RetrogeneDB ID: retro_ocun_94

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:43180044..43181133(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000000070
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000005034
• Aliases: None
• Description: None

Sequence

>retro_ocun_94
GACCTGAAGAACCAGCACCTGGCCAAGAAGTCGGAAGTGAATGACAAAAATCACAAGATGGAGGAGATTCGTAAGAAACT
TGGGGGCGCCAACAAGGAAATGACCCATTTACAAAAGGAGGTGACAGCCATCGAGACCAAGCTGGAACAGAAGCGCAGCG
ACCGCCACAACTTGCTCCAGGCCTGCAAGATGCAGGATATCAAGCTGCCGCTGTCGAAGGGCACCATGGATGATATTAGT
CAGGAAGAGGGTAGCTCCCAGGGGGAGGATTCAGTGAGTGCTTCACAAAGAACGTCCAGCATCTACGCACGAGAGGCCCT
CATTGAGATCGACTACGGTGACCTGTGTGAGGATTTGAAGGATGCCCAGGCTGAGGAGGACATCAAACAGGAGATGAGCA
CACTGCAGCAGAAGCTGAATGAGCAGCAGAGTGTGCTTCAGCGTATTGCTGCCCCCAACATGAAAGCCATGGAAAAGCTG
GAGAGTGTCCGTGACAAGTTCCAGGAGACCTCTGATGAGTTTGAGGCAGTCCGAAAGCGAGCAAAGAAGGCCAAGCAGGC
ATTCGAACAGATCAAGAAGGAGCGCTTTGACCGCTTCAATGCTTGTTTTGAATCTGTGGCTACCAACATTGATGAGATCT
ATAAGGCTCTGTCCCACAACAGCAGTGCCCAGGCATTCCTGGGTCCTGAGAACCCAGAGGAGCCCTACTTGGATGGCATC
AACTATAACTGCGTGGCTCCTGGCAAACGCTTCCGGCCTATGGACAACTTGTCAGGAGGGGAGAAGACAGTGGCAGCTTT
GGCCCTGCTTTTTGCCATCCACAGCTACAAGCCAGCCCCCTTCTTCATCCTGGATGAGATCGATGCTGCCTTGGATAACA
CCAACATTGGCAAGGTAGCAAATTACATCAAGGAGCAGTCGACTTGGAACTTCCAGGCCATCGTCATCTCTCTCAAGGAA
GAGTTCTACACCAAGGCTGAGAGCCTCATTGGAGTCTATCCCGAGCAAGGGGACTGTGTGATCAGCAAAGTCCTGACCTT
CGACCTCACCAAGTACCCAGATGCCAACCCCAACCCCAATGAGCAGTAA

Alignment

ORF - retro_ocun_94 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.79 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DLKNQHLAKKSEVNDKNHEMEEIRKKLGGANKEMTHLQKEVTAIETKLEQKRSDRHNLLQACKMQDIKLP
          DLKNQHLAKKSEVNDKNH.MEEIRKKLGGANKEMTHLQKEVTAIETKLEQKRSDRHNLLQACKMQDIKLP
Retrocopy DLKNQHLAKKSEVNDKNHKMEEIRKKLGGANKEMTHLQKEVTAIETKLEQKRSDRHNLLQACKMQDIKLP

Parental  LSKGTMDDISQEEGSSQGEDSVSGSQRTSSIYAREALIEIDYGDLCEDLKDAQAEEEIKQEMNTLQQKLN
          LSKGTMDDISQEEGSSQGEDSVS.SQRTSSIYAREALIEIDYGDLCEDLKDAQAEE.IKQEM.TLQQKLN
Retrocopy LSKGTMDDISQEEGSSQGEDSVSASQRTSSIYAREALIEIDYGDLCEDLKDAQAEEDIKQEMSTLQQKLN

Parental  EQQSVLQRIAAPNMKAMEKLESVRDKFQETSDEFEAARKRAKKAKQAFEQIKKERFDRFNACFESVATNI
          EQQSVLQRIAAPNMKAMEKLESVRDKFQETSDEFEA.RKRAKKAKQAFEQIKKERFDRFNACFESVATNI
Retrocopy EQQSVLQRIAAPNMKAMEKLESVRDKFQETSDEFEAVRKRAKKAKQAFEQIKKERFDRFNACFESVATNI

Parental  DEIYKALSRNSSAQAFLGPENPEEPYLDGINYNCVAPGKRFRPMDNLSGGEKTVAALALLFAIHSYKPAP
          DEIYKALS.NSSAQAFLGPENPEEPYLDGINYNCVAPGKRFRPMDNLSGGEKTVAALALLFAIHSYKPAP
Retrocopy DEIYKALSHNSSAQAFLGPENPEEPYLDGINYNCVAPGKRFRPMDNLSGGEKTVAALALLFAIHSYKPAP

Parental  FFVLDEIDAALDNTNIGKVANYIKEQSTCNFQAIVISLKEEFYTKAESLIGVYPEQGDCVISKVLTFDLT
          FF.LDEIDAALDNTNIGKVANYIKEQST.NFQAIVISLKEEFYTKAESLIGVYPEQGDCVISKVLTFDLT
Retrocopy FFILDEIDAALDNTNIGKVANYIKEQSTWNFQAIVISLKEEFYTKAESLIGVYPEQGDCVISKVLTFDLT

Parental  KYPDANPNPNEQ
          KYPDANPNPNEQ
Retrocopy KYPDANPNPNEQ

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	1.82 RPM	34.27 RPM
SRP017611_kidney	1.93 RPM	25.24 RPM
SRP017611_liver	1.08 RPM	18.58 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_94 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_94 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_94 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000005034	1 retrocopy	retro_ocun_94 ,