RetrogeneDB ID: retro_ocun_123

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 20:21656518..21657400(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023557
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000021090
• Aliases: None
• Description: None

Sequence

>retro_ocun_123
CTCACAGGAGTTACTCTGTACAGACATCTTAAAAACCACCTTCTAACTGAAGAACAGTTGCGTGAAAATAACTACCCTCG
GCCCAACCCTGACAAACCTGGATGCAGTCTTTTAAATCCATGCAGGACAAAAACTTCTGCAAATGATGCTTCTAAGAAGA
TCTGTTGTCGATGTGGCAAAATATATGACGTGACTCCCTCAGGCAAACACAGTAGGGTAGAAGAATGTTACTACCACTTC
GGCCAAGTACGAAGTCATAAAGTCCTTGATGGCTTAGAATCTCGATACAGCTGTTGTGGAGGAGTGCTTGGATCCCGTGG
GTGTCAGGAGTCCAAGCTTCATGTTCATGACCAAAAAGAAAACCTAGAGGGTTTTGTGAAGACTTTGGTCAAAATCCCAC
CTGCTGATGGTAACTATGGCGTGTTTGCAGTAAATTGTCAGATGTGCTATACGGTCAAAGGCTTGGAACTTACTCGAGTG
ACAGTGGTTGACTCCAGCTTCCAGATGGTCTGTGATACATTTGTGAAACCTGATAAAGAAATCATTGACTATAACACTAG
TTTTTCTGGTGTGGTAGAAGATGACTTGAAGAACATTAGAACCTCCAACCGTGACATGCAAGCCATCCTGCTGAACTTGT
TTAGTGCGGATACCATACTAATTGGACATAGCTTTGAACAATGTCTGTACGCTCTTAAGCTAATTCACACTTGCGTTGTG
GACACAACAGTTATGTTCCCTCATCGGCTAGGTCTGCCTCACAAAAGATCCCTTGGGAGTCCAGTGGCTGACTACCTGCG
GAGAATCATTCAGGATGATGGTCACAAGACTAGTGAAAAAGCAAAAGCTTGCATGGAGTTGGTCCTTTGGAAAGTAAAAA
AA

Alignment

ORF - retro_ocun_123 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.94 %
• Parental protein coverage: 70.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTGVTLYRHLRNHLLTEEQLRENNYPRPNPDKPGCVLLNPCMTKTSVNDASKKICCRCGKIYDVTPSGKH
          LTGVTLYRHL.NHLLTEEQLRENNYPRPNPDKPGC.LLNPC.TKTS.NDASKKICCRCGKIYDVTPSGKH
Retrocopy LTGVTLYRHLKNHLLTEEQLRENNYPRPNPDKPGCSLLNPCRTKTSANDASKKICCRCGKIYDVTPSGKH

Parental  SRVEECYYHFGQVRSHKVLDGLESRYSCCGGVLGSPGCQESKLHVHDQKENLEGFVKTSVKIPPADGNYG
          SRVEECYYHFGQVRSHKVLDGLESRYSCCGGVLGS.GCQESKLHVHDQKENLEGFVKT.VKIPPADGNYG
Retrocopy SRVEECYYHFGQVRSHKVLDGLESRYSCCGGVLGSRGCQESKLHVHDQKENLEGFVKTLVKIPPADGNYG

Parental  VFAVNCEMCYTVKGLELTRVTVVDSSFQMVCDTFVKPDEEIIDYNTRFSGVVEDDLKNIRTSIRDVQAIL
          VFAVNC.MCYTVKGLELTRVTVVDSSFQMVCDTFVKPD.EIIDYNT.FSGVVEDDLKNIRTS.RD.QAIL
Retrocopy VFAVNCQMCYTVKGLELTRVTVVDSSFQMVCDTFVKPDKEIIDYNTSFSGVVEDDLKNIRTSNRDMQAIL

Parental  LNLFSADTILIGHSFEQCLYALKLIHTCVVDTTVMFPHRLGLPHKRSLGSLVADYLQRIIQDDVFEGHNT
          LNLFSADTILIGHSFEQCLYALKLIHTCVVDTTVMFPHRLGLPHKRSLGS.VADYL.RIIQDD...GH.T
Retrocopy LNLFSADTILIGHSFEQCLYALKLIHTCVVDTTVMFPHRLGLPHKRSLGSPVADYLRRIIQDD---GHKT

Parental  SEKAKACMELVLWKVKE
          SEKAKACMELVLWKVK.
Retrocopy SEKAKACMELVLWKVKK

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	0.50 RPM
SRP017611_kidney	0.10 RPM	0.51 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_123 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_123 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_123 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000021090	3 retrocopies	retro_ocun_123 , retro_ocun_1327, retro_ocun_201,