RetrogeneDB ID: retro_ocun_69

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 10:33491644..33492982(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025405
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000005367
• Aliases: None
• Description: None

Sequence

>retro_ocun_69
ATGAATGAGGAGTACGACGTGATCGTGCTGGGCACCGGCCTGACGGAATGTATCTTGTCGGGTATCATGTCAGTGAATGG
AAAGAAAGTTCTTCACATGGATCAAAACCCATACTATGGAGGAGAAAGTGCATCTATAACACCTCTGGAAGATTTATACA
AAAGATTTAAAATACCAGGATCACCACCATCATCAATGGGGAGAGGAAGAGACTGGAATGTTGACTTAATTCCCAAGTTC
CTTATGGCTAATGGTCAGCTGGTTAAGATGCTGCTTTATACAGAAGTCACTCGTTATCTGGATTTCAAAGTGACAGAAGG
AAGCTTTGTCTATAAAGGAGGAAAAATCTACAAGGTTCCTTCCACTGAAGCAGAAGCCCTTGCATCTAGCTTAATGGGAC
TATTTGAAAAACGTCGCTTCAGAAAATTCCTGGTGTATGTTGCCAACTTTGATGAAAACGATGCTAGAACTTTTGAAGGT
GTTGATCCCAAGAAGACTGCAATGCGAGATGAGTATAAGAAATTTGATTTGGGCCAAGATGTTATCGATTTTACAGGTCA
TGCTCTTGCACTCTATAGAACTGATGACTACTTAGATCAACCATGTTGTGAAACCATTAATAGAATTAAACTTTACAGTG
AGTCTCTGGCGCGATATGGCAAAAGCCCATACCTTTATCCACTCTATGGCCTTGGGGAACTCCCACAAGGATTTGCAAGG
CTAAGTGCTATTTATGGTGGTACCTACATGCTGAATAAACCTATCGAAGAAATCATTGTGCAGAATGGGAAGGTGGTTGG
TGTAAAATCTGAAGGAGAGATTGCTCGCTGTAAGCAGCTCATCTGTGACCCCAGCTATGTAAAAGATCGGGTGGAGAAAG
TGGGCCAGGTGATAAGAGTTATCTGCATTCTTAGTCATCCCATCAAGAATACCAACGATGCCAACTCCTGCCAGATCATT
ATTCCACAAAACCAAGTCAATCGAAAGTCAGATATCTATGTCTGCATGATTTCCTCTGCACACAATGTGGCAGCACAAGG
GAAGTACATTGCCATAGTCAGTACAACTGTGGAAACCAAGGAACCTGAGAAAGAAATCAGACCAGCTTTGGAACTGTTGG
AACCAATTGAACAGAAATTTGTTAGCATCAGTGACCTCCTTGTGCCAAAAGATTTGGGAAAAGAAAGCCAGATCTTTATT
TCCCGCACATATGATGCTACGACTCACTTTGAGACAACTTGTGATGACATTAAAGACATCTATAAGAGGATGACAGGATC
AGAGTTTGACTTTGAGGAAATGAAGCGCAAGAAAAATGACATCTATGGGGAAGACTAA

Alignment

ORF - retro_ocun_69 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.98 %
• Parental protein coverage: 99.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SECFDQIVLGTDFTKECILSGIMSVNGKKVLHMDQNPYYGGESASITPLEDLYKRFKIPGSPPSSMGRGR
          .E..D.IVLGT..T.ECILSGIMSVNGKKVLHMDQNPYYGGESASITPLEDLYKRFKIPGSPPSSMGRGR
Retrocopy NEEYDVIVLGTGLT-ECILSGIMSVNGKKVLHMDQNPYYGGESASITPLEDLYKRFKIPGSPPSSMGRGR

Parental  DWNVDLIPKFLMANGQLVKMLLYTEVTRYLDFKVTEGSFVYKGGKIYKVPSTEAEALASSLMGLFEKRRF
          DWNVDLIPKFLMANGQLVKMLLYTEVTRYLDFKVTEGSFVYKGGKIYKVPSTEAEALASSLMGLFEKRRF
Retrocopy DWNVDLIPKFLMANGQLVKMLLYTEVTRYLDFKVTEGSFVYKGGKIYKVPSTEAEALASSLMGLFEKRRF

Parental  RKFLVYVANFDENDARTFEGVDPKKTAMRDVYKKFDLGQDVIDFTGHALALYRTDDYLDQPCCETINRIK
          RKFLVYVANFDENDARTFEGVDPKKTAMRD.YKKFDLGQDVIDFTGHALALYRTDDYLDQPCCETINRIK
Retrocopy RKFLVYVANFDENDARTFEGVDPKKTAMRDEYKKFDLGQDVIDFTGHALALYRTDDYLDQPCCETINRIK

Parental  LYSESLARYGKSPYLYPLYGLGELPQGFARLSAIYGGTYMLNKPIEEIIVQNGKVVGVKSEGEIARCKQL
          LYSESLARYGKSPYLYPLYGLGELPQGFARLSAIYGGTYMLNKPIEEIIVQNGKVVGVKSEGEIARCKQL
Retrocopy LYSESLARYGKSPYLYPLYGLGELPQGFARLSAIYGGTYMLNKPIEEIIVQNGKVVGVKSEGEIARCKQL

Parental  ICDPSYVKDRVEKVGQVIRVICILSHPIKNTNDANSCQIIIPQNQVNRKSDIYVCMISSAHNVAAQGKYI
          ICDPSYVKDRVEKVGQVIRVICILSHPIKNTNDANSCQIIIPQNQVNRKSDIYVCMISSAHNVAAQGKYI
Retrocopy ICDPSYVKDRVEKVGQVIRVICILSHPIKNTNDANSCQIIIPQNQVNRKSDIYVCMISSAHNVAAQGKYI

Parental  AIVSTTMETKEPEKEIRPALELLEPIEQKFVSISDLLVPKDLGKESQIFISRTYDATTHFETTCDDIKDI
          AIVSTT.ETKEPEKEIRPALELLEPIEQKFVSISDLLVPKDLGKESQIFISRTYDATTHFETTCDDIKDI
Retrocopy AIVSTTVETKEPEKEIRPALELLEPIEQKFVSISDLLVPKDLGKESQIFISRTYDATTHFETTCDDIKDI

Parental  YKRMTGSEFDFEEMKRKKNDIYGED
          YKRMTGSEFDFEEMKRKKNDIYGED
Retrocopy YKRMTGSEFDFEEMKRKKNDIYGED

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	4.08 RPM	35.93 RPM
SRP017611_kidney	6.89 RPM	49.87 RPM
SRP017611_liver	5.63 RPM	46.01 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_69 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_69 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_69 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005316	1 retrocopy	retro_btau_1208,
Canis familiaris	ENSCAFG00000005223	2 retrocopies	retro_cfam_2196, retro_cfam_886,
Callithrix jacchus	ENSCJAG00000020512	2 retrocopies	retro_cjac_1168, retro_cjac_3115,
Cavia porcellus	ENSCPOG00000013449	1 retrocopy	retro_cpor_696,
Gorilla gorilla	ENSGGOG00000003623	1 retrocopy	retro_ggor_2590,
Mus musculus	ENSMUSG00000021218	2 retrocopies	retro_mmus_2971, retro_mmus_360,
Oryctolagus cuniculus	ENSOCUG00000005367	1 retrocopy	retro_ocun_69 ,
Oryctolagus cuniculus	ENSOCUG00000012819	1 retrocopy	retro_ocun_893,
Ictidomys tridecemlineatus	ENSSTOG00000006449	1 retrocopy	retro_itri_757,
Tupaia belangeri	ENSTBEG00000011523	1 retrocopy	retro_tbel_644,