RetrogeneDB ID: retro_ocun_782

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:152558518..152559084(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARMC1
• Ensembl ID: ENSOCUG00000000392
• Aliases: None
• Description: armadillo repeat containing 1 [Source:HGNC Symbol;Acc:17684]

Sequence

>retro_ocun_782
ACAACTCCAGGAGAAACAAAACTCCTGGCCTCTGAAATCTATGACATTCTTCAATCGTCAAATATGGCAGATGGAGATAG
CGTCAATGAAATGCATTCACGTTGAAAGAAAGCTCAGTTTTTTCTGGGAACTACAAACAAACGTGCTAAAACAGTGGTTT
TGCATAAAGATGGTCTTGATGATACGTCTCAGAGAAATCTATGTGAAGAAGCTTTGTTAAAAATTAAAGATGTTATTGGC
TTTACTTTTCAAATGGCTGTTCAAAGATCTGTGGTGCAAATCCACTCAGATTTGAAGGCAGAGACTTTGACATCAGGGAT
AGCATCAGCCAAGGTTATGGAAGTTCAGCAAGTTGTGAAAAGTGAAGTGGAGAACAGATGCTGGTTCCGGTCCAGGATAC
TCCTGTAGAAGTAGAGCAGAACACAGAGTTGCCTGATTACCTGCCCAAGGATGAGAGTGCCACCAAGGAGCAGGACACAG
CAGTGTCCCGGGTTGGCTCACACCCGGAGGGTGGAGCTAGCTGGCTGAGCACAGCCACAAACTTTTTATCCAGATCATTT
TACTGG

Alignment

ORF - retro_ocun_782 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.32 %
• Parental protein coverage: 67.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TTPGETKLLASEIYDILQSSNMADGDSFSEMNSRRRKAQFFLGTTNKRAKTVVLHIDGLDDTSRRNLCEE
          TTPGETKLLASEIYDILQSSNMADGDS..EM.SR..KAQFFLGTTNKRAKTVVLH.DGLDDTS.RNLCEE
Retrocopy TTPGETKLLASEIYDILQSSNMADGDSVNEMHSR*KKAQFFLGTTNKRAKTVVLHKDGLDDTSQRNLCEE

Parental  ALLKIKGVISFTFQMAVQRCVVRIRSDLKAEALASAIASTKVMKAQQVVKSE-SGEEMLVPFQDTPMEVE
          ALLKIK.VI.FTFQMAVQR.VV.I.SDLKAE.L.S.IAS.KVM..QQVVKSE.SGE.MLVP.QDTP.EVE
Retrocopy ALLKIKDVIGFTFQMAVQRSVVQIHSDLKAETLTSGIASAKVMEVQQVVKSE<SGEQMLVPVQDTPVEVE

Parental  QNTELPDYLPEDESPTKEQDKAVSRVGSHPEGGASWLSTAANFLSRSFYW
          QNTELPDYLP.DES.TKEQD.AVSRVGSHPEGGASWLSTA.NFLSRSFYW
Retrocopy QNTELPDYLPKDESATKEQDTAVSRVGSHPEGGASWLSTATNFLSRSFYW

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	17.16 RPM
SRP017611_kidney	0.00 RPM	9.02 RPM
SRP017611_liver	0.00 RPM	6.78 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_782 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_782 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_782 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015901	1 retrocopy	retro_btau_1447,
Homo sapiens	ENSG00000104442	1 retrocopy	retro_hsap_3100,
Gorilla gorilla	ENSGGOG00000022803	1 retrocopy	retro_ggor_2129,
Myotis lucifugus	ENSMLUG00000014037	1 retrocopy	retro_mluc_2058,
Nomascus leucogenys	ENSNLEG00000003916	1 retrocopy	retro_nleu_1518,
Oryctolagus cuniculus	ENSOCUG00000000392	2 retrocopies	retro_ocun_1437, retro_ocun_782 ,
Pongo abelii	ENSPPYG00000018630	1 retrocopy	retro_pabe_2474,
Pan troglodytes	ENSPTRG00000020298	1 retrocopy	retro_ptro_2096,
Sus scrofa	ENSSSCG00000006220	1 retrocopy	retro_sscr_1027,