RetrogeneDB ID: retro_ocun_805

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:60214349..60215221(+)
• Located in intron of: ENSOCUG00000023825

Retrocopy information

• Ensembl ID: ENSOCUG00000025106
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LDHB
• Ensembl ID: ENSOCUG00000022015
• Aliases: LDHB, LDH-B, LDH-H
• Description: lactate dehydrogenase B [Source:HGNC Symbol;Acc:6541]

Sequence

>retro_ocun_805
TCTCTGGCTGATGAGCTTGCTCTTGTGGATGTCCTGGAAGATAAGCTCAAAGGAGAGATGATGGATCTGCAGCACGGAAG
CTTGTTTCTCCAGACACCCAAAATTGTGGCGGATAAAGACTACTCCGTGACGGCCAATTCTAAGATCATGGTGGTGACCG
TGGGAGTCCGACAGCAGGAGGGGGAGAGCCGTCTCAACCTGGTGCAGAGAAATGTGAATGTCTTCAAGTTCATTATTCCC
CAGATTGTCAAGTACAGTCCCAACTGCATCATCATCGTGGTTTCCAACCCAGTGGACATTCTTATATACGTGACCTGGAA
ACTAGTGGACTGCCCAAGCACTGTGTGATTGGAAGTGGGTGCAATCTGGATTCTGCTAGATTTCACTATCTCATGGCTGA
AAAGCTTGGCATTCATCCCAGCAGCTGCCATGGATGGATTTTGGGAGAACACGGAGACTCAAGTGTGGCTTTCTGGAGTG
GAGTGAATGTGGCAGGTGTTTCTCTCCAGGAACTGAATCCAGAGATGGGAACAGACAGCGATAGTGAAAACTGGAAGGAG
GTGCACAAGATGGTGGTGGACAGTGCCTATGAAGTCATCAAGCTAAAAGGGTACACTAACTGGGCCATTGGATTAAGTGT
GGCTGATCTCATTGAATCCATGATGAAAAATCTCTCCAGGATTCACCCAGTGTCCACAATGGTGAAGGGCATGTATGGCA
TTGAGAACGAAGTCTTCCTGAGCCTTCCGTGCATCCTCAATGCCCGGGGATTAACCAGCGTCATCAACCAGAAGCTCAAG
GACGATGAGGTTGCCCAGCTCAAGAAAAGTGCAGACACCTTGTGGGACATCCAGAAAGACCTCAAAGACCTG

Alignment

ORF - retro_ocun_805 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.58 %
• Parental protein coverage: 87.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLADELALVDVLEDKLKGEMMDLQHGSLFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQR
          SLADELALVDVLEDKLKGEMMDLQHGSLFLQTPKIVADKDYSVTANSKI.VVT.GVRQQEGESRLNLVQR
Retrocopy SLADELALVDVLEDKLKGEMMDLQHGSLFLQTPKIVADKDYSVTANSKIMVVTVGVRQQEGESRLNLVQR

Parental  NVNVFKFIIPQIVKYSPNCIIIVVSNPVDILTYVTWKL-SGLPKHRVIGSGCNLDSARFRYLMAEKLGIH
          NVNVFKFIIPQIVKYSPNCIIIVVSNPVDIL.YVTWKL.SGLPKH.VIGSGCNLDSARF.YLMAEKLGIH
Retrocopy NVNVFKFIIPQIVKYSPNCIIIVVSNPVDILIYVTWKL<SGLPKHCVIGSGCNLDSARFHYLMAEKLGIH

Parental  PSSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPEMGTDNDSENWKEVHKMVVESAYEVIKLKGYTNWA
          PSSCHGWILGEHGDSSVA.WSGVNVAGVSLQELNPEMGTD.DSENWKEVHKMVV.SAYEVIKLKGYTNWA
Retrocopy PSSCHGWILGEHGDSSVAFWSGVNVAGVSLQELNPEMGTDSDSENWKEVHKMVVDSAYEVIKLKGYTNWA

Parental  IGLSVADLIESMLKNLSRIHPVSTMVKGMYGIENEVFLSLPCILNARGLTSVINQKLKDDEVAQLKKSAD
          IGLSVADLIESM.KNLSRIHPVSTMVKGMYGIENEVFLSLPCILNARGLTSVINQKLKDDEVAQLKKSAD
Retrocopy IGLSVADLIESMMKNLSRIHPVSTMVKGMYGIENEVFLSLPCILNARGLTSVINQKLKDDEVAQLKKSAD

Parental  TLWDIQKDLKDL
          TLWDIQKDLKDL
Retrocopy TLWDIQKDLKDL

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	11.09 RPM	434.39 RPM
SRP017611_kidney	21.69 RPM	720.44 RPM
SRP017611_liver	1.85 RPM	49.33 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_805 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_805 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_805 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016175	4 retrocopies	retro_amel_1316, retro_amel_814, retro_amel_882, retro_amel_977,
Bos taurus	ENSBTAG00000019603	4 retrocopies	retro_btau_1589, retro_btau_303, retro_btau_451, retro_btau_647,
Canis familiaris	ENSCAFG00000012195	9 retrocopies	retro_cfam_1068, retro_cfam_111, retro_cfam_1674, retro_cfam_17, retro_cfam_1700, retro_cfam_174, retro_cfam_1836, retro_cfam_701, retro_cfam_93,
Cavia porcellus	ENSCPOG00000007138	1 retrocopy	retro_cpor_762,
Echinops telfairi	ENSETEG00000019955	1 retrocopy	retro_etel_850,
Felis catus	ENSFCAG00000012639	1 retrocopy	retro_fcat_462,
Macropus eugenii	ENSMEUG00000004825	1 retrocopy	retro_meug_311,
Myotis lucifugus	ENSMLUG00000012155	1 retrocopy	retro_mluc_202,
Macaca mulatta	ENSMMUG00000002679	4 retrocopies	retro_mmul_212, retro_mmul_303, retro_mmul_308, retro_mmul_315,
Monodelphis domestica	ENSMODG00000017786	1 retrocopy	retro_mdom_1484,
Mustela putorius furo	ENSMPUG00000000172	5 retrocopies	retro_mputfur_1300, retro_mputfur_1561, retro_mputfur_492, retro_mputfur_539, retro_mputfur_549,
Oryctolagus cuniculus	ENSOCUG00000015939	6 retrocopies	retro_ocun_1597, retro_ocun_1817, retro_ocun_246, retro_ocun_338, retro_ocun_574, retro_ocun_746,
Oryctolagus cuniculus	ENSOCUG00000022015	1 retrocopy	retro_ocun_805 ,
Sorex araneus	ENSSARG00000002565	1 retrocopy	retro_sara_713,
Sus scrofa	ENSSSCG00000000576	1 retrocopy	retro_sscr_37,
Ictidomys tridecemlineatus	ENSSTOG00000022058	2 retrocopies	retro_itri_501, retro_itri_648,