RetrogeneDB ID: retro_ocun_593

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:2262697..2263458(+)
• Located in intron of: ENSOCUG00000026497

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM76B
• Ensembl ID: ENSOCUG00000014549
• Aliases: None
• Description: family with sequence similarity 76, member B [Source:HGNC Symbol;Acc:28492]

Sequence

>retro_ocun_593
GAGTTCTCCCAGGGCCAACAGCTCTGCAGGGAATGTCGGATCGCACATCCTACTGTAAAGTGTACTTACTGCAGATGAGA
ATTCCAACAAGAGAGCAAACGAACACAATCTGTAAGTGCACAAGATGTTAAGGGATTTGGGACACCCAAACCTTGTCGAC
ACTGTAACATGATTGCAGCATTCATTGGTACCAAGTGTCAGCGCTGTACACATTCAGAAAAAAATGCAGACCCCCTCAGA
CCTGTGAACAGTGCGAACGACAGAGAGCTTTTGATGCGAGGGAGGAAAGTAGAAAGGCGGATCGAAAGTAGTTATGCTGG
CGCTGTACTTTACCATACAAGAGTTTTACAGAAGACAAAAGAACAAAGGAAGGCTCTGGGATCCTCGCATTCAGATCCTC
CTCCTCCTCCTCTGAGAAAGACTAGCATCATTCAAAACCTCTCCACCAGCACCACCACCGCCATCCTCTCAGCAGTAGCC
ATCACCAAGTCAGCAGCTGAAGTCCAGAGCGAGAGCAGGGACTGTGGAAACGGCGCCATAAATCCTCTGAAGCAGTTCAG
AATGAAGCTCCAGAGAAACCCCAGCTGGAATCTAAGCCATCGGATGGAGACAGCTCTACAAGTCAGTCAGCACGTGGTGG
GGCAACAGACAGTTTCGTCCTAAGTCAACTGAAAGAAGTGATGTCGCTTAAGCATCTCTTAGAGCAGAGAGACCAGGCCA
TTGTAGAAAAAGACAGACAGTCAACTGAACTAAAGGCAGAT

Alignment

ORF - retro_ocun_593 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.66 %
• Parental protein coverage: 74.08 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QFELGTPL-QECRIAHPIVKCTYCRSEFQQESKTNTICKKCAQNVKQFGTPKPCQYCNIIAAFIGTKCQR
          .F..G..L..ECRIAHP.VKCTYCR.EFQQESK........AQ.VK.FGTPKPC..CN.IAAFIGTKCQR
Retrocopy EFSQGQQLCRECRIAHPTVKCTYCR*EFQQESKRTQSVS--AQDVKGFGTPKPCRHCNMIAAFIGTKCQR

Parental  CTNSEK-KYGPPQTCEQCKQQCAFDRKEEGRRKVDGKLLCWLCTLSYKRVLQKTKEQRKTLGSSH-SNSS
          CT.SEK.K..PPQTCEQC..Q.AFD..EE.R.K.D.K.LCW.CTL.YK.....T...R...GS......S
Retrocopy CTHSEK<KCRPPQTCEQCERQRAFDAREESR-KADRK*LCWRCTLPYKSF---TEDKRTKEGSGILAFRS

Parental  SSSLTEKDQHHSKHHHHHHHHHHRHSSSHHKISSLSPEQEQGLWKQSHKSSAAIQNETPKKKPKLESKPS
          SSS..EKD.HHSK..H.HHH.H...SSSHH..SS.SPE.EQGLWK..HKSS.A.QNE.P..KP.LESKPS
Retrocopy SSSSSEKD*HHSKPLHQHHHRHPL-SSSHHQVSS*SPEREQGLWKRRHKSSEAVQNEAP-EKPQLESKPS

Parental  NGDSSSINQSADSGGTDNFVLISQLKEEVMSLKRLLQQRDQTILEKDKKLTELKAD
          .GDSS...QSA..G.TD.FVL.SQLK.EVMSLK.LL.QRDQ.I.EKD...TELKAD
Retrocopy DGDSST-SQSARGGATDSFVL-SQLK-EVMSLKHLLEQRDQAIVEKDRQSTELKAD

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	0.11 RPM	8.66 RPM
SRP017611_kidney	0.41 RPM	9.22 RPM
SRP017611_liver	0.15 RPM	3.55 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_593 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_593 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_593 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000008119	1 retrocopy	retro_eeur_195,
Oryctolagus cuniculus	ENSOCUG00000014549	1 retrocopy	retro_ocun_593 ,