RetrogeneDB ID: retro_ocun_1905

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:94520164..94520692(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT4
• Ensembl ID: ENSOCUG00000011283
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 4 [Source:HGNC Symbol;Acc:8051]

Sequence

>retro_ocun_1905
ATGATGAAGTTCAAGCCCAACCAGACGCGGACCTATGACCGCGAGGGCTTCAAGAAGCGGGCGGCGTGCCTGTGCTTCCG
GAGCGAGCAGGAGGACGAGGTGCTGTTGGTGAGCAGCAGTCGCTACCCAGACCAATGGATTGTCCCAGGTGGAGGAATGC
AGCCGGAGGAGGAGCCTGGTGGTGCTGCCGTGAGGGAGGCAGGAGTCAAAGGAAAATTAGGCAGACTCCTAGGCATATTT
GAGAACCAAGACTGAAAGCACAGAACATATGTTTATGTTCTTACAGTCACTGAAATACTAGAAGACTGGGAAGATTCTGT
TAATATAGGAAGGAAGAGAGAGTGGTTCAAAGTAGAAGATGCAATCAAAGTTCTCCAGTGTCATAAACCTGTTCATGCAG
AGGATCTGGAAAAACTCAAGCTGGGTTGTTCCCCATCCAATGGAAATTCTGCGGTCCCTTCCCTTCCAGATAATAACACC
TTGTTTGTAAATGCTGCACAGACCTCTGGGGTGCCATCTTGTATAAGA

Alignment

ORF - retro_ocun_1905 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMKFKPNQTRTYDREGFKKRAACLCFRSEQEDEVLLVSSSRYPDQWIVPGGGMEPEEEPGGAAVREVYEE
          MMKFKPNQTRTYDREGFKKRAACLCFRSEQEDEVLLVSSSRYPDQWIVPGGGM.PEEEPGGAAVR....E
Retrocopy MMKFKPNQTRTYDREGFKKRAACLCFRSEQEDEVLLVSSSRYPDQWIVPGGGMQPEEEPGGAAVR----E

Parental  AGVKGKLGRLLGIFEQNQDRKHRTYVYVLTVTEILEDWEDSVNIGRKREWFKVEDAIKVLQCHKPVHAEY
          AGVKGKLGRLLGIFE.NQD.KHRTYVYVLTVTEILEDWEDSVNIGRKREWFKVEDAIKVLQCHKPVHAE.
Retrocopy AGVKGKLGRLLGIFE-NQD*KHRTYVYVLTVTEILEDWEDSVNIGRKREWFKVEDAIKVLQCHKPVHAED

Parental  LEKLKLGCSPSNGNSAVPSLPDNNTLFVNAAQTSGVPSGIR
          LEKLKLGCSPSNGNSAVPSLPDNNTLFVNAAQTSGVPS.IR
Retrocopy LEKLKLGCSPSNGNSAVPSLPDNNTLFVNAAQTSGVPSCIR

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	0.11 RPM	26.55 RPM
SRP017611_kidney	0.81 RPM	43.89 RPM
SRP017611_liver	0.08 RPM	5.47 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1905 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1905 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1905 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009844	2 retrocopies	retro_amel_1401, retro_amel_36,
Dasypus novemcinctus	ENSDNOG00000015207	3 retrocopies	retro_dnov_1906, retro_dnov_2555, retro_dnov_41,
Dipodomys ordii	ENSDORG00000000647	3 retrocopies	retro_dord_26, retro_dord_272, retro_dord_660,
Equus caballus	ENSECAG00000019319	1 retrocopy	retro_ecab_472,
Echinops telfairi	ENSETEG00000013922	2 retrocopies	retro_etel_1627, retro_etel_2111,
	ENSG00000173598	0 retrocopies
Gorilla gorilla	ENSGGOG00000014324	1 retrocopy	retro_ggor_108,
Loxodonta africana	ENSLAFG00000013776	1 retrocopy	retro_lafr_1131,
Microcebus murinus	ENSMICG00000007100	2 retrocopies	retro_mmur_1521, retro_mmur_1565,
Myotis lucifugus	ENSMLUG00000002767	1 retrocopy	retro_mluc_753,
Monodelphis domestica	ENSMODG00000009468	1 retrocopy	retro_mdom_214,
Mus musculus	ENSMUSG00000020029	3 retrocopies	retro_mmus_1201, retro_mmus_1202, retro_mmus_1203,
Oryctolagus cuniculus	ENSOCUG00000011283	1 retrocopy	retro_ocun_1905 ,
Pteropus vampyrus	ENSPVAG00000013730	1 retrocopy	retro_pvam_1423,
Ictidomys tridecemlineatus	ENSSTOG00000020306	1 retrocopy	retro_itri_112,
Tupaia belangeri	ENSTBEG00000012198	7 retrocopies	retro_tbel_1705, retro_tbel_2322, retro_tbel_3443, retro_tbel_3472, retro_tbel_3733, retro_tbel_3739, retro_tbel_4678,
Tursiops truncatus	ENSTTRG00000003309	2 retrocopies	retro_ttru_1625, retro_ttru_1925,
Vicugna pacos	ENSVPAG00000002957	1 retrocopy	retro_vpac_507,