RetrogeneDB ID: retro_ocun_562

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:56392511..56393516(-)
• Located in intron of: ENSOCUG00000016010

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSGEP
• Ensembl ID: ENSOCUG00000005020
• Aliases: None
• Description: O-sialoglycoprotein endopeptidase [Source:HGNC Symbol;Acc:18028]

Sequence

>retro_ocun_562
ATGCCAACGGTGCTGGGGTTTGAAGGCAGCGCCAACAAGATTGGCGTGGGAGTGGTGCGGGATGGCAAGGTGTTGGCCAA
CCCGCGGCGGACCTATGTCAGGCCTCCGGGCACAGGATTCCTTCCAGGTGACACTGCCAGGCACCACTGAGTTGTTATCC
TAGATCTGCTACAGGAGGCGCTGACCAAGGCAGGATTAACCTCCCAGGATATTGAGTGCGTTGCCTACACCAAGGGTCCT
GGCATGGGTGCTCCACTGGTTTCTGTGGCTGTCGTGGCTCGTACTGTGGCCCAGCTGTGGAATAAGCCATTGCTAGGCGT
GAACCACTGTAAAGGCCACATTGAGATGGGCCGTCTCATCACTGGAGCCACCAGCCCAACTGTGCTGTATGTCAGCGGGG
GAAACACACAGGTGATTGCGTACTCAGAACATCTTTACCGCATCTTTGGGGAGACCATCGATATTGCTGTGGGTAACTGT
CTGGATCGTTTTGCCCGAGTGCTCAAGATTTCTAATGACCCAAGTCCTGGCTACAACATTGAACAGATGGCAAAGAGAGG
GAAGAAACTGGTCGAGCTGCCCTACACTGTAAAGGGGATGGATGTCTCATTCTCAGGGATTCTGTCTTTTATTGAGGATG
CAGCTCAGCGGCTGCTGACCACAGGCGAGTGTACTCCTGAGGATCTGTGTTTCTCCTTGCAGGAAACCATGTTTGCAATG
CTGGTAGAGATCACGGAGCGAGCTATGGCGCACTGTGGCTCCCAGGAGGCCATCATTGTGGGAGGTGTGGGGTGTAACAT
GAGGCTACAGGAGATGATGGAGATAATGTGCCAGGAACGCGGAGCTAAGCTTTTTGCCACAGATGAGAGATTCTGCATTG
ATAATGGAGCCATGATAGCCCAGGCCGGCTGGCAGATGTTCCAGGCCGGACACAGAACCCCACTCCGTGATTCTGGGATT
ACACAGAGGTATTGGACAGATGAAGTAGAAGTGACCTGGAGGGAC

Alignment

ORF - retro_ocun_562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPTVLGFEGSANKIGVGVVRDGKVLANPRRTYVTPPGTGFLPGDTARHHRAVILDLLQEALSEAGLTSQD
          MPTVLGFEGSANKIGVGVVRDGKVLANPRRTYV.PPGTGFLPGDTARHH..VILDLLQEAL..AGLTSQD
Retrocopy MPTVLGFEGSANKIGVGVVRDGKVLANPRRTYVRPPGTGFLPGDTARHH*VVILDLLQEALTKAGLTSQD

Parental  IDCIAYTKGPGMGAPLVSVAVVARTVAQLWNKPLLGVNHCIGHIEMGRLITGATSPTVLYVSGGNTQVIA
          I.C.AYTKGPGMGAPLVSVAVVARTVAQLWNKPLLGVNHC.GHIEMGRLITGATSPTVLYVSGGNTQVIA
Retrocopy IECVAYTKGPGMGAPLVSVAVVARTVAQLWNKPLLGVNHCKGHIEMGRLITGATSPTVLYVSGGNTQVIA

Parental  YSERRYRIFGETIDIAVGNCLDRFARVLKISNDPSPGYNIEQMAKRGKKLVELPYTVKGMDVSFSGILSF
          YSE..YRIFGETIDIAVGNCLDRFARVLKISNDPSPGYNIEQMAKRGKKLVELPYTVKGMDVSFSGILSF
Retrocopy YSEHLYRIFGETIDIAVGNCLDRFARVLKISNDPSPGYNIEQMAKRGKKLVELPYTVKGMDVSFSGILSF

Parental  IEDAAQRMLATGECTPEDLCFSLQETVFAMLVEITERAMAHCGSQEALIVGGVGCNVRLQEMMEIMCQER
          IEDAAQR.L.TGECTPEDLCFSLQET.FAMLVEITERAMAHCGSQEA.IVGGVGCN.RLQEMMEIMCQER
Retrocopy IEDAAQRLLTTGECTPEDLCFSLQETMFAMLVEITERAMAHCGSQEAIIVGGVGCNMRLQEMMEIMCQER

Parental  GAKLFATDERFCIDNGAMIAQAGWEMFQAGHRTPLRDSGITQRYRTDEVEVTWRD
          GAKLFATDERFCIDNGAMIAQAGW.MFQAGHRTPLRDSGITQRY.TDEVEVTWRD
Retrocopy GAKLFATDERFCIDNGAMIAQAGWQMFQAGHRTPLRDSGITQRYWTDEVEVTWRD

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	15.23 RPM
SRP017611_kidney	0.00 RPM	18.45 RPM
SRP017611_liver	0.00 RPM	9.33 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_562 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_562 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_562 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014460	1 retrocopy	retro_cpor_734,
Mus musculus	ENSMUSG00000006289	1 retrocopy	retro_mmus_1765,
Oryctolagus cuniculus	ENSOCUG00000005020	1 retrocopy	retro_ocun_562 ,