RetrogeneDB ID: retro_ocun_416

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:192655906..192657290(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000022148
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000011321
• Aliases: None
• Description: None

Sequence

>retro_ocun_416
ATGGCTGCTACTGTGAACTTGGAACTTGACCCTATTTTTTTGAAAGCACTAGGTTTCTTACATTCAAAGAGTAAAGATTC
TGCTGAGAAACTGAAAGCACTACTTGATGAGTCCTTGGCCCGGGGTGTTGATGCGAGTTACCGTCCATCTCAAAAGGATG
TGGAGCCACCCAAAATTTCAAGCACAAAAGCTATTTCTATTAAGCAAGAGCCCAAAACATCATCCATCTTCTTCAGGCAA
TAATAATGGCAAGGTCCTCACAACTGAAAAGGTAAAGAAGGAAGCTGAAAAGAGACCTGCTGATAAAATAAAATCAGATG
TTACTGAAGGAGCTGATATTCCAAAGAAACCTAGACTAGAGAAATCCGAGACGCGGTCCTCTCCCATTACTGTCCAAACC
AGCAAGGATTTAGCTATAGCTGACCTTTCCAGTTTTGAAGAGACCAGTGCTGATGATTTTGCTATGGAGATGGGACTGGT
CTGTGTTGTTTGTAGGCAGATGACAGTAGCATCTGGTAATCAATTAGTCGAATGTCAAGAATGCCATAATCTGTACCACC
AAGACTGCCATAAACCCCAGGTAACAGACAAGGAAGTGAATGACCCTCGCCTGGTGTGGTATTGTGCCCGATGTACCAGA
CAGATGAAAAGAATGGCTCAAAAAACTCAGAAACCACCACAGAAACCAGCTCCTACAGTTGTTTCTGTAGCTCCAGCTGT
CAAAGATCCATTGGTTAAGAAACCAGAAACTAAACTCAAGCAAGAGACAACTTTCCAAGCATTCAAGAGAACAGAAGTCA
AGACATCCACGGTTATTTCAGGACATTCTTCTAGTACCAGTGTTTCCTCTTCGGTAACTAGTGGCCTAACGGGGTGGGCA
GCGTTTGCAGTCAAAACATCTTCTACTGGTCCCTCAACAGCAAAATTGAGTTCTACAACACAAAACAACAGTGGAAAACC
TGCTGCCTCATCAGCCAGCCAGAAGCCTGTGGGTTTGACTGGTCTGGCAACATCTTCCAAAGGTGGAATAGGTTCTAAAA
TAGGTTCCAATAATAGTTCAACACCCACTGTACCACTGAAACCACCTCCACCTCTGACCTTAGGCAAAACTGGCCTTAGT
CGCTCGGTTAGTTGTGATAATGTCAGCAAAGTAGGTCTTCCCAGTCCAAGTAGTTTAGTTCCAGGAAGCAGCAACCAACT
AAGTGGGAATGGAAATAGTGGGACATCAGGCCCTGGTGGAAGTACCACTAGTAAAAGTACTTCAGAATCTAGTAGCTCTT
CCTCAGCATCCCTTAAAGGTCCAACTTCACAAGAATCACAGCTCAATGCTATGAAGAGATTACAGATGGTTAAGAAGAAA
GCCGCCCAAAAGAAACTCAAGAAA

Alignment

ORF - retro_ocun_416 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAATVNLELDPIFLKALGFLHSKSKDSAEKLKALLDESLARGVDASYRPSQKDVEPPKISSTKAISIKQE
          MAATVNLELDPIFLKALGFLHSKSKDSAEKLKALLDESLARGVDASYRPSQKDVEPPKISSTKAISIKQE
Retrocopy MAATVNLELDPIFLKALGFLHSKSKDSAEKLKALLDESLARGVDASYRPSQKDVEPPKISSTKAISIKQE

Parental  PKTSSSL-PSGNNNGKVLTTEKVKKEAEKRPADKIKSDVTEGADIPKKPRLEKSETRSSPITVQTSKDLA
          PKT.SS...SGNNNGKVLTTEKVKKEAEKRPADKIKSDVTEGADIPKKPRLEKSETRSSPITVQTSKDLA
Retrocopy PKT-SSI>SSGNNNGKVLTTEKVKKEAEKRPADKIKSDVTEGADIPKKPRLEKSETRSSPITVQTSKDLA

Parental  IADLSSFEETSADDFAMEMGLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYC
          IADLSSFEETSADDFAMEMGL.CVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYC
Retrocopy IADLSSFEETSADDFAMEMGLVCVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYC

Parental  ARCTRQMKRMAQKTQKPPQKPAPTVVSVAPAVKDPLVKKPETKLKQETTFQAFKRTEVKTSTVISGNSSS
          ARCTRQMKRMAQKTQKPPQKPAPTVVSVAPAVKDPLVKKPETKLKQETTFQAFKRTEVKTSTVISG.SSS
Retrocopy ARCTRQMKRMAQKTQKPPQKPAPTVVSVAPAVKDPLVKKPETKLKQETTFQAFKRTEVKTSTVISGHSSS

Parental  TSVSSSVTSGLTGWAAFAAKTSSTGPSTAKLSSTTQNNSGKPATSSASQKPVGLTGLATSSKGGIGSKIG
          TSVSSSVTSGLTGWAAFA.KTSSTGPSTAKLSSTTQNNSGKPA.SSASQKPVGLTGLATSSKGGIGSKIG
Retrocopy TSVSSSVTSGLTGWAAFAVKTSSTGPSTAKLSSTTQNNSGKPAASSASQKPVGLTGLATSSKGGIGSKIG

Parental  SNNSTTPTVPLKPPPPLTLGKTGLSRSVSCDNVSKVGLPSPSSLVPGSSNQLSGNGNSGTSGPGGSTTSK
          SNNS.TPTVPLKPPPPLTLGKTGLSRSVSCDNVSKVGLPSPSSLVPGSSNQLSGNGNSGTSGPGGSTTSK
Retrocopy SNNSSTPTVPLKPPPPLTLGKTGLSRSVSCDNVSKVGLPSPSSLVPGSSNQLSGNGNSGTSGPGGSTTSK

Parental  STSESSSSSSASLKGPTSQESQLNAMKRLQMVKKKAAQKKLKK
          STSESSSSSSASLKGPTSQESQLNAMKRLQMVKKKAAQKKLKK
Retrocopy STSESSSSSSASLKGPTSQESQLNAMKRLQMVKKKAAQKKLKK

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	0.06 RPM	7.12 RPM
SRP017611_kidney	0.10 RPM	9.73 RPM
SRP017611_liver	0.08 RPM	2.70 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_416 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_416 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_416 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011569	1 retrocopy	retro_chof_2623,
Myotis lucifugus	ENSMLUG00000011757	1 retrocopy	retro_mluc_62,
Mustela putorius furo	ENSMPUG00000008999	1 retrocopy	retro_mputfur_1546,
Oryctolagus cuniculus	ENSOCUG00000011321	1 retrocopy	retro_ocun_416 ,