RetrogeneDB ID: retro_ocun_1906

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:94933945..94935133(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PREP
• Ensembl ID: ENSOCUG00000000188
• Aliases: None
• Description: prolyl endopeptidase [Source:HGNC Symbol;Acc:9358]

Sequence

>retro_ocun_1906
TGGACCCATGATGGGAAGGGATTATTCTACAACTCATACCCCCAACATGATGGAAAAAGTGATGGTACAGAGACATCCAC
TGATCTCCACCAAAAGCTCTGCTATTATGTCTTGGGGACTGATCAGTGAGAAGACATTTTGTGTGCTGAGTTTCCTGATG
AGCCTAAATGGATGGGTGGTGCTGAGTTATCTGATGATGGTTGCTATGTCCTTTTATCAATAAGGGAAGGATGTGATCCA
GTTAACCGACTCTGGTACTGTGATCTACAGCAGGAACCGAATGGCATCACTGGAATCTTGAAGTGGGTAAAGCTGATTGA
CAACTTTGATGGAGAATATGACTATGTCACCAATGAAGGGACAGTGTTCACGTTCAAGACCAATCGCCATTCTCCCAACT
ATCGCCTGATCAATATTGACTTCATGGATCCTGATGAGTCTAAGTGGAAAGTGCTTGTTCCTGAGCATGAGAAAGATGTC
TTAGAATGGGTGGCTTGTATCAGGTCCAACTTCTTGATCTTATGCTACCTCCATGATGTGAAGAACATCCTGAAGCTCCA
TAACCTGACCACCGGTGCTCTCCTCAAGCCCTTCCCACTTGAGGTTGGCAGTGTTGTGGGCTACAGTGGCCAGAAGAAGG
ACACTGAGATCTTCTACCAGTTTACTTCCTTCTTATCTCCAGGTATCATTTATCACTGTGATCTTACCAAAGAGAAGCTG
GAGCCCAGAGTTTTCCGAGAAGTGACTGTAAAAGGAATCAATGCTTCTGAATACCAGACAATCCAGATTTTCTACCCTAG
CAAGGATGGTACAAAGATTCCCATGTTCATTGTGCATAAAAAGGGCATAAAATTGGATGGCTCTCATCCTGCTTTTTTAT
ATGGCTATGGTGGCTTCAACATTTCTATCACACCCACCTACAGTGTGTCCAGGCTTATTTTTGTGAGGCACATGGGTGGC
ATCCTTGCAGTGGCCAACATCAGAGGAGGTGGCGAATATGGAGAGATGTGGCATAAAAGTGGTACCTTGGCCAACAAACA
GAACTGCTTTGATGACTTTCAGTGTGCTGCTGAGTATCTGATCAAGGAAGGTTACACGTCTCCAAAGAGGCTGAGTATTA
ATGGAGGTTCAAATGGAGGCCTCTTAGTGGCTGCTTGTGCAAATCAGCGTCCTGACCTCTTTGGTTGT

Alignment

ORF - retro_ocun_1906 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.94 %
• Parental protein coverage: 61.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WTHDGKGMFYNSYPQQDGKSDGTETSTNLHQKLYYHVLGTDQAEDILCAEFPDEPKWMGGAELSDDGRYV
          WTHDGKG.FYNSYPQ.DGKSDGTETST.LHQKL.Y.VLGTDQ.EDILCAEFPDEPKWMGGAELSDDG.YV
Retrocopy WTHDGKGLFYNSYPQHDGKSDGTETSTDLHQKLCYYVLGTDQ*EDILCAEFPDEPKWMGGAELSDDGCYV

Parental  LLSIREGCDPVNRLWYCDLQQEPNGITGILKWVKLIDNFEGEYDYVTNEGTVFTFKTNRHSPNYRLINID
          LLSIREGCDPVNRLWYCDLQQEPNGITGILKWVKLIDNF.GEYDYVTNEGTVFTFKTNRHSPNYRLINID
Retrocopy LLSIREGCDPVNRLWYCDLQQEPNGITGILKWVKLIDNFDGEYDYVTNEGTVFTFKTNRHSPNYRLINID

Parental  FMDADESKWKVLVPEHEKDVLEWVACVRSNFLVLCYLHDVKNILQLHDLTTGALLKPFPLEVGSVVGYSG
          FMD.DESKWKVLVPEHEKDVLEWVAC.RSNFL.LCYLHDVKNIL.LH.LTTGALLKPFPLEVGSVVGYSG
Retrocopy FMDPDESKWKVLVPEHEKDVLEWVACIRSNFLILCYLHDVKNILKLHNLTTGALLKPFPLEVGSVVGYSG

Parental  QKKDTEIFYQFTSFLSPGIIYHCDLTKEELEPRVFREVTVKGIDASEYQTVQVFYPSKDGTKIPMFIVHK
          QKKDTEIFYQFTSFLSPGIIYHCDLTKE.LEPRVFREVTVKGI.ASEYQT.Q.FYPSKDGTKIPMFIVHK
Retrocopy QKKDTEIFYQFTSFLSPGIIYHCDLTKEKLEPRVFREVTVKGINASEYQTIQIFYPSKDGTKIPMFIVHK

Parental  KGIKLDGSHPAFLYGYGGFNISITPNYSVSRLIFVRHMGGVLAVANIRGGGEYGETWHKGGILANKQNCF
          KGIKLDGSHPAFLYGYGGFNISITP.YSVSRLIFVRHMGG.LAVANIRGGGEYGE.WHK.G.LANKQNCF
Retrocopy KGIKLDGSHPAFLYGYGGFNISITPTYSVSRLIFVRHMGGILAVANIRGGGEYGEMWHKSGTLANKQNCF

Parental  DDFQCAAEYLVKEGYTSPKRLTINGGSNGGLLVAACANQRPDLFGC
          DDFQCAAEYL.KEGYTSPKRL.INGGSNGGLLVAACANQRPDLFGC
Retrocopy DDFQCAAEYLIKEGYTSPKRLSINGGSNGGLLVAACANQRPDLFGC

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	39.13 RPM
SRP017611_kidney	0.00 RPM	27.97 RPM
SRP017611_liver	0.00 RPM	15.11 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1906 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1906 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1906 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
Callithrix jacchus	ENSCJAG00000001710	1 retrocopy	retro_cjac_3109,
Oryctolagus cuniculus	ENSOCUG00000000188	1 retrocopy	retro_ocun_1906 ,