RetrogeneDB ID: retro_ggor_3033

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:73482885..73483761(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000027341
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LDHB
• Ensembl ID: ENSGGOG00000015758
• Aliases: None
• Description: L-lactate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:G3RI82]

Sequence

>retro_ggor_3033
AAATCTCTGACTGATGAATTTGCTTTTGTGGATGTTTTGGAAGATAAGCTTAAAGGAGAAATGATGGATCCGCAGCATGG
GAGCTTATTTCTCCAGACGCTTAAAATTGTGGCGGATAAAGATTATTCTGTGACTGCCAGTTATAAGATTGTAGTGGTAA
CTGCAGGAGTCCTTCAGCAAGAGGGGGAGAGACGTCTCAATTTGTTGCAGAAAAAATGTTAATGTCTTCAAATTCATTAT
TCCTCAAATTGTCAAGTACACTTCTGATTGCACATAATTGTGGTTTCCAACCTAGGGGACATTCTTACATATGTCACCTG
GAAAATAAGTGGATTACTCAAACACCATGTGATTGGAAGTGGATGTAATCCGGATTCTGCTAGATTTCACTGCCTTATGG
CTGAAAAATTTGGCATTCATCCCAGCAGCTGCCATGGAAGGATTTTGGGGGAACATAGTGACTCAAGTGTGGCTGTGTGG
ATTGGCATGAATGTGACAGGTTTTTCTCTCCAGGAATTGAATCCAGAAATAGGAACTGACAATGATAGTGAAAATTGGAA
AGAAGTGCATAAGATGGTGGTTGAAAGTGCCTATGAAGTCATCAAGCTAAATGGATATACCCACTGGGTTATTGGATTAA
GTGTGGCTGGTCTCATTGAATCCATGTTGAAAAATCTATCCAGGATTCATCTCGTGTCATCAATGGTAAAGGGGATGTAT
GGCATCGAGAATGAAGTCTTCCTGAGCCTTCCATATATCCTCAATGCCCGGGGATTAACCAGCGTTATCAACCAGAAGCT
AAAGGATGATGAGGTTGCTCAGTTCAAGAAAAGTACAGATACCCCGTGGGACATCCAGAAGGACCTAAAAGACCTG

Alignment

ORF - retro_ggor_3033 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QSLADELALVDVLEDKLKGEMMDLQHGSLFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQ
          .SL.DE.A.VDVLEDKLKGEMMD.QHGSLFLQT.KIVADKDYSVTA..KIVVVTAGV.QQEGE.RLNL.Q
Retrocopy KSLTDEFAFVDVLEDKLKGEMMDPQHGSLFLQTLKIVADKDYSVTASYKIVVVTAGVLQQEGERRLNLLQ

Parental  -RNVNVFKFIIPQIVKYSPDCI-IIVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLG
          ..NVNVFKFIIPQIVKY..DC..IIVVSN..DILTYVTWK.SGL.KH.VIGSGCN.DSARF..LMAEK.G
Retrocopy >KNVNVFKFIIPQIVKYTSDCT<IIVVSNLGDILTYVTWKISGLLKHHVIGSGCNPDSARFHCLMAEKFG

Parental  IHPSSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPEMGTDNDSENWKEVHKMVVESAYEVIKLKGYTN
          IHPSSCHG.ILGEH.DSSVAVW.G.NV.G.SLQELNPE.GTDNDSENWKEVHKMVVESAYEVIKL.GYT.
Retrocopy IHPSSCHGRILGEHSDSSVAVWIGMNVTGFSLQELNPEIGTDNDSENWKEVHKMVVESAYEVIKLNGYTH

Parental  WAIGLSVADLIESMLKNLSRIHPVSTMVKGMYGIENEVFLSLPCILNARGLTSVINQKLKDDEVAQLKKS
          W.IGLSVA.LIESMLKNLSRIH.VS.MVKGMYGIENEVFLSLP.ILNARGLTSVINQKLKDDEVAQ.KKS
Retrocopy WVIGLSVAGLIESMLKNLSRIHLVSSMVKGMYGIENEVFLSLPYILNARGLTSVINQKLKDDEVAQFKKS

Parental  ADTLWDIQKDLKDL
          .DT.WDIQKDLKDL
Retrocopy TDTPWDIQKDLKDL

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
SRP007412_brain_prefrontal_cortex	5.61 RPM	412.60 RPM
SRP007412_cerebellum	1.97 RPM	218.62 RPM
SRP007412_heart	4.60 RPM	532.24 RPM
SRP007412_kidney	9.28 RPM	735.02 RPM
SRP007412_liver	0.47 RPM	31.31 RPM
SRP007412_testis	1.97 RPM	206.37 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_3033 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_3033 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4863
Pan troglodytes	retro_ptro_3237
Pongo abelii	retro_pabe_3780

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016175	4 retrocopies	retro_amel_1316, retro_amel_814, retro_amel_882, retro_amel_977,
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,
Dasypus novemcinctus	ENSDNOG00000013620	4 retrocopies	retro_dnov_1161, retro_dnov_1511, retro_dnov_1570, retro_dnov_529,
Felis catus	ENSFCAG00000012639	1 retrocopy	retro_fcat_462,
Gorilla gorilla	ENSGGOG00000010350	3 retrocopies	retro_ggor_1698, retro_ggor_349, retro_ggor_619,
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,
Mus musculus	ENSMUSG00000030246	4 retrocopies	retro_mmus_1817, retro_mmus_2035, retro_mmus_2509, retro_mmus_335,
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,
Sus scrofa	ENSSSCG00000000576	1 retrocopy	retro_sscr_37,