RetrogeneDB ID: retro_ocun_1058

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:99668536..99668930(+)
• Located in intron of: ENSOCUG00000029173

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2D4
• Ensembl ID: ENSOCUG00000008900
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2D 4 (putative) [Source:HGNC Symbol;Acc:21647]

Sequence

>retro_ocun_1058
GAACTGACTGACTTACAGAGGGCTCCTGCCCAGTGCTCCATAGTGAGTAATGATTTGTTCCATGGGCAGGCCACCATCAT
GGGCCTCCCTTACCAAGGAGGGGTTTTCTTCCTGACCATCCACTTTCTTACTAATGACCCTTCAAGCCCCCAAAGGTTGC
TCTCACAACCGAAATGCATCATTACAATGTCAACTGCAATGACAGCATCTGCCTCCACATCCTACAATCACAATGGTCCC
CAGAGCTGTGTCCAAAGTCCTCTTGTCCATCTGCTGCTTGCTCTTCAACCCCAATCCTGATGACTCTCTGGTGTCAGAGA
TAGCCCACATCTACAAGGCTGTCAGAGAGATGTACAGCAGACTAGCAAGAGAGTAGACACAGAAATATGCTATC

Alignment

ORF - retro_ocun_1058 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.25 %
• Parental protein coverage: 93.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELTDLQRDPPAQCSAGPVGDDLFHWQATIMGPTDSPYQGGLFFLTIHFPTDY-PFKPPKVAFTTKIYHPN
          ELTDLQR..PAQCS...V..DLFH.QATIMG....PYQGG.FFLTIHF.T...PFKPPKVA.TT...H.N
Retrocopy ELTDLQR-APAQCSI--VSNDLFHGQATIMG---LPYQGGVFFLTIHFLTND<PFKPPKVALTTEMHHYN

Parental  INSNGSICLDILRSQWSPALTVSK-VLLSICSLLCDPNPDDPLVPEIAHTYKADREKYNRLAREWTQKYA
          .N.N.SICL.IL.SQWSP.L......L...C.L...PNPDD.LV.EIAH.YKA.RE.Y.RLARE.TQKYA
Retrocopy VNCNDSICLHILQSQWSPELCPKS<LLSICCLLF-NPNPDDSLVSEIAHIYKAVREMYSRLARE*TQKYA

Parental  L
          .
Retrocopy I

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	0.22 RPM	38.19 RPM
SRP017611_kidney	0.00 RPM	14.60 RPM
SRP017611_liver	0.00 RPM	7.25 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1058 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1058 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1058 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003997	1 retrocopy	retro_btau_1261,
Callithrix jacchus	ENSCJAG00000007875	4 retrocopies	retro_cjac_1660, retro_cjac_3666, retro_cjac_3882, retro_cjac_925,
Dipodomys ordii	ENSDORG00000006888	5 retrocopies	retro_dord_104, retro_dord_345, retro_dord_408, retro_dord_743, retro_dord_760,
Homo sapiens	ENSG00000078967	2 retrocopies	retro_hsap_452, retro_hsap_453,
Gorilla gorilla	ENSGGOG00000003378	3 retrocopies	retro_ggor_1843, retro_ggor_2936, retro_ggor_436,
Myotis lucifugus	ENSMLUG00000011919	3 retrocopies	retro_mluc_1826, retro_mluc_1827, retro_mluc_594,
Macaca mulatta	ENSMMUG00000002410	5 retrocopies	retro_mmul_1067, retro_mmul_1937, retro_mmul_2514, retro_mmul_2515, retro_mmul_531,
Nomascus leucogenys	ENSNLEG00000003364	3 retrocopies	retro_nleu_54, retro_nleu_876, retro_nleu_90,
Oryctolagus cuniculus	ENSOCUG00000002610	3 retrocopies	retro_ocun_826, retro_ocun_932, retro_ocun_937,
Oryctolagus cuniculus	ENSOCUG00000006026	2 retrocopies	retro_ocun_134, retro_ocun_243,
Oryctolagus cuniculus	ENSOCUG00000008900	1 retrocopy	retro_ocun_1058 ,
Oryctolagus cuniculus	ENSOCUG00000029448	10 retrocopies	retro_ocun_1220, retro_ocun_1426, retro_ocun_1536, retro_ocun_1660, retro_ocun_1856, retro_ocun_1941, retro_ocun_261, retro_ocun_467, retro_ocun_887, retro_ocun_988,
Pongo abelii	ENSPPYG00000029727	1 retrocopy	retro_pabe_3573,
Sus scrofa	ENSSSCG00000016722	2 retrocopies	retro_sscr_671, retro_sscr_79,
Tupaia belangeri	ENSTBEG00000003691	9 retrocopies	retro_tbel_1273, retro_tbel_2535, retro_tbel_2782, retro_tbel_307, retro_tbel_367, retro_tbel_37, retro_tbel_4118, retro_tbel_4163, retro_tbel_4312,
Tarsius syrichta	ENSTSYG00000000595	14 retrocopies	retro_tsyr_1007, retro_tsyr_1145, retro_tsyr_1162, retro_tsyr_1314, retro_tsyr_1392, retro_tsyr_1415, retro_tsyr_1677, retro_tsyr_1694, retro_tsyr_1859, retro_tsyr_683, retro_tsyr_789, retro_tsyr_836, retro_tsyr_838, retro_tsyr_919,