RetrogeneDB ID: retro_ocun_1317

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:107004688..107005426(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000021848
• Aliases: None
• Description: None

Sequence

>retro_ocun_1317
CTTGGCCAGAGACGTGATCAAGAGGGACTTCCTGGGATGGGATGCCGGAAGCAGCAATTTCACAAGGAGTGAGAGCAGCC
ATCCAGATTTACATGGTTTTGGTCCTTTAAGTACAAGTATACCATGTGCTGTAAGGCATCATTGAGATGGCGAAGCAGCA
GCAAGACCAAGTAGCCCAAAACATCAAGGAAGGTCCTGAGAAGATGGAGACAGAGATGGAGATGGATGCTGCTCTCCGTG
AGTACCAGCTCATGCTAATGAGGCAGGATTTCATGAAGCTCCAAGACCTTTGGAGAATGGAAGAGCTGCGCAAACAAAAG
GTGCAAAAGCGAAAGTAACTGGAGCTCAGGCAGGAAGAGGAGGGCAATTGCCATGAGGAAGAGATGTAGAGGTAGCAGGA
AGAAATGATTCAGCAACAGCAAGAAGGATGCGTGGGAACCTTTCCTGATGAGAGTAGACAGGAGATACAGATGGGCCATA
TGGCCGTGGGAGATGTTATCAGCCTGAACAGCATAGGTGCCATGCTTGCCCACCCCACTGCCCCCACCGACTCCTGTGCC
AGCTGTTACCCCAGCACCTCCAAGATCTGCCACTATGATGCTGGACAGGACCTTGGGATTGACCCCACCAATGACCGAGT
TATTTGGCCAAGCTGCTACAATGGAAGGAATTAGCAAAACTGGTGGAACCCCTCCTGCATTCAGCCATTCAGCCCCTAGA
GCTGAATTTGTTCCAAAC

Alignment

ORF - retro_ocun_1317 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.8 %
• Parental protein coverage: 50.42 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGSFEYEYAMRWKA-LIEMEKQQQDQVDRNIKEAREK
          ..Q..D.EGLP.......QQFHKE.EQP.RF....SF.Y.Y.M..KA..IEM.KQQQDQV..NIKE..EK
Retrocopy LGQRRDQEGLPG-MGCRKQQFHKE*EQPSRFTWFWSFKYKYTMCCKA<IIEMAKQQQDQVAQNIKEGPEK

Parental  LE--MEMEAARHEHQVMLMRQDLMRRQEELRRMEELHNQEVQKRKQLELRQEEERRRREEEMRRQQEEMM
          .E..MEM.AA..E.Q.MLMRQD.M..Q..L.RMEEL..Q.VQKRK.LELRQEEE....EEEM.R.QEEM.
Retrocopy METEMEMDAALREYQLMLMRQDFMKLQD-LWRMEELRKQKVQKRK*LELRQEEEGNCHEEEM*R*QEEMI

Parental  RRQQEGFKGTFPDAREQEIRMGQMAMGGAMGINNRGAM-PPAPVPAGTPAP---PGP---ATMMPDGTLG
          ..QQEG..GTFPD...QEI.MG.MA.G.....N..GAM..P.P.P..TP.P...P.P...ATMM.D.TLG
Retrocopy QQQQEGCVGTFPDESRQEIQMGHMAVGDVISLNSIGAM>LPTPLPPPTPVPAVTPAPPRSATMMLDRTLG

Parental  LTPPTTERFGQAATMEGIGAIGGTPPAFNRAAPGAEFAPN
          LTPP.TE.FGQAATMEGI...GGTPPAF...AP.AEF.PN
Retrocopy LTPPMTELFGQAATMEGISKTGGTPPAFSHSAPRAEFVPN

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	42.44 RPM
SRP017611_kidney	0.00 RPM	41.66 RPM
SRP017611_liver	0.00 RPM	29.67 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1317 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1317 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1317 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016057	2 retrocopies	retro_amel_1438, retro_amel_795,
Bos taurus	ENSBTAG00000012152	2 retrocopies	retro_btau_1027, retro_btau_313,
Canis familiaris	ENSCAFG00000017071	1 retrocopy	retro_cfam_98,
Callithrix jacchus	ENSCJAG00000036744	1 retrocopy	retro_cjac_3990,
Equus caballus	ENSECAG00000008502	2 retrocopies	retro_ecab_357, retro_ecab_427,
Felis catus	ENSFCAG00000014807	2 retrocopies	retro_fcat_1219, retro_fcat_147,
Homo sapiens	ENSG00000147140	1 retrocopy	retro_hsap_1699,
Gorilla gorilla	ENSGGOG00000006194	1 retrocopy	retro_ggor_1273,
Microcebus murinus	ENSMICG00000000232	1 retrocopy	retro_mmur_569,
Myotis lucifugus	ENSMLUG00000002489	1 retrocopy	retro_mluc_622,
Mustela putorius furo	ENSMPUG00000004937	1 retrocopy	retro_mputfur_937,
Mus musculus	ENSMUSG00000031311	2 retrocopies	retro_mmus_3652, retro_mmus_632,
Nomascus leucogenys	ENSNLEG00000001278	1 retrocopy	retro_nleu_1344,
Oryctolagus cuniculus	ENSOCUG00000001877	1 retrocopy	retro_ocun_1834,
Oryctolagus cuniculus	ENSOCUG00000021848	2 retrocopies	retro_ocun_1317 , retro_ocun_1804,
Otolemur garnettii	ENSOGAG00000004834	3 retrocopies	retro_ogar_1525, retro_ogar_546, retro_ogar_593,
Pongo abelii	ENSPPYG00000020451	1 retrocopy	retro_pabe_1398,
Pan troglodytes	ENSPTRG00000022010	1 retrocopy	retro_ptro_1150,
Pteropus vampyrus	ENSPVAG00000016503	1 retrocopy	retro_pvam_444,
Rattus norvegicus	ENSRNOG00000003689	2 retrocopies	retro_rnor_1178, retro_rnor_1503,
Sorex araneus	ENSSARG00000007959	2 retrocopies	retro_sara_661, retro_sara_663,
Drosophila melanogaster	FBgn0004227	1 retrocopy	retro_dmel_11,