RetrogeneDB ID: retro_ocun_739

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:14594924..14595617(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000003891
• Aliases: None
• Description: None

Sequence

>retro_ocun_739
CTTGGTGTGAGTCATCCTGTCCGCAAACAAGTTACTGAATGATTTCTGGATATGAGGGGTGGGCTTGGTTTGGCTGGTGC
AAAGGCTGAATACAGTGGAGGTGAAATCTGAGAACAGACCGGAGATGGTCTTGTCTATGCTGCTCTTATAGCATAAAGTG
CTGCAATGGGAAGTGCAGAGGCAAGTGTATTTAGTGTCCTTCAGCATGTCCTCAGTGCTGGACCCCATGTCAAGAGGGGC
AGCAATGCCACTAGCTTCGTATACCAGGCGGTTGCCAAGGGAACTCACCAGCCATCTGATGCTTCTGCTTTTAATGCCAG
TCACTCAGGTTCTGGACTCTTCAGGATTTACTCTATCTCCCAGGCAGCCACTGATAGAGATGCTTTCACGGCTGCCTACA
AAAAAGTGAAACCAGTTGCTCAAGGAAACCTTTCCAGTGCAGATGTCCAAGCTGCCAAGAACAACCTGCAAGCTGGATGT
CTCATGTTGGTAGAGTCTTTGGAGGGCTTCCTGGATGAAGTTGGGTCCCAAGCTCTTGTTGCTAGTTCTTATGTGCCACT
GTCCACAGTCGTTCAGCAGAGTGACTTGGTGACTGATGCTGATATCATAAATGCTGTGAAGAAGTTTGTTTCTGGCCAGA
AGTTGATGGCAGCAAGTGGAAATCTGGGTCATATACCTTTTGTTGATGAGTTA

Alignment

ORF - retro_ocun_739 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.35 %
• Parental protein coverage: 50.99 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGVSHPVLKQVAEQFLNMRGGLGLAGVKARYRGGEIREQTGDSLVHAAVVAESAAMGSAEANAFSVLQHV
          LGVSHPV.KQV.E.FL.MRGGLGLAG.KA.Y.GGEI.EQTGD.LV.AA..A.SAAMGSAEA..FSVLQHV
Retrocopy LGVSHPVRKQVTE*FLDMRGGLGLAGAKAEYSGGEI*EQTGDGLVYAALIA*SAAMGSAEASVFSVLQHV

Parental  LGAGPHVKRGSNATSLLYQAVAKGTHQPFDVSAFNASYTDSGLFGIYTISQAAAAGDVIKAAYNQVKTVA
          L.AGPHVKRGSNATS..YQAVAKGTHQP.D.SAFNAS...SGLF.IY.ISQAA...D...AAY..VK.VA
Retrocopy LSAGPHVKRGSNATSFVYQAVAKGTHQPSDASAFNASHSGSGLFRIYSISQAATDRDAFTAAYKKVKPVA

Parental  QGNLSSADVQAAKNKLKAGYLMSVESSEGFLDEVGSQALIAGSYVPPSTVLQQIDSVADADIVNAAKKFV
          QGNLSSADVQAAKN.L.AG.LM.VES.EGFLDEVGSQAL.A.SYVP.STV.QQ.D.V.DADI.NA.KKFV
Retrocopy QGNLSSADVQAAKNNLQAGCLMLVESLEGFLDEVGSQALVASSYVPLSTVVQQSDLVTDADIINAVKKFV

Parental  SGQKSMAASGNLGHTPFVDEL
          SGQK.MAASGNLGH.PFVDEL
Retrocopy SGQKLMAASGNLGHIPFVDEL

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	157.45 RPM
SRP017611_kidney	0.00 RPM	222.27 RPM
SRP017611_liver	0.00 RPM	65.82 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_739 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_739 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_739 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021651	2 retrocopies	retro_btau_1008, retro_btau_1668,
Canis familiaris	ENSCAFG00000017756	1 retrocopy	retro_cfam_2075,
Callithrix jacchus	ENSCJAG00000009116	1 retrocopy	retro_cjac_222,
Echinops telfairi	ENSETEG00000001084	1 retrocopy	retro_etel_2087,
Homo sapiens	ENSG00000140740	1 retrocopy	retro_hsap_2785,
Gorilla gorilla	ENSGGOG00000015379	1 retrocopy	retro_ggor_1941,
Myotis lucifugus	ENSMLUG00000003345	2 retrocopies	retro_mluc_1391, retro_mluc_770,
Macaca mulatta	ENSMMUG00000018287	2 retrocopies	retro_mmul_1442, retro_mmul_683,
Monodelphis domestica	ENSMODG00000007645	1 retrocopy	retro_mdom_327,
Mustela putorius furo	ENSMPUG00000016849	1 retrocopy	retro_mputfur_1042,
Nomascus leucogenys	ENSNLEG00000012185	1 retrocopy	retro_nleu_685,
Oryctolagus cuniculus	ENSOCUG00000003891	2 retrocopies	retro_ocun_604, retro_ocun_739 ,
Otolemur garnettii	ENSOGAG00000005478	4 retrocopies	retro_ogar_1113, retro_ogar_112, retro_ogar_1934, retro_ogar_82,
Ochotona princeps	ENSOPRG00000000419	1 retrocopy	retro_opri_455,
Pongo abelii	ENSPPYG00000007174	1 retrocopy	retro_pabe_2232,
Pan troglodytes	ENSPTRG00000007871	1 retrocopy	retro_ptro_1886,
Sorex araneus	ENSSARG00000010670	1 retrocopy	retro_sara_231,
Tupaia belangeri	ENSTBEG00000010785	1 retrocopy	retro_tbel_3988,
Vicugna pacos	ENSVPAG00000010914	1 retrocopy	retro_vpac_640,