RetrogeneDB ID: retro_ocun_604

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:29951644..29953003(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023193
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_ocun_604
ATGAAGCTATTAACCAGAGCCGGGTCCTTTTCGAGATTTTATTCCCTCCAAGTTGCTCCCAAAGTGAAAGCCTCGGCTGC
CCCCGCAGGAGCGCCTCTGCACCCTCAGGACCTTGAATCCACCAAATTACCAAATGGCTTAGTGATTGCTTCTCTGGAAA
ACTATGCTCCTGCATCCAGAATTGGCTTGTTCATCAAAGCACGCAGTAGATACGAGGACTCCAACAACTTAGGGACCTCT
CATTTGCTGCGTCTTGCATCCAGTTTGACAACTAATGGAGCTTCCTCGTTCAAGATAACACGTGGAATTGAGGCAGTTGG
CGGTACACTAAGTGTGACTGCAACAAGGGAAAAGATGGCACACACGGTGGAATGCCTGTGGGACAATGTTGATATTCTAA
TGGAGTTCCTACTCAACGTCACCACATCACCAGAATTTCGTCGCTGGGAAGTAACTGCACTTCAGTCTCAGCTAAGGATT
GACAAAGCTGTGGCTTTTCAGAATCCACAGACGCATGTCATTGAAAATTTGCATGCTGCAGCCTACCAGAATGCCTTGGC
TAATTCCTTGTATTGTCCTGACTATAGGATTGGAAAAGTGACACCAGAAGAGTTAGATTACTATGTTCAGAACCACTTCA
CAAGTGCAAGAATGGCTTTGATTGGACTTGGTGTGAGTCATTCTGTCCTCAAGCAAGTTGCTGAGCAATTCCTCAACATG
AGGGGTGGGCTTGGCTTGGCTGGTGTAAAGGCCAGATACCGTGGAGGTGAAATCCGAGAACAGACTGGAGACAGCCTTGT
CCATGCTGCGGTTGTAGCAGAAAGCGCTGCCATGGGAAGCGCAGAAGCAAATGCATTCAGTGTCCTTCAGCACTTCCCTG
GTGCCGGGCCCCACGTCAAAAGGGGCAGCAACGCCACCAGCCTCCTATACCAGGCTGTCGCCAAGGGGACTCACCAGCCA
TTTGATGTTTCCGCTTTTAATGCCAGTTACACGGATTCTGGACTCTTCAGGATTTACACTACCTCCCAGGCAGCAGCTGC
TGGAGATGTTATCAAGGCTGCCTACAACCAAGTAAAAACAGTTGCTCAAGGAAACCTTTCCAGTGCAGATGTCCAAGCTG
CCAAGAACAAGCTGAAAGCTGGATACCTAATGTCAGTAGAGTCTTCGGAGGGCTTCCTGGATGAGGTTGGGTCCCAGGCT
CTGATAACTGGTTCTTGCGTGCCACCATCCACAGTCCTTCAGCAGATGGACTCGGTGGCTGATGCTGATATCGTAAATGC
TGCAAAGAAGTTTGTTTCTGGCCAGAAGTCCATGGCAGGAAGAGGAAATTTGGGTCATACACCTTTTGTTGATGAGTTA

Alignment

ORF - retro_ocun_604 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.36 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKLLTRAGSFSRFYSLKVAPKVKASAAPAGAPLHPQDLEFTKLPNGLVIASLENYAPASRIGLFIKAGSR
          MKLLTRAGSFSRFYSL.VAPKVKASAAPAGAPLHPQDLE.TKLPNGLVIASLENYAPASRIGLFIKA.SR
Retrocopy MKLLTRAGSFSRFYSLQVAPKVKASAAPAGAPLHPQDLESTKLPNGLVIASLENYAPASRIGLFIKARSR

Parental  YEDSNNLGTSHLLRLASSLTTKGASSFKITRGIEAVGGTLSVTATREKMAYTVECLRDDVDILMEFLLNV
          YEDSNNLGTSHLLRLASSLTT.GASSFKITRGIEAVGGTLSVTATREKMA.TVECL.D.VDILMEFLLNV
Retrocopy YEDSNNLGTSHLLRLASSLTTNGASSFKITRGIEAVGGTLSVTATREKMAHTVECLWDNVDILMEFLLNV

Parental  TTSPEFRRWEVAALQSQLRVDKAVAFQNPQTHVIENLHAAAYRNALANSLYCPDYRIGKVTPEELHYYVQ
          TTSPEFRRWEV.ALQSQLR.DKAVAFQNPQTHVIENLHAAAY.NALANSLYCPDYRIGKVTPEEL.YYVQ
Retrocopy TTSPEFRRWEVTALQSQLRIDKAVAFQNPQTHVIENLHAAAYQNALANSLYCPDYRIGKVTPEELDYYVQ

Parental  NHFTSARMALIGLGVSHPVLKQVAEQFLNMRGGLGLAGVKARYRGGEIREQTGDSLVHAAVVAESAAMGS
          NHFTSARMALIGLGVSH.VLKQVAEQFLNMRGGLGLAGVKARYRGGEIREQTGDSLVHAAVVAESAAMGS
Retrocopy NHFTSARMALIGLGVSHSVLKQVAEQFLNMRGGLGLAGVKARYRGGEIREQTGDSLVHAAVVAESAAMGS

Parental  AEANAFSVLQHVLGAGPHVKRGSNATSLLYQAVAKGTHQPFDVSAFNASYTDSGLFGIYTISQAAAAGDV
          AEANAFSVLQH..GAGPHVKRGSNATSLLYQAVAKGTHQPFDVSAFNASYTDSGLF.IYT.SQAAAAGDV
Retrocopy AEANAFSVLQHFPGAGPHVKRGSNATSLLYQAVAKGTHQPFDVSAFNASYTDSGLFRIYTTSQAAAAGDV

Parental  IKAAYNQVKTVAQGNLSSADVQAAKNKLKAGYLMSVESSEGFLDEVGSQALIAGSYVPPSTVLQQIDSVA
          IKAAYNQVKTVAQGNLSSADVQAAKNKLKAGYLMSVESSEGFLDEVGSQALI.GS.VPPSTVLQQ.DSVA
Retrocopy IKAAYNQVKTVAQGNLSSADVQAAKNKLKAGYLMSVESSEGFLDEVGSQALITGSCVPPSTVLQQMDSVA

Parental  DADIVNAAKKFVSGQKSMAASGNLGHTPFVDEL
          DADIVNAAKKFVSGQKSMA..GNLGHTPFVDEL
Retrocopy DADIVNAAKKFVSGQKSMAGRGNLGHTPFVDEL

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	6.18 RPM	157.45 RPM
SRP017611_kidney	15.71 RPM	222.27 RPM
SRP017611_liver	2.70 RPM	65.82 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_604 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_604 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_604 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,