RetrogeneDB ID: retro_ocun_315

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:147686697..147687458(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000022999
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LDB1
• Ensembl ID: ENSOCUG00000025582
• Aliases: None
• Description: LIM domain binding 1 [Source:HGNC Symbol;Acc:6532]

Sequence

>retro_ocun_315
TTTGTGTCCCTCGACTGTGACCAGGGTAGCAGGGTGACCCAGCACGGCAAACCCATGTTCACTCAGGTGTGCGTGGAGGG
CCGGCTATACCTGGAGTTCATGTGCGACGACATGATGAGGATAAAGACGTGGCACTTCAGCATCCGGCAGCACCGAGAGC
TCATCCCCTGCAGCATCCTTGCCATGCACGCCCAGGACCCCCAGATGTTGGATCAGCTGTCCAAAAACATCACACGGTGT
GGGCTGTCCAACTCCACTCTCAACTACCTCCGACACTGTGTGATACTCGAGCCCATGCAGGAGCTCATGTCCTGCCACAA
GACTTACAGCCTCAGCCCCCAAGACTGCCTCAAGACCTGCCTTTTCCAGAAGTGGCAGCGCATGGTAGCACCCCCCGCGG
AACCCGCACGGCAGCAGCCCAGCAAGCGGCGGAAACGGAAGATGTCAGGGGCAGCATCATGAGTTCGGAGGGTGGCTACA
CCAACAACAGCAACAGCAAGAAGAAGAGCCCGGCCAGCACCTTCGCCCTCTCCAGCCAGGATGTGATGGTGGTGGGGGAG
CCCACCCTGATGGGCGGGGAGTTCGGGGACGAGGACGAGAGGCTCATCACCCGTCTGGAGAACACCCAGTTTGACGCGGC
CAACGGCATTGACGACAGCTTTAACAACTCCCCTGCACTGGGTGCCAACAGCCCCTGGAACAGCAAGCCTCCGTCCAGCC
AAGAAAGCAAATCGGAGAACCCCACGTCACAGGCCTCCCAG

Alignment

ORF - retro_ocun_315 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.59 %
• Parental protein coverage: 62.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FVSLDCDQGSMVTQHGKPMFTQVCVEGRLYLEFMFDDMMRIKTWHFSIRQHRELIPRSILAMHAQDPQML
          FVSLDCDQGS.VTQHGKPMFTQVCVEGRLYLEFM.DDMMRIKTWHFSIRQHRELIP.SILAMHAQDPQML
Retrocopy FVSLDCDQGSRVTQHGKPMFTQVCVEGRLYLEFMCDDMMRIKTWHFSIRQHRELIPCSILAMHAQDPQML

Parental  DQLSKNITRCGLSNSTLNYLRLCVILEPMQELMSRHKTYSLSPRDCLKTCLFQKWQRMVAPPAEPARQQP
          DQLSKNITRCGLSNSTLNYLR.CVILEPMQELMS.HKTYSLSP.DCLKTCLFQKWQRMVAPPAEPARQQP
Retrocopy DQLSKNITRCGLSNSTLNYLRHCVILEPMQELMSCHKTYSLSPQDCLKTCLFQKWQRMVAPPAEPARQQP

Parental  SKRRKRKMSG-GSTMSSGGGNTNNSNSKKKSPASTFALSSQVPDVMVVGEPTLMGGEFGDEDERLITRLE
          SKRRKRKMSG.GS.MSS.GG.TNNSNSKKKSPASTFALSSQ..DVMVVGEPTLMGGEFGDEDERLITRLE
Retrocopy SKRRKRKMSG<GSIMSSEGGYTNNSNSKKKSPASTFALSSQ--DVMVVGEPTLMGGEFGDEDERLITRLE

Parental  NTQFDAANGIDDEDSFNNSPALGANSPWNSKPPSSQESKSENPTSQASQ
          NTQFDAANGID..DSFNNSPALGANSPWNSKPPSSQESKSENPTSQASQ
Retrocopy NTQFDAANGID--DSFNNSPALGANSPWNSKPPSSQESKSENPTSQASQ

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	0.44 RPM	42.38 RPM
SRP017611_kidney	1.01 RPM	25.95 RPM
SRP017611_liver	0.08 RPM	11.10 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_315 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_315 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_315 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	ENSOCUG00000025582	1 retrocopy	retro_ocun_315 ,