RetrogeneDB ID: retro_ocun_1158

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:16796111..16796760(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000006233
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: APOBEC1
• Ensembl ID: ENSOCUG00000025736
• Aliases: None
• Description: apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 (APOBEC1), mRNA [Source:RefSeq mRNA;Acc:NM_001082341]

Sequence

>retro_ocun_1158
CCCTGGGAATTTGAAGTCTTCTTTGACCCCCAGAACTGCGTAAAGGGGCCTGCCTGCTCCATGAAATAAAGTGGGGGGCA
AGCTCCACGACCTGGCGCAGCTCAGGCAAGAACACCACCAATCACGTGGAAGTCAACTTCATAGAAAAGCGGACTTCAGA
GAGGCGGCTTTGCCCATCCACCTGCTGCTCCCTCCCCTGGCTCTTGCCTTGGAGCCCCTGCTGGGAATGCTCCAGGGAGA
TCAGAGAATTTTTGAGCCAACACCCGGATGTGACTCTGGCTATTTTTGTAGCTCGGCTATTTCAGCACATGGATCACCGG
AACCGGCAAGGGCTCAAGGACCTTGTTACCAGCGGCGTAACTGTCCGGATTATGAGCGTCTCAGAGCATTGTTACTGCAG
GAAGAATTTTGTCAACTACCCACCAGGGAAAGCAGCTCAGTGGCCAAGGTGCCCACTTCAGTGGATGATGATGTACGCAC
TGGAACTCCACTGCGCCGTTCTCAGTCTCCCACCCTGCTAAAGATTTCACGAAGACCTCAAAATCAGCTTACATTTTTCC
GCCTTACTCCTCAACATGGCCATTATCAGATGATTCCACCATACATCCTTTTAGCTACAGGATTGTTACAACCTTCTGAG
ACTTGGAGA

Alignment

ORF - retro_ocun_1158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.19 %
• Parental protein coverage: 81.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PWEFEVFFDPQ-ELRKEACLLYEIKWGASSKTWRSSGKNTTNHVEVNFLEKLTSEGRLGPSTCCSITWFL
          PWEFEVFFDPQ.ELRK.ACLL.EIKWGASS.TWRSSGKNTTNHVEVNF.EK.TSE.RL.PSTCCS..W.L
Retrocopy PWEFEVFFDPQ<ELRKGACLLHEIKWGASSTTWRSSGKNTTNHVEVNFIEKRTSERRLCPSTCCSLPWLL

Parental  SWSPCWECSTAIREFLSQHPGVTLVIFVARLFQHMDRRNRQGLKDLVTSGVTVQVMSVSEYCYCWENFVN
          .WSPCWECS..IREFLSQHP.VTL.IFVARLFQHMD.RNRQGLKDLVTSGVTV..MSVSE.CYC..NFVN
Retrocopy PWSPCWECSREIREFLSQHPDVTLAIFVARLFQHMDHRNRQGLKDLVTSGVTVRIMSVSEHCYCRKNFVN

Parental  YPPGKAAQWPRYPPRWMLMYALELYCIILGLPPC-LKISRRHQKQLTFFSLTPQYCHYKMIPPYILLATG
          YPPGKAAQWPR.P..WM.MYALEL.C..L.LPPC.LKISRR.Q.QLTFF.LTPQ..HY.MIPPYILLATG
Retrocopy YPPGKAAQWPRCPLQWMMMYALELHCAVLSLPPC<LKISRRPQNQLTFFRLTPQHGHYQMIPPYILLATG

Parental  LLQPSVPWR
          LLQPS..WR
Retrocopy LLQPSETWR

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	0.88 RPM
SRP017611_kidney	0.00 RPM	0.10 RPM
SRP017611_liver	0.00 RPM	3.85 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1158 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1158 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1158 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	ENSOCUG00000025736	1 retrocopy	retro_ocun_1158 ,