LVLASDLGKEKAKQLRSDLSSFDMLRYVETLLTHMGVNPLEAE
          LVLASDLGKEKAKQL.SD.S.F......E.LL...G.N..E.E
Retrocopy LVLASDLGKEKAKQLNSDMSFFNHVAFCELLLVFVGLNWMEEE

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	9.99 RPM
SRP017611_kidney	0.00 RPM	23.17 RPM
SRP017611_liver	0.20 RPM	5.51 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2515 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2515 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2515 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010897	1 retrocopy	retro_amel_419,
Bos taurus	ENSBTAG00000019166	1 retrocopy	retro_btau_1387,
Canis familiaris	ENSCAFG00000012419	2 retrocopies	retro_cfam_1427, retro_cfam_379,
Choloepus hoffmanni	ENSCHOG00000003695	1 retrocopy	retro_chof_577,
Dipodomys ordii	ENSDORG00000003880	1 retrocopy	retro_dord_677,
Equus caballus	ENSECAG00000016651	2 retrocopies	retro_ecab_109, retro_ecab_465,
Erinaceus europaeus	ENSEEUG00000014906	1 retrocopy	retro_eeur_124,
Felis catus	ENSFCAG00000003647	1 retrocopy	retro_fcat_994,
Homo sapiens	ENSG00000107672	1 retrocopy	retro_hsap_43,
Loxodonta africana	ENSLAFG00000004214	1 retrocopy	retro_lafr_1051,
Macaca mulatta	ENSMMUG00000012044	1 retrocopy	retro_mmul_716,
Mustela putorius furo	ENSMPUG00000002960	1 retrocopy	retro_mputfur_396,
Nomascus leucogenys	ENSNLEG00000016919	1 retrocopy	retro_nleu_2073,
Otolemur garnettii	ENSOGAG00000010026	1 retrocopy	retro_ogar_280,
Pongo abelii	ENSPPYG00000002712	1 retrocopy	retro_pabe_878,
Pteropus vampyrus	ENSPVAG00000017186	2 retrocopies	retro_pvam_1163, retro_pvam_795,
Rattus norvegicus	ENSRNOG00000020452	1 retrocopy	retro_rnor_2515 ,
Ictidomys tridecemlineatus	ENSSTOG00000011112	1 retrocopy	retro_itri_36,
Vicugna pacos	ENSVPAG00000006534	1 retrocopy	retro_vpac_260,