RetrogeneDB ID: retro_ocun_685

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:7255676..7256120(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLLP
• Ensembl ID: ENSOCUG00000007353
• Aliases: None
• Description: plasmolipin [Source:HGNC Symbol;Acc:18553]

Sequence

>retro_ocun_685
AATCTGAGCTTCCCAAGCTGCAGCCTGGGCGAACTCATGCTGCCGTGGCTGGTGCGGGAGCCGCTGCCGTGGACCCACAT
TTCCAGAACCCAGTGCACCCATTCCCAGCCTATGGCTGAGTGATAGTTGTGGCTGTCTTGCTCTGGCTGCTGACAATCAC
GTTCCTCTTCCACGTGTTTCAGCTGCATGTGAAATGGTCCATGGTGCCCTGAGCACTGGTGTTGATCTTTAATGTCAGTG
TCACCATGCCCTACATCAACACCTTTGTCACCTTTTCTGTTGCAGTCGGACTGACATCCCTGAGGGGACACATGTTTATT
ATCTGCGTGCTGCTGCCTCCTTCTTTGCTTGTTTAGTCATGAGTGCCAATGGGTGAGTGTTGTTTTCGGCTTCCAGGCCT
GGTGACGAGTGGGCAGCAATGTGGTCACCAGTCAGGTGGAGGGA

Alignment

ORF - retro_ocun_685 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.55 %
• Parental protein coverage: 82.97 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DLGFVRSTVGALMLLQLVLGLLVWALIADT-PYHLYPAYGWVMFVAVFLWLVTIVFFIFYLLQLHQKWYT
          .L.F.....G.LML..LV...L.W..I..T.P.H..PAYG.V..VAV.LWL.TI.F..F...QLH.KW..
Retrocopy NLSFPSCSLGELMLPWLVREPLPWTHISRT<PVHPFPAYG*VIVVAVLLWLLTITF-LFHVFQLHVKWSM

Parental  VPWPLVLMVFNASATVLYITAFITCSAVVDLTSLKG-SRPYNQRAAASFFACLVMIAYG-VSTFFSFQAW
          VP..LVL..FN.S.T..YI..F.T.S..V.LTSL.G....Y..RAAASFFACLVM.A.G.VS..F.FQAW
Retrocopy VP*ALVL-IFNVSVTMPYINTFVTFSVAVGLTSLRG<THVYYLRAAASFFACLVMSANG<VSVVFGFQAW

Parental  RGVGSNAATSQMAG
          ..VGSN..TSQ..G
Retrocopy *RVGSNVVTSQVEG

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	48.51 RPM
SRP017611_kidney	0.00 RPM	93.25 RPM
SRP017611_liver	0.00 RPM	10.33 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_685 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_685 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_685 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012103	1 retrocopy	retro_cjac_4155,
Homo sapiens	ENSG00000102934	1 retrocopy	retro_hsap_4816,
Loxodonta africana	ENSLAFG00000008636	1 retrocopy	retro_lafr_145,
Macaca mulatta	ENSMMUG00000008924	1 retrocopy	retro_mmul_2569,
Nomascus leucogenys	ENSNLEG00000002825	1 retrocopy	retro_nleu_2191,
Oryctolagus cuniculus	ENSOCUG00000007353	1 retrocopy	retro_ocun_685 ,
Pongo abelii	ENSPPYG00000007385	1 retrocopy	retro_pabe_3744,
Pan troglodytes	ENSPTRG00000008151	1 retrocopy	retro_ptro_3205,