RetrogeneDB ID: retro_ocun_1287

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:6777968..6778767(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000002129
• Aliases: None
• Description: None

Sequence

>retro_ocun_1287
TCTAGATGTCAACCAAAAGCCTGTGGCTTGAGACTTATTGAGTCTGCACACAACAGTGATCTCAGATGACTACAAAACTG
AGTGACTTCAAAGTAAAAGATCTTACTCTCAGTTTTTCGGCTTTGACACAAACATTTTCTCTAGCTATGAATTTCCTGGA
CAAATTCCTGTCCAAAATGAAGGTACAGCCCAAGCACCTTGGATGTGTCAGTCTGAGCTGTTTTTATTTTGCTGTAAAAA
TCAGTAGAAGAGGAAAGGAATGTCCCATTGGCAACTGAGTTGATCCGGATAAGTCAGTATATTTTTCATGGTTTCAGGCT
TGATGAGAATGGAAAAGATTGCATTGGAGAAATTGTGTTGGAAAGTCAGAGCTACTAGTATCTTTCAGTTTCTGCAACTC
TTATTCACTCATTTAAGATAACTTGCCATTTGAAAGGGGAAATAGCCTTAATTTTGAAAGACTGGAAGCTCAACTTAAGG
CATGTCACTGCAGGATCATATTTTCTAAAACGAAGCCTCTGTGCTGGCTTTGTCTATCACTGCATTGGAGATCCAAGCAC
AGAAGTATTTAGAGTTAACAGAAGGAATAGAATGACTTCAGAAACATACCAAAATAAATGGCAGAGATTTGACCTTCTAG
CAAGAGCTTGTATTGAAGTGCTTAACTGAGCACTCATCAAACAAGTGTTCGAAACTGAATGTTCGGGAGTTGAAATGGAT
TGTCTGGGCATACTGCATGGCAGTTGAAGCTAGTTACTATAGCATAACTCACCTTCCAACAATTCCTGAAATGGTTCCT

Alignment

ORF - retro_ocun_1287 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.28 %
• Parental protein coverage: 91.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SRCQPKVCGLRLIESAHDNGLR-MTARLRDFEVKDLLSLTQFFGFDTETFSLAVNLLDRFLSKMKVQPKH
          SRCQPK.CGLRLIESAH...LR.MT..L.DF.VKD...LT..F...T.TFSLA.N.LD.FLSKMKVQPKH
Retrocopy SRCQPKACGLRLIESAHNSDLR<MTTKLSDFKVKD---LTLSFSALTQTFSLAMNFLDKFLSKMKVQPKH

Parental  LGCVGLSCFYLAVK-SIEEERNVPLATDLIRISQYRF-TVSDLMRMEKIVLEKVCWKVKATT-AFQFLQL
          LGCV.LSCFY.AVK.S.EEERNVPLAT.LIRISQY.F..VS.LMRMEKI.LEK.CWKV.AT...F.F...
Retrocopy LGCVSLSCFYFAVK>SVEEERNVPLATELIRISQYIF>MVSGLMRMEKIALEKLCWKVRATS>SFSFCNS

Parental  YYSLIQENLPFERRNNLNFERLEAQLKACHCRIIFSKAKP-SVLALSIIALEIQAQQCVELTEGIECLQK
          Y.SLI..NLPFER.N.LNFERLEAQLKACHCRIIFSK.KP.SVLALSI.ALEIQAQ...ELTEGIE.LQK
Retrocopy Y-SLI*DNLPFERGNSLNFERLEAQLKACHCRIIFSKTKP<SVLALSITALEIQAQKYLELTEGIE*LQK

Parental  HSKINGRDLTFWQELVSKCLTEYSSNKCSKPNVQKLKWIVSGRTARQLKHSYYRIAHLPTIPEMVP
          H.KINGRDLTF.QELV.KCLTE.SSNKCSK.NV..LKWIV..........SYY.I.HLPTIPEMVP
Retrocopy HTKINGRDLTF*QELVLKCLTEHSSNKCSKLNVRELKWIV-WAYCMAVEASYYSITHLPTIPEMVP

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	46.58 RPM
SRP017611_kidney	0.00 RPM	72.47 RPM
SRP017611_liver	0.00 RPM	34.38 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1287 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1287 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1287 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006607	2 retrocopies	retro_btau_1064, retro_btau_763,
Canis familiaris	ENSCAFG00000017207	1 retrocopy	retro_cfam_1657,
Callithrix jacchus	ENSCJAG00000015341	1 retrocopy	retro_cjac_2319,
Cavia porcellus	ENSCPOG00000000880	1 retrocopy	retro_cpor_771,
Dasypus novemcinctus	ENSDNOG00000015166	1 retrocopy	retro_dnov_1275,
Dipodomys ordii	ENSDORG00000014293	1 retrocopy	retro_dord_486,
Equus caballus	ENSECAG00000018880	1 retrocopy	retro_ecab_152,
Felis catus	ENSFCAG00000027366	1 retrocopy	retro_fcat_763,
Myotis lucifugus	ENSMLUG00000001667	1 retrocopy	retro_mluc_1341,
Monodelphis domestica	ENSMODG00000007651	1 retrocopy	retro_mdom_1018,
Mus musculus	ENSMUSG00000020326	1 retrocopy	retro_mmus_1534,
Oryctolagus cuniculus	ENSOCUG00000002129	3 retrocopies	retro_ocun_1287 , retro_ocun_512, retro_ocun_615,
Otolemur garnettii	ENSOGAG00000007639	1 retrocopy	retro_ogar_2452,
Pongo abelii	ENSPPYG00000016016	1 retrocopy	retro_pabe_3373,
Pteropus vampyrus	ENSPVAG00000017902	1 retrocopy	retro_pvam_1027,
Sarcophilus harrisii	ENSSHAG00000007465	2 retrocopies	retro_shar_328, retro_shar_490,
Vicugna pacos	ENSVPAG00000008340	1 retrocopy	retro_vpac_351,