RetrogeneDB ID: retro_ocun_1931

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:59000369..59000874(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: M6PR
• Ensembl ID: ENSOCUG00000017823
• Aliases: None
• Description: mannose-6-phosphate receptor (cation dependent) [Source:HGNC Symbol;Acc:6752]

Sequence

>retro_ocun_1931
CTCAATCAGACTCACATCTTCAATGGAAGTCATTTGGATCCTGCTGTTCTATAAAGGAGGTGATGAATGTGGCAATCACT
GTAGAAAGGAAAAATGTTGCACAAAAATGATAATCTTCTAATATCTACATATTCTAATAGACAATTTTAACCCTATGTCT
GAGGAGCGAGATGATTGCTTTCTACCTCTCTGAGATGGATAACAGCCTGGCTTATTCCCCCAGAGATCTCCAACATCAGG
GTAAGCTCTTTCTCAACACATTTGCATCAGTGGTTATTCTCTATGTCATCAGGAGGATCTTCTACCAGCAACCAATCATG
GGAGCCAAGATAATGGAGCAGCTTCGCTGCTACTCTTCTAGCAGTATCTTGGCAATGTGGTAGTAGATGGTAGTGATTTT
GTGTGTCGTTTAAAACCCCAAAATACACCTGTTGCATATCACAGTGTGGTGGATGATACGCTTTGGGAGGAGTCAAAATA
AAAGGGTGATGATTTATTACCAATA

Alignment

ORF - retro_ocun_1931 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.41 %
• Parental protein coverage: 61.87 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LNETHIFNGSD-WIMLIYKGGDEYDRHCGKEQRRAVVMISCNRHTLADNFNPVSEERGKVQDCF-YLFEL
          LN.THIFNGS..WI.L.YKGGDE...HC.KE.......I....H.L.DNFNP.SEER....DCF.YL.E.
Retrocopy LNQTHIFNGSH>WILLFYKGGDECGNHCRKEKCCTKMIIF*YLHILIDNFNPMSEER---DDCF>YLSEM

Parental  DSSLACPP-EVSHLSVGSVLLVTFASLVTVYIIGGFLYQRLVVGAKGMEQF-PHLAFWQDLGNLVADGCD
          D.SLA..P....H...G...L.TFAS.V..Y.I....YQ....GAK.MEQ....L.F.Q.LGN.V.DG.D
Retrocopy DNSLAYSPRDLQHQ--GKLFLNTFASVVILYVIRRIFYQQPIMGAKIMEQL<SLLLF*QYLGNVVVDGSD

Parental  FVCRSKPRNVPAAYRGVGDDQLGEESEERDDHLLPM
          FVCR.KP.N.P.AY..V.DD.L.EES....D.LLP.
Retrocopy FVCRLKPQNTPVAYHSVVDDTLWEESK*KGDDLLPI

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	46.80 RPM
SRP017611_kidney	0.00 RPM	94.77 RPM
SRP017611_liver	0.00 RPM	40.62 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1931 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1931 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1931 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000003538	1 retrocopy	retro_dnov_2250,
Mus musculus	ENSMUSG00000007458	1 retrocopy	retro_mmus_2192,
Oryctolagus cuniculus	ENSOCUG00000017823	1 retrocopy	retro_ocun_1931 ,
Otolemur garnettii	ENSOGAG00000005610	1 retrocopy	retro_ogar_629,
Tarsius syrichta	ENSTSYG00000005689	2 retrocopies	retro_tsyr_1665, retro_tsyr_882,