RetrogeneDB ID: retro_ptro_3237

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:76162380..76163382(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LDHB
• Ensembl ID: ENSPTRG00000004762
• Aliases: None
• Description: Pan troglodytes lactate dehydrogenase B (LDHB), mRNA. [Source:RefSeq mRNA;Acc:NM_001098561]

Sequence

>retro_ptro_3237
ATAGCAACTCTTAAGGGAAAACTCATTGTACCAGTTGCGGAAGAAGAGGCAACAGTCCAAAACAATAAGATCACTGTAGT
GAGTGTTGGACAAGTTGGTATGGCGTGTGCTATCAGCATTCTGGGAAAATCTCTGGCTGATGAATTTGCTTTTGTGGATG
TTTTGGAAGATAAGCTTAAAGGAGAAATGATGAATCTGCAGCATGAGAGCTTATTTCTCAAGACGCTTAAAATTGTGGCA
GATAAAGATTATTCTGTGACTGCCAGTTATAAGATTGTAGTGGTAACTGCAGGAGTCCTTCAGCAAGAGGGGGAGAGGCG
TCTCAATTTGGTGCAGAAAAAATGTTAATGTCTTCAAATTCATTATTCCTCAAACTGTCAAGTACACTTCTGATTGCACA
TAATTGTGGTTTCCAACCTAGGGGACATTCTTACATATGTTACCTGGAAAATAAGTGGATTACTCAAACATCATGTGATT
GGAAGTGGATGTAATCCGGATTCTGCTAGATTTCACTGCCTTATGGATGAAAAATTTGGCATTCATCCCAGCAGCTGCCA
TGGAAGGATTTTGGGGGAACATAGTGACTCAAGTGTGGCTGTGTGGATTGGCATGAATGTGACAGGTTTTTCTCTCCAGG
AATTGAATCCAGAAATAGGAACTGACAATGATAGTGAAAATTGGAAAGAAGTGCATAAGATGGTGGTTGAAAATGCCTAT
GAAGTCAACAAACTAAATGGATATACCCACTGGGATACTGGATTAAGTGTGGCTGATCTCATTGAATCCATGTTGAAAAA
TCTATCCAGGATTCATCTCGTGTCAATAATGGTAAAGGGGATGTATGGCATCGAGAATGAAGTCTTCCTGAGCCTTCCAT
ATATCCTCAATGCCCGGGGATTAACCAGCGTTATCAACCAGAAGCTAAAGGATGATGAGGTTGCTCAGTTCAAGAAAAGT
ACAGATACCCCGTGGGACATACAGAAGGACCTTAAAGACCTG

Alignment

ORF - retro_ptro_3237 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATLKEKLIAPVAEEEATVPNNKITVVGVGQVGMACAISILGKSLADELALVDVLEDKLKGEMMDLQHGS
          .ATLK.KLI.PVAEEEATV.NNKITVV.VGQVGMACAISILGKSLADE.A.VDVLEDKLKGEMM.LQH.S
Retrocopy IATLKGKLIVPVAEEEATVQNNKITVVSVGQVGMACAISILGKSLADEFAFVDVLEDKLKGEMMNLQHES

Parental  LFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQ-RNVNVFKFIIPQIVKYSPDCI-IIVVS
          LFL.T.KIVADKDYSVTA..KIVVVTAGV.QQEGE.RLNLVQ..NVNVFKFIIPQ.VKY..DC..IIVVS
Retrocopy LFLKTLKIVADKDYSVTASYKIVVVTAGVLQQEGERRLNLVQ>KNVNVFKFIIPQTVKYTSDCT<IIVVS

Parental  NPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVA
          N..DILTYVTWK.SGL.KH.VIGSGCN.DSARF..LM.EK.GIHPSSCHG.ILGEH.DSSVAVW.G.NV.
Retrocopy NLGDILTYVTWKISGLLKHHVIGSGCNPDSARFHCLMDEKFGIHPSSCHGRILGEHSDSSVAVWIGMNVT

Parental  GVSLQELNPEMGTDNDSENWKEVHKMVVESAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMV
          G.SLQELNPE.GTDNDSENWKEVHKMVVE.AYEV.KL.GYT.W..GLSVADLIESMLKNLSRIH.VS.MV
Retrocopy GFSLQELNPEIGTDNDSENWKEVHKMVVENAYEVNKLNGYTHWDTGLSVADLIESMLKNLSRIHLVSIMV

Parental  KGMYGIENEVFLSLPCILNARGLTSVINQKLKDDEVAQLKKSADTLWDIQKDLKDL
          KGMYGIENEVFLSLP.ILNARGLTSVINQKLKDDEVAQ.KKS.DT.WDIQKDLKDL
Retrocopy KGMYGIENEVFLSLPYILNARGLTSVINQKLKDDEVAQFKKSTDTPWDIQKDLKDL

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	0.05 RPM	370.61 RPM
SRP007412_cerebellum	0.04 RPM	385.16 RPM
SRP007412_heart	0.29 RPM	1606.74 RPM
SRP007412_kidney	0.13 RPM	806.42 RPM
SRP007412_liver	0.00 RPM	20.10 RPM
SRP007412_testis	0.00 RPM	94.95 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3237 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3237 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3237 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4863
Gorilla gorilla	retro_ggor_3033
Pongo abelii	retro_pabe_3780

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 42 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,
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,
Pan troglodytes	ENSPTRG00000003421	5 retrocopies	retro_ptro_1540, retro_ptro_1618, retro_ptro_2039, retro_ptro_259, retro_ptro_2875,
Pan troglodytes	ENSPTRG00000003423	1 retrocopy	retro_ptro_62,
Pan troglodytes	ENSPTRG00000004762	1 retrocopy	retro_ptro_3237 ,
Sus scrofa	ENSSSCG00000000576	1 retrocopy	retro_sscr_37,
Tarsius syrichta	ENSTSYG00000013759	7 retrocopies	retro_tsyr_1130, retro_tsyr_1532, retro_tsyr_1860, retro_tsyr_2051, retro_tsyr_334, retro_tsyr_64, retro_tsyr_986,