RetrogeneDB ID: retro_ocun_1754

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018854:231667..232307(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000003280
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DSCC1
• Ensembl ID: ENSOCUG00000017952
• Aliases: None
• Description: DNA replication and sister chromatid cohesion 1 [Source:HGNC Symbol;Acc:24453]

Sequence

>retro_ocun_1754
ATGACCCAGTTGCAAGTTCTAAATGCCTGTGAGATTGGAGGTTATTGGAGAATTCTTGAATTTGACTATGAGATGAAACT
TCTGAATCATGTAACTCAGCTTGTGGATTCTGAATCTTGGTCGTTTAATAAAGTTCCTTTGAGTACATGTCTTCAGGAAC
TTGGACCATTGGAGCCAGAAGAAATGATAGAACACTGTCTTAAATGTTATGGAAAGAAATACATAGACGAAGGTGAAGTT
TATTTTGAACTGAGTGCTGATAAAATATGCAGAGCAACAGCACAGATGCTTCTTCAGAATGCAGTGAAATTCAATCTTGC
TGAGTTTCAAGAAGTGTGGCAACAGTGTCCCTGAAGGAATGATAACTAGGCTTGATCAGCTTAAGGGTTTAGCATTGGTT
GATAGAAATTCAAGGCCAGAAATCATATTTTTGCTGAAAGTTGATGACTTACCTGAAGGTGATCAGGAACGTTTTAATAG
TCTGTTCTCTATAAGAGAGAAGTGGACAGAAGAAGATATTGCTCCATATATTCAAGATTTATGCGGAGAAAAGCAAACCA
TAGGTGCATTACTCACTAAATATTCTCGTTCTTCAATGCAGAATGGTGTCAAAGTTTATAATTCAAAAAGACCCATTTCT

Alignment

ORF - retro_ocun_1754 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTQLQVLNACEIGGYWRILEFDYEMKLLNHVTQLVDSESWSFNKVPLSTCLQELGPLEPEEMIEHCLKCY
          MTQLQVLNACEIGGYWRILEFDYEMKLLNHVTQLVDSESWSFNKVPLSTCLQELGPLEPEEMIEHCLKCY
Retrocopy MTQLQVLNACEIGGYWRILEFDYEMKLLNHVTQLVDSESWSFNKVPLSTCLQELGPLEPEEMIEHCLKCY

Parental  GKKYIDEGEVYFELSADKICRATAQMLLQNAVKFN-LAEFQEVWQQSVPEGMITRLDQLKGLALVDRNSR
          GKKYIDEGEVYFELSADKICRATAQMLLQNAVKFN.L..F......SVPEGMITRLDQLKGLALVDRNSR
Retrocopy GKKYIDEGEVYFELSADKICRATAQMLLQNAVKFN>LLSFKKCGN-SVPEGMITRLDQLKGLALVDRNSR

Parental  PEIIFLLKVDDLPEGDQERFNSLFSIREKWTEEDIAPYIQDLCGEKQTIGALLTKYSRSSMQNGVKVYNS
          PEIIFLLKVDDLPEGDQERFNSLFSIREKWTEEDIAPYIQDLCGEKQTIGALLTKYSRSSMQNGVKVYNS
Retrocopy PEIIFLLKVDDLPEGDQERFNSLFSIREKWTEEDIAPYIQDLCGEKQTIGALLTKYSRSSMQNGVKVYNS

Parental  RRPIS
          .RPIS
Retrocopy KRPIS

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	0.11 RPM	0.77 RPM
SRP017611_kidney	0.00 RPM	0.30 RPM
SRP017611_liver	0.15 RPM	0.77 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1754 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1754 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1754 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000017952	1 retrocopy	retro_ocun_1754 ,