RetrogeneDB ID: retro_cpor_762

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_27:4175848..4176483(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000021820
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LDHB
• Ensembl ID: ENSCPOG00000007138
• Aliases: None
• Description: lactate dehydrogenase B [Source:HGNC Symbol;Acc:6541]

Sequence

>retro_cpor_762
CAAATGATGGATTGGCAGAATGGAATTGTGTTTCTTCAGACATCTAAAATTGTGGCAGACAAATACTACTCTGCCAACTC
TAAGATTGTGGTTGTCACCACCAGGATTTGTCAGCAGGAAGGGGAGAGTTGGCTCAGTGTGATGCAGAGAAATGTTAATG
TCTTCAAGTTCATTATTCCTCACATCATCAGGTGTAGTCCTGACTGCACCATCATTGTGATTTCCATCCCCATGGACATT
CTCACATATGCTGCCTGGAAACTAGGTGGATTGCCCAAGCACTGTCTGATTGGAAGCAGATTCAATCTGGATTCTGCTAG
ATTTTGCTATCTTACATCTGAAAAACTTGGCATTCATCCCAGTGGCTGCCAGGATGGATTGTGGGAGAACATGGCAACAG
CAGTGTGGCTGTCTGGAGTGGAGTGAATATAGCAGATGTTTCCCCCCAGGAACTGAATCTGGAAATGGGCACAGACAATG
AGAGTGAAAATTGGAAGGAAGTGTGTAATATGGTAGCAGAAAGTGCCTATGTAGTCATCAGGCTAAAAGATTATACCAAC
TGGGTCATAGGGTTAAGTGTGGCTAAGCTTGCTGAGTCCATCTTGAATCTATCCAAGGTTCATCCAGTGTCATCA

Alignment

ORF - retro_cpor_762 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.15 %
• Parental protein coverage: 64.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EMMDLQHGSLFLQTSKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPD
          .MMD.Q.G..FLQTSKIVADK.YS..ANSKIVVVT....QQEGES.L...QRNVNVFKFIIP.I...SPD
Retrocopy QMMDWQNGIVFLQTSKIVADKYYS--ANSKIVVVTTRICQQEGESWLSVMQRNVNVFKFIIPHIIRCSPD

Parental  CTIIVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCH-GWILGEHGDSSVA
          CTIIV.S.P.DILTY..WKL.GLPKH..IGS..NLDSARF.YL..EKLGIHPS.C..GWI.GEHG.SSVA
Retrocopy CTIIVISIPMDILTYAAWKLGGLPKHCLIGSRFNLDSARFCYLTSEKLGIHPSGCQ<GWIVGEHGNSSVA

Parental  VWSGVNVAGVSLQELNPEMGTDNDSENWKEVHKTVVDSAYEVIKLKGYTNWAIGLSVADLIESILKNLSR
          VWSGVN.A.VS.QELN.EMGTDN.SENWKEV...V..SAY.VI.LK.YTNW.IGLSVA.L.ESIL.NLS.
Retrocopy VWSGVNIADVSPQELNLEMGTDNESENWKEVCNMVAESAYVVIRLKDYTNWVIGLSVAKLAESIL-NLSK

Parental  IHPVST
          .HPVS.
Retrocopy VHPVSS

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	308.52 RPM
SRP017611_kidney	0.00 RPM	859.17 RPM
SRP017611_liver	0.00 RPM	65.77 RPM
SRP040447_lung	0.00 RPM	129.11 RPM
SRP040447_skeletal_muscle	0.00 RPM	553.11 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_762 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_762 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 67 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 ,
Cavia porcellus	ENSCPOG00000011926	2 retrocopies	retro_cpor_1055, retro_cpor_427,
Dasypus novemcinctus	ENSDNOG00000013620	4 retrocopies	retro_dnov_1161, retro_dnov_1511, retro_dnov_1570, retro_dnov_529,
Echinops telfairi	ENSETEG00000019955	1 retrocopy	retro_etel_850,
Felis catus	ENSFCAG00000012639	1 retrocopy	retro_fcat_462,
Gorilla gorilla	ENSGGOG00000015758	1 retrocopy	retro_ggor_3033,
Loxodonta africana	ENSLAFG00000000972	2 retrocopies	retro_lafr_197, retro_lafr_315,
Macropus eugenii	ENSMEUG00000004825	1 retrocopy	retro_meug_311,
Microcebus murinus	ENSMICG00000017183	2 retrocopies	retro_mmur_275, retro_mmur_300,
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,
Mus musculus	ENSMUSG00000030246	4 retrocopies	retro_mmus_1817, retro_mmus_2035, retro_mmus_2509, retro_mmus_335,
Oryctolagus cuniculus	ENSOCUG00000022015	1 retrocopy	retro_ocun_805,
Otolemur garnettii	ENSOGAG00000004763	9 retrocopies	retro_ogar_1469, retro_ogar_2093, retro_ogar_2344, retro_ogar_2459, retro_ogar_3288, retro_ogar_3342, retro_ogar_3383, retro_ogar_689, retro_ogar_721,
Pteropus vampyrus	ENSPVAG00000002462	3 retrocopies	retro_pvam_1487, retro_pvam_320, retro_pvam_673,
Rattus norvegicus	ENSRNOG00000013000	3 retrocopies	retro_rnor_2697, retro_rnor_2749, retro_rnor_2834,
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,