RetrogeneDB ID: retro_ocun_861

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 16:27626488..27629408(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000006539
• Aliases: None
• Description: None

Sequence

>retro_ocun_861
TTGATCCAGGGGAATGACCTGAAGAATGACGAGAGCTCTCTCACGGGGGAGTCCGACCACGTCCGGAAGTCCCTGGACAA
AGACCCATGCTGCTCTCAGGGACCCATGTCATAGAAGGCTCTGGCCGGATGGTGGTGACCGCTTTGGTGTCAACTCGCAG
ACCGGGATCATCTTCACTCTGCTGGGGGCCAGTGAGGATGACGAGGAGGAGATGAAGAAGAAAGGTAAAAAACAAGGAGT
CCCTGAAAATCACAACAAAACAAAGACCCAGGACGCTGTGGCCCTGGAGATCCAGCCACTCAGCAGCCAGGAGGGGGCCG
ACAACGAGGACAAGGACAAGAAGGCCAGCAAGGTGCACAAGAAGAAGTCGGTGCTGCAGGGCAAGCTGACGCGCCTGGCC
GTCCAGATCAGGAAAGCCGGTCTCATCATGTCCGCCGTGACCTTCGTCATCCTGATCCTGTACTTCATGATCGACAACTT
CGTGATCCAGGGCAGACCGTGGCTCACCGAGTGCACCCCCGTCTATATCCAGTACTTCATCAAGTTCTTCATCATCGGCG
TCACCGTGCTGGTGGTGGCTGTGCCCAAGGGGCTGCTGCTGGCTGTCACCATCTCCCTGGCCAACTCTGTAAAGAAAATG
ATGAAAGACAACAACCTGGTGCGGCACCTGGATGCCTGTGAGACGATGGGCAATGCCACGGCCATCTGCTCCAACAAGAC
CGGCATGCTGACCATGAACCGCATGACTGTGGTGCAGGCCTACATTGGGGGCACCCACTACCACCAGGTGCCCAGCCCCG
ACGTCTTCCTGCCCAAGGTCCTGGACCACATCGTCAATGGCATTGCCATCAACAGCGCTTACACATCCAAGATCCTGCCT
CCGGAGAAGGAGGGAGGCCTGCTGCGGCAGGTGAGCAACAAGACCGAGTGTGATCTGCTGGGCTTTGTCGCAGATCTGAA
GCAGAACTACCAGGCGGTGTGCAACGAGGTGCCCGAGGAGCAGCTCTACAAGGTGTACACCTTCAACTCGTTGCGCAAGT
CCATGAGCACAGTCGTCCGGAAGCCTGCCGGCGGCTTCCACATGTACAGCAAGGGCGCCTCGGAGATCATGCTTCGCAAG
TGCAATCGGATCCTGGACAAGAAGGGGGAGGCGGTCCCGTTCAAGAACAAGGGCTGCTACGACAAGGTGCACAGTGTCAT
TGAACCCATGGCCTGCAAGGGGCTGCGCACCATCTGCACAGCCTACTGGGACTTCGATGACGCTGAGCCCTCCTGGGACA
ACGAGAGCAAGGTCCTCACCGAGCTCACCTGCATTGCCATCATGGGCATTGAGGACCCTGTGCACCCAGAGGTCCCAGAA
GCTATCGCCAAATGCAAGCAAGCTGGCATCACTGTCAGAATGGTGACCAGGGACAATGTCAACACAGCCCGAGCCATCGC
CACCAAATGTGGCATCCTGACATCTGGTGATGACTTCCTGTGCTTAGAAGGCAAAGAATTCAACTGACTCATTCGCAATG
AAAAGGGAGAGGTAGAACAAGAGAAGCTGCACAAGATCTAACCCAAGCTTTGGGTCCTGGCCTGGTCCTTGCCCACAGAC
AAGCACACGCTGGTGAAAGGCATCATTGACAGCACCGTTGGGGATCAGCGGCAGGTGGTGGCTGTCACCAGTGATGGCAC
AAACGATGGGCCGGCCCTCAAGAAGGCAGACGTTGGTTTTACCATGGGGATTGCAGGCACAGACATGGCAAAGGAAGCCT
CGGACATCATCCTCACTGATGACAACTTCACCAACATTGTCAAGGCCGTGATGTGGGGGCGGAACGTCTACAACAGCATC
TCCAAGTTCCTGCAGTTCCAGCTCACCATCAACATGGTGGCCGTGATCATGGCCTTCACGGGTACCTGCATCACTCAGGA
CTCCCCACTGAAAGCCATGCAGATGCTGTGGGTGAACCTGATCATGGACACTTTCGCTTCACTGGCCCTGGCCGCCGAGC
CCCCCACCGACGCACTGCTGAGGCAGCGCCCCTACCGCCGAAACAAGCCCCTGATCTCGCGGACCATGATGAAGAACATC
CTGGGCCACGCCGTCTATCAGCTCACCGTCATCTTTTTCCTGGTCTTTGCTGGTGAGAAATTCTTCAACATTGACAATAG
GAGGAAGGCCCCACTCCACTCGCTGCCCAGACAGCACTACACCATCGTTTTCAACACCTTCGTGCTGATGCAGCTCTTCA
ACGAGATCAACTCCCGCAAGATCCATGGCGAGAGGAACGTGTTCGCCGGCATGTACCACAACCTCAACTTCTGCTCGGTG
GTCCTGGGCACGTTCATCAGCCAGGTTCTCATTGTGGAATCTGGGGGCAAGCCCTTCAGTTGCACAAAGCTCAGCCTGTT
GCAGTGGCTGTGGTGTCTCTTCATTGGGATTGGAGAACTCCTGTGGGGCCAGATCATCTCTACGATACCCACGCAATCCC
TGAAGTTCCTGAAGGAGGCCGGGCACAGCACCACCAAGGAGGAGATCAGCAAGGATGCCGAGGGGCTGGATGAGATCGAC
CACGCCAAGATGGAGCTGCGCCGAGGCCAGATCCTCTGGTTCCAGGGCCTGAACCGGATCCAGACCCAGATCAAGGTGGT
CAGAGCATTCCATAGCTCCCTCCACGAAAGCATTCAGAAGCCCAGGAACCAGAACTCCATCCACAACTTCATGACCCACC
CTGAATTCGCCATAGATGAGGAGTCGCCGCAAACACCCTTCCTAGATAAGCAGGATGACAGTCTGCACGAGGCCCTGGAC
TCTGGGTCCAAGGTGTTCCCGCCGGACGGTGACAAAAACAACAACGCGGTGGACTGCAAGCCATCGCCAGCCGCCGCATC
CCGCTCCGACAGCCCTCTGTACAGCCTGGAGACCTCCGTG

Alignment

ORF - retro_ocun_861 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.33 %
• Parental protein coverage: 81.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LIQGNDLKIDESSLTGESDHVRKSLDKDP-MLLSGTHVMEGSGRMVVTAV-GVNSQAGIIFTLLGASEDD
          LIQGNDLK.DESSLTGESDHVRKSLDKDP.MLLSGTHV.EGSGRMVVTA..GVNSQ.GIIFTLLGASEDD
Retrocopy LIQGNDLKNDESSLTGESDHVRKSLDKDP<MLLSGTHVIEGSGRMVVTAL<GVNSQTGIIFTLLGASEDD

Parental  EEEKKKKGKKQGVPENRNKAKTQDGVALEIQPLNSQEGADNEDKDKKASKVHKKEKSVLQGKLTRLAVQI
          EEE.KKKGKKQGVPEN.NK.KTQD.VALEIQPL.SQEGADNEDKDKKASKVHKK.KSVLQGKLTRLAVQI
Retrocopy EEEMKKKGKKQGVPENHNKTKTQDAVALEIQPLSSQEGADNEDKDKKASKVHKK-KSVLQGKLTRLAVQI

Parental  GKAGLIMSAVTVVILILYFVIDNFVIQGRPWLAECTPVYIQYFVKFFIIGVTVLVVAVPEGLPLAVTISL
          .KAGLIMSAVT.VILILYF.IDNFVIQGRPWL.ECTPVYIQYF.KFFIIGVTVLVVAVP.GL.LAVTISL
Retrocopy RKAGLIMSAVTFVILILYFMIDNFVIQGRPWLTECTPVYIQYFIKFFIIGVTVLVVAVPKGLLLAVTISL

Parental  AYSVKKMMKDNNLVRHLDACETMGNATAICSDKTGTLTMNRMTVVQAYVGGTHYHQVPSPDVFLPKVLDL
          A.SVKKMMKDNNLVRHLDACETMGNATAICS.KTG.LTMNRMTVVQAY.GGTHYHQVPSPDVFLPKVLD.
Retrocopy ANSVKKMMKDNNLVRHLDACETMGNATAICSNKTGMLTMNRMTVVQAYIGGTHYHQVPSPDVFLPKVLDH

Parental  IVNGIAINSAYTSKILPPEKEGGLPRQVGNKTECALLGFVADLKQDYQAVRNEVPEEQLYKVYTFNSVRK
          IVNGIAINSAYTSKILPPEKEGGL.RQV.NKTEC.LLGFVADLKQ.YQAV.NEVPEEQLYKVYTFNS.RK
Retrocopy IVNGIAINSAYTSKILPPEKEGGLLRQVSNKTECDLLGFVADLKQNYQAVCNEVPEEQLYKVYTFNSLRK

Parental  SMSTVVRKPAGGFRMYSKGASEIMLRKCNRILDKKGEAVPFKNKDRDDMVRSVIEPMACEGLRTICIAYR
          SMSTVVRKPAGGF.MYSKGASEIMLRKCNRILDKKGEAVPFKNK...D.V.SVIEPMAC.GLRTIC.AY.
Retrocopy SMSTVVRKPAGGFHMYSKGASEIMLRKCNRILDKKGEAVPFKNKGCYDKVHSVIEPMACKGLRTICTAYW

Parental  DFDDAEPSWDNESEVLTELTCIAVVGIEDPVRPEVPEAISKCKRAGITVRMVTGDNVNTARAIATKCGIL
          DFDDAEPSWDNES.VLTELTCIA..GIEDPV.PEVPEAI.KCK.AGITVRMVT.DNVNTARAIATKCGIL
Retrocopy DFDDAEPSWDNESKVLTELTCIAIMGIEDPVHPEVPEAIAKCKQAGITVRMVTRDNVNTARAIATKCGIL

Parental  TPGDDFLCLEGKEFNRLIRNEKGEVEQEKLDKIWPKLRVLARSSPTDKHTLVKGIIDSTVGDQRQVVAVT
          T.GDDFLCLEGKEFN.LIRNEKGEVEQEKL.KI.PKL.VLA.S.PTDKHTLVKGIIDSTVGDQRQVVAVT
Retrocopy TSGDDFLCLEGKEFN*LIRNEKGEVEQEKLHKI*PKLWVLAWSLPTDKHTLVKGIIDSTVGDQRQVVAVT

Parental  GDGTNDGPALKKADVGFAMGIAGTDVAKEASDIILTDDNFTSIVKAVMWGRNVYDSISKFLQFQLTVNVV
          .DGTNDGPALKKADVGF.MGIAGTD.AKEASDIILTDDNFT.IVKAVMWGRNVY.SISKFLQFQLT.N.V
Retrocopy SDGTNDGPALKKADVGFTMGIAGTDMAKEASDIILTDDNFTNIVKAVMWGRNVYNSISKFLQFQLTINMV

Parental  AVIVAFTGACITQDSPLKAVQMLWVNLIMDTFASLALATEPPTDALLRRRPYGRNKPLISRTMMKNILGH
          AVI.AFTG.CITQDSPLKA.QMLWVNLIMDTFASLALA.EPPTDALLR.RPY.RNKPLISRTMMKNILGH
Retrocopy AVIMAFTGTCITQDSPLKAMQMLWVNLIMDTFASLALAAEPPTDALLRQRPYRRNKPLISRTMMKNILGH

Parental  AVYQLTIIFFLVFAGEKFFHIDSGRKAPLHSPPSQHYTIVFNTFVLMQLFNEINSRKIHGERNVFAGIYH
          AVYQLT.IFFLVFAGEKFF.ID..RKAPLHS.P.QHYTIVFNTFVLMQLFNEINSRKIHGERNVFAG.YH
Retrocopy AVYQLTVIFFLVFAGEKFFNIDNRRKAPLHSLPRQHYTIVFNTFVLMQLFNEINSRKIHGERNVFAGMYH

Parental  NLIFCSVVLGTFISQVLIVEFGGKPFSCTKLSLSQWLWCLFFGIGELLWGQIISAIPTQSLKFLKEAGHG
          NL.FCSVVLGTFISQVLIVE.GGKPFSCTKLSL.QWLWCLF.GIGELLWGQIIS.IPTQSLKFLKEAGH.
Retrocopy NLNFCSVVLGTFISQVLIVESGGKPFSCTKLSLLQWLWCLFIGIGELLWGQIISTIPTQSLKFLKEAGHS

Parental  TTKEEISKDAEGLDEIDHAEMELRRGQILWFRGLNRIQTQIKVVRAFHSSLHESIQKPRNQNSIHNFMTH
          TTKEEISKDAEGLDEIDHA.MELRRGQILWF.GLNRIQTQIKVVRAFHSSLHESIQKPRNQNSIHNFMTH
Retrocopy TTKEEISKDAEGLDEIDHAKMELRRGQILWFQGLNRIQTQIKVVRAFHSSLHESIQKPRNQNSIHNFMTH

Parental  PEFAIDEESPRTPFLDEQEDDSLHEALDSGSKVFPPDGEAAPYANKNNNAVDCKPSRAAASRSDSPLHSL
          PEFAIDEESP.TPFLD.Q.DDSLHEALDSGSKVFPPDG......N.N.......P..A..S..DSPL.SL
Retrocopy PEFAIDEESPQTPFLDKQ-DDSLHEALDSGSKVFPPDGD----KNNNAVDCKPSPAAASRS--DSPLYSL

Parental  ETSV
          ETSV
Retrocopy ETSV

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	69.59 RPM
SRP017611_kidney	0.00 RPM	21.69 RPM
SRP017611_liver	0.00 RPM	3.24 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_861 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_861 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_861 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
Myotis lucifugus	ENSMLUG00000009948	1 retrocopy	retro_mluc_39,
Oryctolagus cuniculus	ENSOCUG00000006539	1 retrocopy	retro_ocun_861 ,