RetrogeneDB ID: retro_ocun_1056

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:97683354..97684830(+)
• Located in intron of: ENSOCUG00000024654

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAR1
• Ensembl ID: ENSOCUG00000004336
• Aliases: None
• Description: fatty acyl CoA reductase 1 [Source:HGNC Symbol;Acc:26222]

Sequence

>retro_ocun_1056
ATGGTGTCAATCCCAGAATACTATGAAGGCAAGAATGTTCTGCTCACTGGAGCTACTGGCTTCCTAGGAAAAGTGCTTCT
GGAGAAGTTGCTGAGGTCTTGTCCAAAGGTGAATTCAGTATATGTTTTGGTGAGGCAGAAAGCTGGGCAGACCCCTCAAG
AACGAGTGGAACAAGTCTTGAGTGGCAAGCTGTTTGATCGATTGAGAGGTGAAAATCCAGATTTTAGAGAGAAAATAATA
GCAATCAACAGCGAACTTACTCAACCTAAACTGGCTCTTAGTGAGGAAGATGAAGAGGTCATCGTAGATTCCACCAATAT
TATATTCCACTGTGCAGCCACCGTAAGGTTTAATGAAAATTTAAGAGATGCTGTTCAGTTAAATGTGACTGCTACAAGAC
AGCTTATTCTCCTTGCACAACAAATGAAGAACTTGGAGGTGTTCATGCATGTATCAACAGCATATGCCTACTGCAATCGA
AAGCATATTGATGAAGTAGTATATCCACCCCCAGTAGACCCCAAGAAGCTGATTGACTCTTTAGAGTGGATGGATGATGG
CCTAGTAACTGATATCACACCCAAACTGATAGGAGATAGACCTAATACGTACATATACACGAAAGCATTGGCAGAATATG
TTGTACAACAAGAAGGAGCAAAGCTAAACGTGGCGATTGTAAGGCCATCGATTGTCGGTGCCACTTGGAAAGAACCCTTT
CCAGGATGGATTGATAACTTTAATGGACCAAGTGGTCTCTTCATTGCGGCAGGGAAAGGAATTCTTCGAACAATGCGTGC
CTCCAACAGTGCCCTTGCAGATCTTGTTCCTGTAGATGTAGTTGTCAACACGAGTCTTGCAGCAGCCTGGTATTCCGGAG
TTAATAGACCAAGAAACATCATGGTATACAACTGCACAACAGGCAGCACTAATCCATTCCACTGGGGTGAAGTTGAATAC
CATGTAATTTCCACCTTTAGGAGAAATCCTCTCGAACAGGCCTTCAGGTGGCCCAATGTAAATCTAACCTCCAATCACCT
CTCATATCATTTCTGGATTGCTGTAAGCCATAAGGCCCCAGCATTCCTGTATGATATCTACCTCAGGATGACTGGAAGAA
GCCCAAGGATGATGAAAACAATAACTCGTCTTCACAAAACTATCGTCTTTCTTGAATATTTCACAAGTAATTCTTGGGTT
TGGAATACTGACAATGTGAATATGTTAATGAATCAACTAAATCCTGAAGACAGAAAGACCTTCAATATTGATGTACGGCA
GTTACGTTGGGCTGCGTATATAGAGAACTACTGCATGGGAACTAAGAAATACGTGTTAAATGAAGAAATGTCTGGCCTCC
CTGCTGCTAGAAAGCATCTGAACAAATTGCGGAACCTACGTTATGGCTTCAATACCATTCTCGTGATTCTGATCTGGCAC
ATTTTTATTACAAGATCACAAATGGCAAGAAACATC

Alignment

ORF - retro_ocun_1056 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVSIPEYYEGKNVLLTGATGFLGKVLLEKLLRSCPKVNSVYVLVRQKAGQTPQERVEEILSGKLFDRLRD
          MVSIPEYYEGKNVLLTGATGFLGKVLLEKLLRSCPKVNSVYVLVRQKAGQTPQERVE..LSGKLFDRLR.
Retrocopy MVSIPEYYEGKNVLLTGATGFLGKVLLEKLLRSCPKVNSVYVLVRQKAGQTPQERVEQVLSGKLFDRLRG

Parental  ENPDFREKIIAINSELTQPKLALSEEDKEVIVDSTNIIFHCAATVRFNENLRDAVQLNVIATRQLILLAQ
          ENPDFREKIIAINSELTQPKLALSEED.EVIVDSTNIIFHCAATVRFNENLRDAVQLNV.ATRQLILLAQ
Retrocopy ENPDFREKIIAINSELTQPKLALSEEDEEVIVDSTNIIFHCAATVRFNENLRDAVQLNVTATRQLILLAQ

Parental  QMKNLEVFMHVSTAYAYCNRKHIDEVVYPPPVDPKKLIDSLEWMDDGLVNDITPKLIGDRPNTYIYTKAL
          QMKNLEVFMHVSTAYAYCNRKHIDEVVYPPPVDPKKLIDSLEWMDDGLV.DITPKLIGDRPNTYIYTKAL
Retrocopy QMKNLEVFMHVSTAYAYCNRKHIDEVVYPPPVDPKKLIDSLEWMDDGLVTDITPKLIGDRPNTYIYTKAL

Parental  AEYVVQQEGAKLNVAIVRPSIVGASWKEPFPGWIDNFNGPSGLFIAAGKGILRTMRASNNALADLVPVDV
          AEYVVQQEGAKLNVAIVRPSIVGA.WKEPFPGWIDNFNGPSGLFIAAGKGILRTMRASN.ALADLVPVDV
Retrocopy AEYVVQQEGAKLNVAIVRPSIVGATWKEPFPGWIDNFNGPSGLFIAAGKGILRTMRASNSALADLVPVDV

Parental  VVNTSLAAAWYSGVNRPRNIMVYNCTTGSTNPFHWGEVGYYLNHFFKMNPLNQVFRRPNIKLYSNNLLLH
          VVNTSLAAAWYSGVNRPRNIMVYNCTTGSTNPFHWGEV.Y.....F..NPL.Q.FR.PN..L.SN.L..H
Retrocopy VVNTSLAAAWYSGVNRPRNIMVYNCTTGSTNPFHWGEVEYHVISTFRRNPLEQAFRWPNVNLTSNHLSYH

Parental  YWKGVRHTVPALLLDLALRLTGQKPWMMKTITRLHKAMVFLEYFTSNSWVWNTDNVNMLMNQLNPEDKKT
          .W..V.H..PA.L.D..LR.TG..P.MMKTITRLHK..VFLEYFTSNSWVWNTDNVNMLMNQLNPED.KT
Retrocopy FWIAVSHKAPAFLYDIYLRMTGRSPRMMKTITRLHKTIVFLEYFTSNSWVWNTDNVNMLMNQLNPEDRKT

Parental  FNIDVRQLHWAEYIENYCMGTKKYVLNEEMSGLPAARKHLNKLRNIRYGFNTILVILIWRIFIARSQMAR
          FNIDVRQL.WA.YIENYCMGTKKYVLNEEMSGLPAARKHLNKLRN.RYGFNTILVILIW.IFI.RSQMAR
Retrocopy FNIDVRQLRWAAYIENYCMGTKKYVLNEEMSGLPAARKHLNKLRNLRYGFNTILVILIWHIFITRSQMAR

Parental  NI
          NI
Retrocopy NI

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	0.50 RPM	45.48 RPM
SRP017611_kidney	0.30 RPM	31.72 RPM
SRP017611_liver	0.00 RPM	1.77 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1056 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1056 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1056 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003490	2 retrocopies	retro_chof_1358, retro_chof_1733,
Callithrix jacchus	ENSCJAG00000010077	1 retrocopy	retro_cjac_545,
Cavia porcellus	ENSCPOG00000002654	1 retrocopy	retro_cpor_267,
Homo sapiens	ENSG00000197601	1 retrocopy	retro_hsap_1225,
Gorilla gorilla	ENSGGOG00000001180	1 retrocopy	retro_ggor_958,
Macaca mulatta	ENSMMUG00000011990	1 retrocopy	retro_mmul_1301,
Nomascus leucogenys	ENSNLEG00000017695	1 retrocopy	retro_nleu_698,
Oryctolagus cuniculus	ENSOCUG00000004336	2 retrocopies	retro_ocun_1056 , retro_ocun_790,
Otolemur garnettii	ENSOGAG00000005064	2 retrocopies	retro_ogar_1353, retro_ogar_341,
Pongo abelii	ENSPPYG00000003470	1 retrocopy	retro_pabe_1019,
Pan troglodytes	ENSPTRG00000024190	1 retrocopy	retro_ptro_840,
Rattus norvegicus	ENSRNOG00000013176	1 retrocopy	retro_rnor_467,