RetrogeneDB ID: retro_ocun_1671

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018754:877883..878273(-)
• Located in intron of: ENSOCUG00000000722

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000016529
• Aliases: None
• Description: None

Sequence

>retro_ocun_1671
AAACACAAGGCCTTGAAAACATATGCACCCCTGACTACACTTGCAATTTTATCTACTACAGTTGCTTACAAGCTCCTTGC
AACCGATGCTTTGCATTCAGGAAACAGAGGTAAGGAAAATTGTGTCCTTAGAAGCTCACTGATGGGCACGGTATGTGGTG
TTTTATATCCCTGTGGCTTGGCTTTTTCTAAAAACGGATGCCTGGCAGTTGGATATCACAAAGCTCCACTGCCACCAAAA
GCAAGGGTTTTACTCCACTGGCTGCTGCTTTGTCAAACGGAGCTGAAGGCAATGGTGATTCCTCTAGTCTTTCAGACAGC
ATTTGGAACACTTACCATATAGAATTATTCAGTATTTGAAAAGATATTTGAGAAAACGGCACACGAAGAT

Alignment

ORF - retro_ocun_1671 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.81 %
• Parental protein coverage: 56.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KHDALKTYASLTTLPFLSTIVAYKLLVTDALYSGNISKENCVLRSSLVGIVCGILYPSSLAFSKNGRLAV
          KH.ALKTYA.LTTL..LST.VAYKLL.TDAL.SGN..KENCVLRSSL.G.VCG.LYP..LAFSKNG.LAV
Retrocopy KHKALKTYAPLTTLAILSTTVAYKLLATDALHSGNRGKENCVLRSSLMGTVCGVLYPCGLAFSKNGCLAV

Parental  RYHTVPLPPKGRVLLHWMLLCQTEIKAMVIPLVFQTMFGILIGLQHYSLFEKTLAKTVHED
          .YH..PLPPK.RVLLHW.LLCQTE.KAMVIPLVFQT.FG.L.....YS.FEK...KT.HED
Retrocopy GYHKAPLPPKARVLLHWLLLCQTELKAMVIPLVFQTAFGTLT-I*NYSVFEKIFEKTAHED

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	0.06 RPM	7.23 RPM
SRP017611_kidney	0.00 RPM	6.79 RPM
SRP017611_liver	0.00 RPM	1.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1671 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1671 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1671 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020596	1 retrocopy	retro_btau_420,
Echinops telfairi	ENSETEG00000008939	1 retrocopy	retro_etel_200,
Mus musculus	ENSMUSG00000030614	1 retrocopy	retro_mmus_1618,
Oryctolagus cuniculus	ENSOCUG00000016529	3 retrocopies	retro_ocun_1656, retro_ocun_1671 , retro_ocun_607,
Oryctolagus cuniculus	ENSOCUG00000016534	1 retrocopy	retro_ocun_1120,
Sus scrofa	ENSSSCG00000014905	1 retrocopy	retro_sscr_452,