RetrogeneDB ID: retro_ocun_358

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:42741442..42742015(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RDM1
• Ensembl ID: ENSOCUG00000022704
• Aliases: None
• Description: RAD52 motif 1 [Source:HGNC Symbol;Acc:19950]

Sequence

>retro_ocun_358
GCGAGGGACGCGCGCAGAGCCCAGGCGGCCTGTGACCGGAAGCTGCTTTTCCAGGAGACTCCAGTGAAGGTTCGTCTTGG
CCCCAGACATAAGGCAGTTCAACATCAGGCCCTTGCCCTAAACGGCTCCTGATGCCAAGAGCTGGCAAACTACTGCTTGG
GTTTCAATGGATGGTCAAAAAGGATCATCAAGCTTCAGGAGCTCTCCGACCTTGAAGAGAGGGAAAATGAAGAGACGGAG
CGGCGACTTGCGGAGCGGAGCCTGAAGGTCTTCTGTGCCTCGGAGGTGGTGCTGCCATCCTATGAGTGCTCGAGTCGTGG
AGTCGGCGTGGCCGAGGAGCCGCTGGATACGCTGGAGGAGGAAGGACCATTGTTGTTCCTTATGAAGAAGAAGACAGCCC
AGAACCTTGCCATTCAGAAGGCTTTGTCAAATGCGTTCCAGAAACTGTCGATTGTGGTTTTAGAAAGTGGTAAAATAGCC
GTGGAGTACAGACCCGGTGAAGAGATCCTAGATACCGGAAGCGAAGAAGAACTACACAACTTGATTGAAGTATGTGGAGA
TGAAAGCTGGAGT

Alignment

ORF - retro_ocun_358 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.81 %
• Parental protein coverage: 73.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ARDARRAQAACDRKLLFQETPVKVRLGTRHKAVQHQALALNGSRCQELANYYLGFNGWSKRIIKLQELSA
          ARDARRAQAACDRKLLFQETPVKVRLG.RHKAVQHQALALNGS.CQELANY.LGFNGWSKRIIKLQELS.
Retrocopy ARDARRAQAACDRKLLFQETPVKVRLGPRHKAVQHQALALNGS*CQELANYCLGFNGWSKRIIKLQELSD

Parental  LEERENEETARRLAERSLKVFCALEVVLPSYECSSRGVGVAEEPLDTLQEEGPLLFLMKKKTAQNLAIQK
          LEERENEET.RRLAERSLKVFCA.EVVLPSYECSSRGVGVAEEPLDTL.EEGPLLFLMKKKTAQNLAIQK
Retrocopy LEERENEETERRLAERSLKVFCASEVVLPSYECSSRGVGVAEEPLDTLEEEGPLLFLMKKKTAQNLAIQK

Parental  ALSNAFQKLSIVVLESGKIAVEYRPGEEILDTGSEE-LHNLIEVCGDESWS
          ALSNAFQKLSIVVLESGKIAVEYRPGEEILDTGSEE.LHNLIEVCGDESWS
Retrocopy ALSNAFQKLSIVVLESGKIAVEYRPGEEILDTGSEEELHNLIEVCGDESWS

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	8.50 RPM
SRP017611_kidney	0.00 RPM	0.61 RPM
SRP017611_liver	0.00 RPM	0.23 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_358 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_358 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_358 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000030	1 retrocopy	retro_btau_1640,
Oryctolagus cuniculus	ENSOCUG00000022704	1 retrocopy	retro_ocun_358 ,
Tursiops truncatus	ENSTTRG00000006200	1 retrocopy	retro_ttru_1156,