RetrogeneDB ID: retro_nleu_2319

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397343.1:5926226..5927050(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PKM2
• Ensembl ID: ENSNLEG00000013869
• Aliases: None
• Description: Pyruvate kinase [Source:UniProtKB/TrEMBL;Acc:G1RUB3]

Sequence

>retro_nleu_2319
ATGTTGAAGCCCCATAGTGAAGCCAGGGCTGCCTTCATTCAGACCCAGCAGCTGCACGCAGCCATGGCTGACACATTCTT
GGAGCACATGTGCTGCCTGGACACTGACTTGCCAACCATTACAGCCTGGAGCACTGGCATCATCAGTACTACGGGCCCAG
CTTCCCCATTGTTAGAGATGCTGAAGAAAACGATTAAGTCTGGAATGAATGTGGCTCATCTGAACTCTCATGGAACTCAT
GAGTACCATACAGAGACCATCAAGAACGTGTGCACAGCCACGGAAAGCTTCGCTTCTGACTCCATCCTCTACCGGCCCAT
TGCTATGGCTCTGGACACTAAAGGACCTGAGATCCCAACTGGGAGCATCAAGGGCAGTGGCACTGCAGAGGCGGAGCTGG
AGAAGGGAGCCACTCTCAAATTCACGCTGGATAAAACCTCCATGGAAAAGTGTAAGAGAACATCCTGTGGCTGGACTACA
AGAACATCTGCAAGGTGGCGGAAGTGGGCTGCAAGATCTACATGGATGATGGGCTAATTTCTCTCTAAGTGAAGCAGAAG
GATGCTCACTTTCTGGTGACAGAGGTGGAAAATGGTGGCTCCTTGGGCAGCAAGAAGGATGTGAACCTTCCTGGGGCTGC
CGTGGACCTGCCTGCCATATGGGAGAAGGACATCCAGGACCTGAAGTCTGGGGGCGAGCAAGATGTCGATATGATGTTTT
CGTCATCCATCCGCAAGACATCTGATGTCCATGAAGTTAGGAAGGTCTTGGGAGAGAAAGGAAAGAACATCAAGATAATC
AGCAAAATTGAGAATCATGACGGG

Alignment

ORF - retro_nleu_2319 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.95 %
• Parental protein coverage: 51.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMN
          M.KPHSEA..AFIQTQQLHAAMADTFLEHMC.LD.D.P.ITA..TGII.T.GPAS...E.LK..IKSGMN
Retrocopy MLKPHSEARAAFIQTQQLHAAMADTFLEHMCCLDTDLPTITAWSTGIISTTGPASPLLEMLKKTIKSGMN

Parental  VARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATL
          VA.LN.SHGTHEYH.ETIKNV.TATESFASD.ILYRP.A.ALDTKGPEI.TG.IKGSGTAE.EL.KGATL
Retrocopy VAHLN-SHGTHEYHTETIKNVCTATESFASDSILYRPIAMALDTKGPEIPTGSIKGSGTAEAELEKGATL

Parental  KITLDNAYMEKCD-ENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGV
          K.TLD...MEKC..ENILWLDYKNICKV.EVG.KIY.DDGLISL.VKQK.A.FLVTEVENGGSLGSKK.V
Retrocopy KFTLDKTSMEKCK<ENILWLDYKNICKVAEVGCKIYMDDGLISL*VKQKDAHFLVTEVENGGSLGSKKDV

Parental  NLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEG
          NLPGAAVDLPA..EKDIQDLK.G.EQDVDM.F.S.IRK.SDVHEVRKVLGEKGKNIKIISKIENH.G
Retrocopy NLPGAAVDLPAIWEKDIQDLKSGGEQDVDMMFSSSIRKTSDVHEVRKVLGEKGKNIKIISKIENHDG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_2319 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys 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 11 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013504	1 retrocopy	retro_chof_1430,
Callithrix jacchus	ENSCJAG00000018473	1 retrocopy	retro_cjac_236,
Felis catus	ENSFCAG00000000653	1 retrocopy	retro_fcat_105,
Homo sapiens	ENSG00000067225	2 retrocopies	retro_hsap_210, retro_hsap_3418,
Gorilla gorilla	ENSGGOG00000005062	1 retrocopy	retro_ggor_281,
Macropus eugenii	ENSMEUG00000004506	3 retrocopies	retro_meug_1482, retro_meug_2043, retro_meug_912,
Macaca mulatta	ENSMMUG00000023454	1 retrocopy	retro_mmul_183,
Nomascus leucogenys	ENSNLEG00000013869	3 retrocopies	retro_nleu_1859, retro_nleu_2319 , retro_nleu_2716,
Pan troglodytes	ENSPTRG00000007246	2 retrocopies	retro_ptro_2322, retro_ptro_335,
Rattus norvegicus	ENSRNOG00000011329	6 retrocopies	retro_rnor_1120, retro_rnor_2050, retro_rnor_2253, retro_rnor_2703, retro_rnor_515, retro_rnor_830,
Sarcophilus harrisii	ENSSHAG00000010300	1 retrocopy	retro_shar_90,