RetrogeneDB ID: retro_rnor_1707

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:262033905..262034628(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Metap2
• Ensembl ID: ENSRNOG00000021881
• Aliases: Metap2, Amp2, Mnpep, p67
• Description: methionine aminopeptidase 2 [Source:RefSeq peptide;Acc:NP_071984]

Sequence

>retro_rnor_1707
GGACCAAGAGTTCAAACAGACCCTCCCTCAGTTCCAATATGTGACCTGTATCCTAATGGTGTATTTCCCAAAGGACAAGA
GTGTGAATACCCACCCACCCAAGATGGGCGGACAGCTGCTTGGAGAACCACAAGTGAAGAGAAAAAGGCGGTAGACCAGG
CTAGTGAGGAGATTTGGAACGACTTCCGAGAAGCTGCCGAAGCACACTGGCAAGTTAGGAAATACGTCATGAGCTGGATC
AAGCCTGGGATGACAATGCTAGAAATATGTGAGAAGTTGGAAGACTGTTCCCGAAAGCTCATAAAGGAGAATGCAGGCCT
GGCCTTTCCCACTGGGTGTTCTCTCAACAACTGTGCTGCACATTACACTCCCAATGCTGGTGACACGACAGTCTTCCAGT
ACGACGACATCTGTAAGATCGACTTTGGAACGCATATAAGTGGTAGAATAATTGATTGTGCTTTTACTGTTACTTTTAAT
TCCAAATATGACATATTATTACAAGCTGTAAAAGATGCCACCAATACTGGAATGAAGTGTACTGGGATTGATGTCCGTCT
CTGTGATGTTGGTGAGGCCATTCAAGAAGTTATGGAGTCCTATGAAGTAGAAATAGATGGGAAGACCTATCAAGTGAAAC
CCATACGGAACTTAAATGGACATTCAATTGGGCCATATAGAATTCACACTGGAAAAACAGTGCCCATTGTGAAAGGAGGG
GAG

Alignment

ORF - retro_rnor_1707 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.08 %
• Parental protein coverage: 56.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPRVQTDPPSVPICDLYPNGVFPKGQECEYPPTQDGRTAAWRTTSEEKKALDQASEEIWNDFREAAEAHR
          GPRVQTDPPSVPICDLYPNGVFPKGQECEYPPTQDGRTAAWRTTSEEKKA.DQASEEIWNDFREAAEAH.
Retrocopy GPRVQTDPPSVPICDLYPNGVFPKGQECEYPPTQDGRTAAWRTTSEEKKAVDQASEEIWNDFREAAEAHW

Parental  QVRKYVMSWIKPGMTMIEICEKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDI
          QVRKYVMSWIKPGMTM.EICEKLEDCSRKLIKE...NAGLAFPTGCSLNNCAAHYTPNAGDTTV.QYDDI
Retrocopy QVRKYVMSWIKPGMTMLEICEKLEDCSRKLIKE---NAGLAFPTGCSLNNCAAHYTPNAGDTTVFQYDDI

Parental  CKIDFGTHISGRIIDCAFTVTFNPKYDILLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEIDG
          CKIDFGTHISGRIIDCAFTVTFN.KYDILL.AVKDATNTG.KC.GIDVRLCDVGEAIQEVMESYEVEIDG
Retrocopy CKIDFGTHISGRIIDCAFTVTFNSKYDILLQAVKDATNTGMKCTGIDVRLCDVGEAIQEVMESYEVEIDG

Parental  KTYQVKPIRNLNGHSIGPYRIHAGKTVPIVKGGE
          KTYQVKPIRNLNGHSIGPYRIH.GKTVPIVKGGE
Retrocopy KTYQVKPIRNLNGHSIGPYRIHTGKTVPIVKGGE

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	0.14 RPM	25.31 RPM
SRP017611_kidney	0.00 RPM	36.98 RPM
SRP017611_liver	0.00 RPM	15.94 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1707 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1707 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1707 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006353	1 retrocopy	retro_cfam_1330,
Monodelphis domestica	ENSMODG00000008173	1 retrocopy	retro_mdom_297,
Mus musculus	ENSMUSG00000036112	2 retrocopies	retro_mmus_3689, retro_mmus_770,
Otolemur garnettii	ENSOGAG00000008469	1 retrocopy	retro_ogar_2163,
Rattus norvegicus	ENSRNOG00000021881	2 retrocopies	retro_rnor_1707 , retro_rnor_547,