RetrogeneDB ID: retro_ocun_1529

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: AAGW02077833:361..940(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPD1L
• Ensembl ID: ENSOCUG00000010093
• Aliases: None
• Description: glycerol-3-phosphate dehydrogenase 1-like [Source:HGNC Symbol;Acc:28956]

Sequence

>retro_ocun_1529
GACATTGACATTAGTATGCTGATGAGTGCCAACACTGCCAGCAAAGTGGCTACAGAGTTCTGTGAAACCACTATCAGCAG
CTAAGTGACAGAGAATGGCCTTTTTTTCAAAGAACTTTTGCAGACTCCAATTCTTTAATGACTGTGGTTGCTGATGCAAA
CACTGTTGGACTTTGTGGTACTCTTAAAAACATCATGGCCTTAGGAACTGGGTTCTGTGACTACCTCTGCTGTGGTGACA
ACATTAAAGCTGCCATCATCCACATGTGCCTCATGGAAATATTTGCTTTTTCCAGGATCTCTGCTAGGGTCAGGAGTCCA
CAGTCACTGTCCTAGAGAGCTGCCAGGTGGCTAACCTGATTGTCACCTGCTACACAGGGTGGAACCACAGGTGACCAAGG
CATTTGCCAGAACTAGGAAGACCACTGAAGAATTGGAGGAGATGCTGAATGGGTAGAAGTCTCAAGGACCTCAGACTTCT
GAAGTGTATCACATCCTCAAACAGAAAGAACCAGCTGACAAGTTTCCATCTGCAGTATATCAGATCTGTGAAGGCAGACT
CTTCCTAGAGATGTCGTCT

Alignment

ORF - retro_ocun_1529 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.1 %
• Parental protein coverage: 59.88 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EVPLSALGSKPKAAKLSERRFNHLSTGSKVMENGLLFKELLQTP-NFRITVVDDADTVELCGALKNIVAV
          ....S.L.S...A.K.....F......S.V.ENGL.FKELLQTP.N...TVV.DA.TV.LCG.LKNI.A.
Retrocopy DIDISMLMSANTASKVATE-FCETTISS*VTENGLFFKELLQTP<NSLMTVVADANTVGLCGTLKNIMAL

Parental  GAGFCDGLRCGDNTKAAVIRLGLMEMIAFAKI-FCRGQVSTATFLESCGVADLITTCYGGRNRR-VAEAF
          G.GFCD.L.CGDN.KAA.I...LME..AF..I..C.GQ.ST.T.LESC.VA.LI.TCY.G.N.R.V..AF
Retrocopy GTGFCDYLCCGDNIKAAIIHMCLMEIFAFSRI<LC*GQESTVTVLESCQVANLIVTCYTGWNHR<VTKAF

Parental  ARTGKTIEELEKEMLNGQKLQGPQTSAEVYRILSQKGLTDRFPLFTAVYQICYEGRPVQEMLS
          ART.KT.EELE.EMLNG.K.QGPQTS.EVY.IL.QK...D.FP...AVYQIC.EGR...EM.S
Retrocopy ARTRKTTEELE-EMLNG*KSQGPQTS-EVYHILKQKEPADKFP--SAVYQIC-EGRLFLEMSS

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	0.61 RPM	94.32 RPM
SRP017611_kidney	0.41 RPM	57.98 RPM
SRP017611_liver	0.23 RPM	8.25 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1529 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1529 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1529 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009826	1 retrocopy	retro_btau_1671,
Choloepus hoffmanni	ENSCHOG00000012633	5 retrocopies	retro_chof_1033, retro_chof_306, retro_chof_340, retro_chof_620, retro_chof_724,
Loxodonta africana	ENSLAFG00000013996	1 retrocopy	retro_lafr_101,
Microcebus murinus	ENSMICG00000011060	1 retrocopy	retro_mmur_1205,
Mus musculus	ENSMUSG00000050627	3 retrocopies	retro_mmus_1348, retro_mmus_2552, retro_mmus_3695,
Oryctolagus cuniculus	ENSOCUG00000010093	2 retrocopies	retro_ocun_1529 , retro_ocun_1588,
Otolemur garnettii	ENSOGAG00000013243	1 retrocopy	retro_ogar_285,
Procavia capensis	ENSPCAG00000016132	1 retrocopy	retro_pcap_316,
Rattus norvegicus	ENSRNOG00000026455	2 retrocopies	retro_rnor_2035, retro_rnor_2474,
Sus scrofa	ENSSSCG00000021977	1 retrocopy	retro_sscr_154,