RetrogeneDB ID: retro_ocun_1892

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:63714744..63715280(+)
• Located in intron of: ENSOCUG00000016267

Retrocopy information

• Ensembl ID: ENSOCUG00000024343
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C1orf52
• Ensembl ID: ENSOCUG00000002803
• Aliases: None
• Description: chromosome 1 open reading frame 52 [Source:HGNC Symbol;Acc:24871]

Sequence

>retro_ocun_1892
GCAGCGGAGAAGGACCACCTGAGCTATTTCACAGTTTATAGGAGCAGTAGTTCGGCTCCTCTGGCGAGAAGGACAACAGC
AAGCTGGATGAGACGGATCACAGGGCTCCGAATGCAGCGAAGTCAGGGGGCGGCTGCAAGAATAAGGTGGAGAAGCAGCT
GCCAGGACCTGACGCACTGTTCCGGAGTGTGACTCGTTGGGCCTTTCTCTACAATCCACTCAACAAGCAGACAGACTGGG
AAAGGCAAGTTGTCAAGGCGCCCGAGGAGCCTCCAAAGGAGTTCAAAATATGGAAGTCAAACTATGTGCGCCTTCCAGAG
ACCTACACAACGGAGAAGAAACCTCTGCCTCCAGAGCTGGACATGGTAATACGATGGTCTAACATATATGAGGACAAAGG
CGATGATGCCCCGCAGAATGCTAAGAAAGCTAGGCTTCTACCGGAAGGGGAGGAGACGTTGGAGTCAGATGATGAAAAAG
ATGAGCATACTTCTCAAAAGTGCAAAGTAGAACCAGGAGAACCAGCAAAGAAGAAA

Alignment

ORF - retro_ocun_1892 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.22 %
• Parental protein coverage: 98.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AEEKDPLSYFAAYGSSSS-GSSGEEDNSEPEETGRRASDAAKSAGGCGNKAEKRLPGPDELFRSVTRPAF
          A.EKD.LSYF..Y.SSSS.GSSGE.DNS...ET..RA..AAKS.GGC.NK.EK.LPGPD.LFRSVTR.AF
Retrocopy AAEKDHLSYFTVYRSSSS<GSSGEKDNSKLDETDHRAPNAAKSGGGCKNKVEKQLPGPDALFRSVTRWAF

Parental  LYNPLNKQIDWERHVVKAPEEPPKEFKIWKSNYVPPPETYTAEKKPPPPELDMAIKWSNIYEDNGDDAPQ
          LYNPLNKQ.DWER.VVKAPEEPPKEFKIWKSNYV..PETYT.EKKP.PPELDM.I.WSNIYED.GDDAPQ
Retrocopy LYNPLNKQTDWERQVVKAPEEPPKEFKIWKSNYVRLPETYTTEKKPLPPELDMVIRWSNIYEDKGDDAPQ

Parental  NAKKARLLPEGEETLESDDEKDEHTSKKRKVEPGEPTKKK
          NAKKARLLPEGEETLESDDEKDEHTS.K.KVEPGEP.KKK
Retrocopy NAKKARLLPEGEETLESDDEKDEHTSQKCKVEPGEPAKKK

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	19.37 RPM
SRP017611_kidney	0.00 RPM	7.80 RPM
SRP017611_liver	0.00 RPM	3.24 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1892 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1892 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1892 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012863	1 retrocopy	retro_chof_384,
Oryctolagus cuniculus	ENSOCUG00000002803	2 retrocopies	retro_ocun_1489, retro_ocun_1892 ,