RetrogeneDB ID: retro_ocun_516

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:87432963..87433881(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000004833
• Aliases: None
• Description: None

Sequence

>retro_ocun_516
TTTAGGGGAGGAGGAAGGATGCAGAGAGAACGGAGAGGTAAAAATGTGGTTCATCAACTCTCGGTAACCTTAGAAGATTT
ATATAATGGTGCAACAAGGAAACTAGCTCTACAGAAGAATGTGATTTGTGACAAATGTGAAGGCCGAGGCGGTAAGAAAG
GAGCAGTAGAGTGCTGTCCCAATTGCCGAGGTACTGGAATGCAAATAAGGATTCATCAGATAGGACCTGGAATGGTTCAG
CAGATTCAGTCTGTATGCATGGAGTGCCAGGGCCATGGGGAACGCATCAGTCCTAAAGATAGATGTAAAAGCTGCAATGG
AAGGAAAATAGTTCGAGAGAAGAAAATTCTAGAAGTTCATATTGACAAAGGCATGAAAGATGGCCAGAAGATAACATTCC
ATGGTGAAGGAGACCAAGAACCAGGACTGGAGCCAGGAGATATTATCATTGTGTTAGATCAGAAGGACCATGCTGTTTTT
ACCCGACGAGGAGAAGACCTTTTTATGTGTATGGACATACAATTGGTCGAAGCATTATGTGGTTTCCAAAAGCCAATATC
CACTCTTGACAACCGAACCATAGTCATCACCTCTCATCCAGGTCAGATTGTCAAGCATGGAGATATCAAGTGTGTGCTAA
ATGAAGGCATGCCAATTTATCGTAGACCTTATGAAAAGGGTCGCCTAATCATTGAATTCAAGGTAAACTTCCCTGAAAAT
GGCTTTCTCTCTCCTGATAAACTCTCTTTGCTGGAAAAACTTCTCCCTGAGAGGAAGGAAGTAGAAGAGACTGATGAAAT
GGATCAGGTAGAACTCGTGGACTTTGATCCAAATCAGGAAAGACGGCGCCATTATAATGGAGAAGCATACGAGGATGATG
AACATCATCCCAGAGGGGGTGTTCAGTGTCAGACCTCC

Alignment

ORF - retro_ocun_516 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.67 %
• Parental protein coverage: 77.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGRGGKKGAVECCPNCRGTGMQIR
          F.GGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGRGGKKGAVECCPNCRGTGMQIR
Retrocopy FRGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGRGGKKGAVECCPNCRGTGMQIR

Parental  IHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKILEVHIDKGMKDGQKITFHGEGDQE
          IHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKILEVHIDKGMKDGQKITFHGEGDQE
Retrocopy IHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKILEVHIDKGMKDGQKITFHGEGDQE

Parental  PGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLVEALCGFQKPISTLDNRTIVITSHPGQIVKHGDIK
          PGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLVEALCGFQKPISTLDNRTIVITSHPGQIVKHGDIK
Retrocopy PGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLVEALCGFQKPISTLDNRTIVITSHPGQIVKHGDIK

Parental  CVLNEGMPIYRRPYEKGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERKEVEETDEMDQVELVDFDPNQE
          CVLNEGMPIYRRPYEKGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERKEVEETDEMDQVELVDFDPNQE
Retrocopy CVLNEGMPIYRRPYEKGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERKEVEETDEMDQVELVDFDPNQE

Parental  RRRHYNGEAYEDDEHHPRGGVQCQTS
          RRRHYNGEAYEDDEHHPRGGVQCQTS
Retrocopy RRRHYNGEAYEDDEHHPRGGVQCQTS

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	3.31 RPM	65.12 RPM
SRP017611_kidney	1.42 RPM	31.62 RPM
SRP017611_liver	1.70 RPM	30.75 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_516 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_516 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_516 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 118 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007589	4 retrocopies	retro_amel_1509, retro_amel_455, retro_amel_756, retro_amel_946,
Bos taurus	ENSBTAG00000016265	6 retrocopies	retro_btau_1440, retro_btau_1599, retro_btau_1800, retro_btau_1826, retro_btau_574, retro_btau_828,
Canis familiaris	ENSCAFG00000001818	23 retrocopies	retro_cfam_1111, retro_cfam_1153, retro_cfam_1218, retro_cfam_1229, retro_cfam_1315, retro_cfam_1352, retro_cfam_1420, retro_cfam_1457, retro_cfam_1520, retro_cfam_1668, retro_cfam_1833, retro_cfam_1941, retro_cfam_1949, retro_cfam_1994, retro_cfam_2004, retro_cfam_2162, retro_cfam_352, retro_cfam_391, retro_cfam_419, retro_cfam_749, retro_cfam_751, retro_cfam_923, retro_cfam_993,
Choloepus hoffmanni	ENSCHOG00000000631	9 retrocopies	retro_chof_1760, retro_chof_186, retro_chof_2020, retro_chof_2541, retro_chof_2694, retro_chof_287, retro_chof_417, retro_chof_498, retro_chof_946,
Dasypus novemcinctus	ENSDNOG00000018342	3 retrocopies	retro_dnov_1139, retro_dnov_640, retro_dnov_884,
Felis catus	ENSFCAG00000008729	5 retrocopies	retro_fcat_1241, retro_fcat_1407, retro_fcat_1502, retro_fcat_1984, retro_fcat_811,
Homo sapiens	ENSG00000086061	4 retrocopies	retro_hsap_2331, retro_hsap_2569, retro_hsap_3647, retro_hsap_4889,
Gorilla gorilla	ENSGGOG00000007030	3 retrocopies	retro_ggor_1603, retro_ggor_2463, retro_ggor_418,
Loxodonta africana	ENSLAFG00000001527	2 retrocopies	retro_lafr_1019, retro_lafr_936,
Macaca mulatta	ENSMMUG00000007740	6 retrocopies	retro_mmul_1313, retro_mmul_1802, retro_mmul_2477, retro_mmul_2482, retro_mmul_2625, retro_mmul_400,
Monodelphis domestica	ENSMODG00000003384	7 retrocopies	retro_mdom_1140, retro_mdom_1253, retro_mdom_1451, retro_mdom_1627, retro_mdom_1824, retro_mdom_742, retro_mdom_874,
Nomascus leucogenys	ENSNLEG00000005268	4 retrocopies	retro_nleu_1255, retro_nleu_2550, retro_nleu_2793, retro_nleu_509,
Oryctolagus cuniculus	ENSOCUG00000004833	2 retrocopies	retro_ocun_516 , retro_ocun_70,
Oryctolagus cuniculus	ENSOCUG00000004839	1 retrocopy	retro_ocun_1126,
Pongo abelii	ENSPPYG00000019141	4 retrocopies	retro_pabe_1892, retro_pabe_2111, retro_pabe_2559, retro_pabe_2994,
Pan troglodytes	ENSPTRG00000020852	4 retrocopies	retro_ptro_1499, retro_ptro_1705, retro_ptro_177, retro_ptro_2472,
Sarcophilus harrisii	ENSSHAG00000012366	1 retrocopy	retro_shar_762,
Sus scrofa	ENSSSCG00000011000	2 retrocopies	retro_sscr_134, retro_sscr_984,
Tupaia belangeri	ENSTBEG00000000596	23 retrocopies	retro_tbel_1281, retro_tbel_134, retro_tbel_1529, retro_tbel_1542, retro_tbel_2260, retro_tbel_2293, retro_tbel_2316, retro_tbel_2428, retro_tbel_2445, retro_tbel_2917, retro_tbel_2965, retro_tbel_2972, retro_tbel_329, retro_tbel_3345, retro_tbel_3353, retro_tbel_3692, retro_tbel_4014, retro_tbel_4223, retro_tbel_432, retro_tbel_591, retro_tbel_617, retro_tbel_634, retro_tbel_842,
Tursiops truncatus	ENSTTRG00000007387	4 retrocopies	retro_ttru_1181, retro_ttru_1551, retro_ttru_567, retro_ttru_783,
Vicugna pacos	ENSVPAG00000001299	1 retrocopy	retro_vpac_367,