RetrogeneDB ID: retro_ocun_969

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 18:21450284..21451172(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C14orf28
• Ensembl ID: ENSOCUG00000008733
• Aliases: None
• Description: chromosome 14 open reading frame 28 [Source:HGNC Symbol;Acc:19834]

Sequence

>retro_ocun_969
ATGAAGACACTGTTTGAAGAGATCAAAGCATCAGTTAAAAATAACTGTAACCAAGATCGATCGTTTTGGAGGCCTGTTAT
TCCTTGGGGAGGTGTTTTTACTATCAAAGCTGGCCGCAAAGCAGTATCCTGTACACCACTCTATGTTGAAATAAGACTGA
AAAATCCCTGCACCATAGATGGATTCCTGATGTTGTTATATGTCATTCTGAATGAAAATGAAAATTTCCCCAGGGAACTC
TCTCTTCATCTTGGTAGAGAGTTTGTAGACTATTTCCTTTATTTAATGGACACCTACAGCTTTACAACTGTGAAGCTACT
TTGGATTTGGGACAAGATGGAAAAATAGCAATACAAATCTGAAGTTCATAAAGCATCATTAATAATTGATTTATTTGGGA
ATGAACATGATAACTTTACCAAAAATCTGGAAAATCTTATGTCTAGCATTCAAGAGAGTTACTGTTCCAACTGGAGATAC
CCAACTCGAGTGCAGGAAGATCAGCAGCGTACCATTAATATAAATCCTCCCCAAGAAATTCCACATGGAAACTTAATACG
ACTGGCTGTGGCTGAGTTATTCTGTTCCAAGATTGAACTGTGTGAAGAGCGTGGTTGTGGTGGCTTAAGAGAATTTGCCC
AGCGAGTTTTCCGTCACAGGGCACCCCCTTTTGTTGTCTTAAATATGCAGCATTGGAAATCCGAAGATCTGGCATATGTA
CCTTATTATTTGGATTTATCTGATCACAAATATTTATTGGAAGGCGCAACATTATTTAACAAAGATGAGCATCATTATTC
TGCAGCTTTCCAGACTGATGGACATTGGATGCACTATGATGGCCTCAGAAATGTGAACTTAATTTTGTTAAATAAACCCC
CAGAGTTT

Alignment

ORF - retro_ocun_969 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.28 %
• Parental protein coverage: 95.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKTLFEEIKASIKNNYNQDRSFWRPVLPWGGVFTIKAGRKAVSCTPLYVEIRLKNTCTIDGFLMLLYVIL
          MKTLFEEIKAS.KNN.NQDRSFWRPV.PWGGVFTIKAGRKAVSCTPLYVEIRLKN.CTIDGFLMLLYVIL
Retrocopy MKTLFEEIKASVKNNCNQDRSFWRPVIPWGGVFTIKAGRKAVSCTPLYVEIRLKNPCTIDGFLMLLYVIL

Parental  NENENFPRELSLHLGREFVDYFLYLMDTYSFTTVKLLWIWDKMEKQQYKSEVHKASLIIDLFGNEHDNFT
          NENENFPRELSLHLGREFVDYFLYLMDTYSFTTVKLLWIWDKMEK.QYKSEVHKASLIIDLFGNEHDNFT
Retrocopy NENENFPRELSLHLGREFVDYFLYLMDTYSFTTVKLLWIWDKMEK*QYKSEVHKASLIIDLFGNEHDNFT

Parental  KNLENLMSTIQESYCSNWRCPTRVQEDQQRTININPPQEIPHGNLIRLAVDELFCSKIELCEERGCGGLR
          KNLENLMS.IQESYCSNWR.PTRVQEDQQRTININPPQEIPHGNLIRLAV.ELFCSKIELCEERGCGGLR
Retrocopy KNLENLMSSIQESYCSNWRYPTRVQEDQQRTININPPQEIPHGNLIRLAVAELFCSKIELCEERGCGGLR

Parental  EFAQRVFCHGAPPFVVLNMQHWKSEDLAYVPYYLDLSDHKYLLEGATLFNKDEHHYSAAFQIDGHWMHYD
          EFAQRVF.H.APPFVVLNMQHWKSEDLAYVPYYLDLSDHKYLLEGATLFNKDEHHYSAAFQ.DGHWMHYD
Retrocopy EFAQRVFRHRAPPFVVLNMQHWKSEDLAYVPYYLDLSDHKYLLEGATLFNKDEHHYSAAFQTDGHWMHYD

Parental  GLRNVNLILLNKPPEF
          GLRNVNLILLNKPPEF
Retrocopy GLRNVNLILLNKPPEF

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	2.76 RPM
SRP017611_kidney	0.00 RPM	2.94 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_969 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_969 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_969 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	ENSOCUG00000008733	1 retrocopy	retro_ocun_969 ,