RetrogeneDB ID: retro_ocun_49

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:9303818..9305696(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000024832
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000012468
• Aliases: None
• Description: None

Sequence

>retro_ocun_49
ATGTGTGGCATTTGCTGTTCTGTAAGCTTTTCTGTTGAACACTGGAGAAAAGATTTGAAAGAAGATCTACTATATAATCT
TAAACGTCGGGGTCCTGAGAGCAGTAAACAGTTGTTAAAATGTTATATGAACTACCAGTGTGTGTTTTCTGGCCATGTCC
TTCACTTGAGGGGTGTTTTGACTGCCCAGCCTATGGAAGATGAAAGAGGCAATGTGTTCCTATGGAATGGAGAAGTCTTT
AGTGGAATAAAGGTTGAAGAAATAGAGAATGATACTCTTTCCTCTTGTAAGAGTGAATCTGATATTATGTCCCTCTTCTC
AGAAGTCCAAGGTCCTTGGTCTTTTATATATTATCAAGCATCTAGTCACAGTTTATGGTTTGGTAGGGATTTTTTTGGTT
GCCATAGTTTGCTTTGGCATTTTAATAATTTGGACAAGAGTTTCTGCCTCTCTTCAGTTGGCCCCCAGACATATGGAGTG
GCAAATCAGTGGCAAGAAGTTCCAGCATCTGGAATTTTCAGAATTGATCTCCAGTCTGCTGCCATGGCCAAACATGTAAG
GTTGCAGTTGTATCCTTGGGAATGTATTTCTAGGGAGAATGCTACTGAAGAGTGCAGTACCAGCCTGACTCATGTTTCAG
CAGACTTGCCGACATTTGTATCAGTGGTGGCAAATGAAGCCAAACTACATCTTGGAACGCCTATTTCTCCTTTAAATATG
ACGTTGCCACAAGCTCCATTGGCGACTCATTGCAGTCACATTTCCAGTATCCCATTCTCAAGAGAGACCCTTCAGGTCTG
CCTTACTGATGGACACATGAGAGAAGTAGTTGAAAAGTTCATTGATGTCCTTAGTGTCGCAGTCAAGAGACGTGTCTTGT
GTCTACAGAGGGACGAAAACCTGGTACCAAATGGAGTTTTGAAGACGGGTGATAGGAAAGCAAATGTTGCCGTCCTGTTT
TCTGGAGGCATCGATTCCATGGTTATTGCTACCCTTGCTGATCGTCATATTCCTTTAGGTGAACCAGTTGATCTCCTGAA
TGTAGCTTTCATGACCAAAGAAAAGACCGTTCCAAGTAGCCGTAACAAAAGACCGAGTAAACAGAAAAATCATGAAATGC
CTTCTGAGGAGTTCTCTGTAGGTACTGCTGCCCGTGGTGCTGATAGTCCTGATGAGAAATACAGTGTACCAGATAGAGTC
ACAGGAAAGGCAGGACTAAAGGAACTGCAAGCTGTTAACCCTTCTCGAATGTGGAATTTTGTTGAAATTAATGTTTCTCT
GGAAGAACTGCAACAATTAAGAAGAACTCAAATAAGTCACTTAGTTCAGCCCCTGGATACGGTTTTGGATGATAGCATTG
GCTGTGCAGTCTGGTTTGCTTCCAGAGGAACTGGCTGGCTAGTGACTCAGGATGAAGTGAAGTCCTATCAGAGCAGTGCA
AAGGTAGTTCTCACTGGAATTGGTGCAGATGAGCAACTTGCAGGTTATTCCCGTCATCGTGTTCACTTCCGTACGCATGG
ACCGGGAGGACTGAACAAGGAAATAACGATGGAACTGGGTCGAATTTCTTCTAGAAACCTTGGTCGTGATGACAGAGTAA
TTGGTGATCATGGAAAAGAAGCAAGATTTCCCTTCCTGAATGAAAATGTTGTCTCCTTTCTAAATTCCCTACCCATCTGG
GAAAAGGCAAACCTGACTCTACCCCGAGGAATTGGTGAGAAACTAATTTTACGTCTGGCAGCTGTGGAACTCGGCCTTAC
AGCCTCTGCTCTCCTGCCAAAGTGGGCCATGCAGTTTGGATCCAGAATTGCAAAGATGGAAAACAGTAATGAAAAGGCAT
CTGATAAGTGTGGAAGGCTCCAGATTATTTCCTTATAA

Alignment

ORF - retro_ocun_49 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.87 %
• Parental protein coverage: 83.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSSCKSESDIMSLFSEVQGPWSFIYYQASSHSLWFGRDFFGRRSLLWHFNDVDKSVCLSSVGPQTPGVAN
          LSSCKSESDIMSLFSEVQGPWSFIYYQASSHSLWFGRDFFG..SLLWHFN..DKS.CLSSVGPQT.GVAN
Retrocopy LSSCKSESDIMSLFSEVQGPWSFIYYQASSHSLWFGRDFFGCHSLLWHFNNLDKSFCLSSVGPQTYGVAN

Parental  QWQEVPASGIFRIDLQSAAMAKHVRLQLYPWECISRENATEECDKSLTHASADLPMFVSVVANEAKLHLG
          QWQEVPASGIFRIDLQSAAMAKHVRLQLYPWECISRENATEEC..SLTH.SADLP.FVSVVANEAKLHLG
Retrocopy QWQEVPASGIFRIDLQSAAMAKHVRLQLYPWECISRENATEECSTSLTHVSADLPTFVSVVANEAKLHLG

Parental  TPVSPLNMTLPQAPLATHCSNISSVPPSRETLQVCLTDGHMKEVVEKFIDVLSVAVKRRVLCLQRDENPV
          TP.SPLNMTLPQAPLATHCS.ISS.P.SRETLQVCLTDGHM.EVVEKFIDVLSVAVKRRVLCLQRDEN.V
Retrocopy TPISPLNMTLPQAPLATHCSHISSIPFSRETLQVCLTDGHMREVVEKFIDVLSVAVKRRVLCLQRDENLV

Parental  PNGVLKTGDRKANVAILFSGGIDSMVIATLADRHIPLGEPIDLLNVAFVTKEKTVLSSRNKRTRKQKNHE
          PNGVLKTGDRKANVA.LFSGGIDSMVIATLADRHIPLGEP.DLLNVAF.TKEKTV.SSRNKR..KQKNHE
Retrocopy PNGVLKTGDRKANVAVLFSGGIDSMVIATLADRHIPLGEPVDLLNVAFMTKEKTVPSSRNKRPSKQKNHE

Parental  MPPEEFSEGTAARGAGSPDENYSVPDRVTGKAGLKELQAVNPSRMWNFVEINVSLEELQQLRRTQISHLV
          MP.EEFS.GTAARGA.SPDE.YSVPDRVTGKAGLKELQAVNPSRMWNFVEINVSLEELQQLRRTQISHLV
Retrocopy MPSEEFSVGTAARGADSPDEKYSVPDRVTGKAGLKELQAVNPSRMWNFVEINVSLEELQQLRRTQISHLV

Parental  QPLDTVLDDSIGCAVWFASRGTGWLVTQGEVKPYQSSAKVVLTGIGADEQLAGYSRHRVRFQTRGPEALN
          QPLDTVLDDSIGCAVWFASRGTGWLVTQ.EVK.YQSSAKVVLTGIGADEQLAGYSRHRV.F.T.GP..LN
Retrocopy QPLDTVLDDSIGCAVWFASRGTGWLVTQDEVKSYQSSAKVVLTGIGADEQLAGYSRHRVHFRTHGPGGLN

Parental  REIAMELGRISSRNLGRDDRVIGDHGKEARFPFLDENVVSFLNSLPIWEKANLTLPRGIGEKLILRLAAV
          .EI.MELGRISSRNLGRDDRVIGDHGKEARFPFL.ENVVSFLNSLPIWEKANLTLPRGIGEKLILRLAAV
Retrocopy KEITMELGRISSRNLGRDDRVIGDHGKEARFPFLNENVVSFLNSLPIWEKANLTLPRGIGEKLILRLAAV

Parental  ELGLTASALLPKRAMQFGSRIAKMENSNEKASDKCGRLRIISL
          ELGLTASALLPK.AMQFGSRIAKMENSNEKASDKCGRL.IISL
Retrocopy ELGLTASALLPKWAMQFGSRIAKMENSNEKASDKCGRLQIISL

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	2.81 RPM	45.31 RPM
SRP017611_kidney	1.72 RPM	23.11 RPM
SRP017611_liver	0.46 RPM	8.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_49 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_49 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_49 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
Bos taurus	ENSBTAG00000000492	1 retrocopy	retro_btau_1365,
Oryctolagus cuniculus	ENSOCUG00000012468	1 retrocopy	retro_ocun_49 ,