RetrogeneDB ID: retro_nleu_2716

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397406.1:594312..595569(-)
• Located in intron of: ENSNLEG00000000983

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_2716
ATGTCGAAGCCCGATAGTGAAGCCGGGACTGCCTTCATTCAGACCCAGCAGCTGCACGCAGCCATGGCTGACGCATTCCT
GGAGCACCTGTACCGCCTGGACGTTGATTCACCGCCCATCACAGCCCGGAACACTGGCATCCTCTGTACCATTGGCCCAG
CTTCCCGATCAGTGGAGACGTTGAAGGAGATGATTAAGTCTGGAATGAATGTGGCTCGTCTGAACTTCTCTCATGGAACT
CACGAGTACCACGCGGAGACCATCAGGAATGTGCGCACAGCCACGGAAAGCTTTGCTTCTGACCAGCCCGTTGCTGTGGC
TGTAGACACTAAAGGACCTGAGATCCGAACTGGGCTCATCAAGGGTGGCGGCACTGCAGAGGTGGAGCCGAAGAAGGGAG
CCACTCTCAAAATCACGCTGGATAACGCCTACGTGGAAACGTGTGACGAGAACACCCTGTGGCTGGACTACAAGAACATC
TGCAAGGTGGCGGAAGTGGGCAGCAAGATCTACGTGGGTGACGGGCTTATTTCTCTCCAGGTGAAGCAGAAAGGTGCCGA
CTTCCTGGTGACGGAGGTGGAAAATGGTGGCTCCTTGGGCAGCAAGAAGGGCGTGAACCTTCCTGGGGCTGCTGTGGACT
TGCCTGCTGTGTCGGAGAAGGACATCCAGGATCTGTAAGTTTGGGGTCGAGCAGGATGTTGACACGGTGTTTGCGTCATT
CATCCGCAAGGCATCTGATGTCCGTGAAGTGAGGAAGGTCCTGGGAGAGAAGGGAAAGAACATCAAGATAATCGGCAAAA
TCGAGAATCGTGAGCGGGTTCGGAGGTTTCATGAAATCCTGGAGGCCAGTGATGGGATCACGGTGGCTCGTGGTGATCTA
GGCATTGAGACTCCTGCAGAGAAGGTCTTCCTTGCTCAGAAGATGGTGATTGGACGGCGCAACCGAGCTGGGAAGCCTGT
CATCTGTGCTCCTCAGATGCTGGAGAGCGTGATCAAGAAGGCCCGCCCCACTCGGGCTGAAGGCAGTGATGTGGCCAGTG
CAGTCCTGGATGGAGCCGACTGCATCATGCTGTCTGGAGAAACAGCCAAAGGGGAAGGTCCTCTGGAGGCTGTCCGCATG
CAGCACCTGACTGCCCGGGAGGCAGAGGCCGCCATCTACCGCTCGCATCATCTGAGGAACTCCGCCGCCTGGCGCCCATT
ACCAGCGACCCCACAGAAGCCACCGCCGCGGGTGCCGTGGAGGCCTCCTTCGAGTGC

Alignment

ORF - retro_nleu_2716 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.82 %
• Parental protein coverage: 79.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMN
          MSKP.SEAGTAFIQTQQLHAAMAD.FLEH..RLD.DSPPITARNTGI.CTIGPASRSVETLKEMIKSGMN
Retrocopy MSKPDSEAGTAFIQTQQLHAAMADAFLEHLYRLDVDSPPITARNTGILCTIGPASRSVETLKEMIKSGMN

Parental  VARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATL
          VARLNFSHGTHEYHAETI.NVRTATESFASD.....PVAVA.DTKGPEIRTGLIKG.GTAEVE.KKGATL
Retrocopy VARLNFSHGTHEYHAETIRNVRTATESFASD----QPVAVAVDTKGPEIRTGLIKGGGTAEVEPKKGATL

Parental  KITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVN
          KITLDNAY.E.CDEN.LWLDYKNICKV.EVGSKIYV.DGLISLQVKQKGADFLVTEVENGGSLGSKKGVN
Retrocopy KITLDNAYVETCDENTLWLDYKNICKVAEVGSKIYVGDGLISLQVKQKGADFLVTEVENGGSLGSKKGVN

Parental  LPGAAVDLPAVSEKDIQDL-KFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRR
          LPGAAVDLPAVSEKDIQDL.KFGVEQDVD.VFASFIRKASDV.EVRKVLGEKGKNIKII.KIEN.E.VRR
Retrocopy LPGAAVDLPAVSEKDIQDL>KFGVEQDVDTVFASFIRKASDVREVRKVLGEKGKNIKIIGKIENRERVRR

Parental  QVPVVPAPVPXXXXXXDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVA
          ......A.........DLGIE.PAEKVFLAQKM.IGR.NRAGKPVICA.QMLES.IKK.RPTRAEGSDVA
Retrocopy FHEILEASDGITVARGDLGIETPAEKVFLAQKMVIGRRNRAGKPVICAPQMLESVIKKARPTRAEGSDVA

Parental  NAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAMFHRKLF-EELVRASSHSTDLMEAMAMGSVE
          .AVLDGADCIMLSGETAKG..PLEAVRMQHL.AREAEAA........EEL.R......D..EA.A.G.VE
Retrocopy SAVLDGADCIMLSGETAKGEGPLEAVRMQHLTAREAEAAIYRSHHL<EELRRLAPITSDPTEATAAGAVE

Parental  ASYKC
          AS..C
Retrocopy ASFEC

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_2716 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,