RetrogeneDB ID: retro_ocun_301

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:122922652..122923167(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000000270
• Aliases: None
• Description: None

Sequence

>retro_ocun_301
AATTTAACGAGGTATTAAATGAATAATGGCAGTCTTCTCACAGAAGGGGCAGCACATGCATTTTCCCTGTACAACATGGA
TCAGTTCACACCTGTGAAGATAGAAGGATATGAAGATCAGTTCTCAATTACAGAGCACAGTGACATGGGTAAAAGCAGGT
TTTTAGATCCAAGAAACAAAATTTCATTAAGTTTGATCACTTACAGAAAAAAAGCAAGTGATCCCCAGCCAGAAGAAATA
GATGAAAGCTTGAAGTCTTGGAGAGAATCTTCTGACAGTGCTTTATGAGCTTATGTGAAAGATCACTATTCCAACAGCTT
CTATACTGTGTTTGCTACAACTACAGACAGGCAACAGATTTTTATTACATGTATTGAAAGCCATCAGTTTCAATTGAAAA
ACTTCTGGAGTGGTAATTGAGGATCAGAGCATAAATTCACCACCACACCACCTATAGCCAAGTGGTTGGAGTGTTTAAGA
TTCAGGTTCTCTAGTCTGAAGATGATAATGTTCAA

Alignment

ORF - retro_ocun_301 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.73 %
• Parental protein coverage: 60.28 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NDVRLLLNNDNLLREGAAHAFAQYNMDQFTPVKIEGYEDQVLITEHGDLGNSRFLDPRNKIS-FKFDHL-
          N..R...NN..LL.EGAAHAF..YNMDQFTPVKIEGYEDQ..ITEH.D.G.SRFLDPRNKIS..KFDHL.
Retrocopy NLTRY*MNNGSLLTEGAAHAFSLYNMDQFTPVKIEGYEDQFSITEHSDMGKSRFLDPRNKIS<IKFDHL>

Parental  RKEASDPQPEEVDGGLKSWRESCDSALRAYVKDHYSNGFCTVVYAKTIDGQQTIIACIESHQFQPKNFWN
          RK.ASDPQPEE.D..LKSWRES.DSAL.AYVKDHYSN.F.T.V.A.T.D.QQ..I.CIESHQFQ.KNFW.
Retrocopy RKKASDPQPEEIDESLKSWRESSDSAL*AYVKDHYSNSFYT-VFATTTDRQQIFITCIESHQFQLKNFWS

Parental  GRWRSEWKFTITPPTA-QVVGVLKIQVHYYEDGNVQ
          G...SE.KFT.TPP.A.QVVGV.KIQV...ED.NVQ
Retrocopy GN*GSEHKFTTTPPIA<QVVGVFKIQVL*SEDDNVQ

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	20.70 RPM
SRP017611_kidney	0.00 RPM	21.99 RPM
SRP017611_liver	0.00 RPM	13.72 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_301 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_301 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_301 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003570	1 retrocopy	retro_amel_219,
Choloepus hoffmanni	ENSCHOG00000004131	8 retrocopies	retro_chof_1008, retro_chof_1419, retro_chof_1499, retro_chof_1704, retro_chof_1861, retro_chof_2129, retro_chof_625, retro_chof_711,
Callithrix jacchus	ENSCJAG00000013548	3 retrocopies	retro_cjac_2259, retro_cjac_2850, retro_cjac_4125,
Cavia porcellus	ENSCPOG00000014532	1 retrocopy	retro_cpor_1155,
Dipodomys ordii	ENSDORG00000000671	3 retrocopies	retro_dord_224, retro_dord_265, retro_dord_44,
Felis catus	ENSFCAG00000013303	2 retrocopies	retro_fcat_700, retro_fcat_746,
Homo sapiens	ENSG00000116489	2 retrocopies	retro_hsap_2338, retro_hsap_4871,
Gorilla gorilla	ENSGGOG00000023677	1 retrocopy	retro_ggor_1216,
Latimeria chalumnae	ENSLACG00000017963	1 retrocopy	retro_lcha_20,
Myotis lucifugus	ENSMLUG00000009796	1 retrocopy	retro_mluc_2483,
Macaca mulatta	ENSMMUG00000015668	2 retrocopies	retro_mmul_2612, retro_mmul_942,
Mustela putorius furo	ENSMPUG00000004977	1 retrocopy	retro_mputfur_616,
Mus musculus	ENSMUSG00000070372	4 retrocopies	retro_mmus_179, retro_mmus_1828, retro_mmus_3370, retro_mmus_349,
Nomascus leucogenys	ENSNLEG00000004191	1 retrocopy	retro_nleu_1689,
Oryctolagus cuniculus	ENSOCUG00000000270	6 retrocopies	retro_ocun_1315, retro_ocun_1417, retro_ocun_1787, retro_ocun_301 , retro_ocun_527, retro_ocun_555,
Oryctolagus cuniculus	ENSOCUG00000003591	2 retrocopies	retro_ocun_1531, retro_ocun_873,
Otolemur garnettii	ENSOGAG00000014074	4 retrocopies	retro_ogar_1640, retro_ogar_2159, retro_ogar_3217, retro_ogar_845,
Pongo abelii	ENSPPYG00000001021	2 retrocopies	retro_pabe_2116, retro_pabe_3789,
Pan troglodytes	ENSPTRG00000001110	2 retrocopies	retro_ptro_1710, retro_ptro_3245,
Rattus norvegicus	ENSRNOG00000013538	1 retrocopy	retro_rnor_77,
Sorex araneus	ENSSARG00000001278	1 retrocopy	retro_sara_166,
Ictidomys tridecemlineatus	ENSSTOG00000015956	1 retrocopy	retro_itri_1044,
Tupaia belangeri	ENSTBEG00000001727	5 retrocopies	retro_tbel_1870, retro_tbel_3525, retro_tbel_4327, retro_tbel_638, retro_tbel_868,
Tarsius syrichta	ENSTSYG00000006259	2 retrocopies	retro_tsyr_179, retro_tsyr_471,
Vicugna pacos	ENSVPAG00000005361	1 retrocopy	retro_vpac_579,