RetrogeneDB ID: retro_ggor_281

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:117575211..117576204(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PKM2
• Ensembl ID: ENSGGOG00000005062
• Aliases: None
• Description: Pyruvate kinase [Source:UniProtKB/TrEMBL;Acc:G3QQT8]

Sequence

>retro_ggor_281
CAGCACTGGAGGACCTCAGCAGCCATGTCGAAGCCCCATAGTGAAGCCGGGACTGCCTTCATTCAGACCCAGCAGCTACA
TGCAGCCATGGCTGACACATTCCTGGAGCACATGTGCCACCTGGACATTCACACACCACCCATCCCAGGCTGGAACACTG
GCATCATCTGTACCATTAGCCCAGCTTCCCAATCAGTGGAGATGTTGAAGGAGATGACTAAGTCTGGAATGAATGTGGCT
TGTCTGAACTTCTCTCATGGAACTCATGAGTACCACATGGAGACCATCAAGAACATGTGCACAGCCACGGAAAGCTTTGC
TGCTGACCCCATCCTCTACCGGCCTGTTGCTTTGGGTCTGGATACTAAAGGACCTGAGATCCGAACTGGGCTCATCAAGG
GCAGCAGCACCATGGAGGTGGGGCTGAAGATGGGAGCCACTCTCAAAATCATGCTGGATAACACCTACATGAAAAAGTGT
GACGAGAACAACCTGTGGCTGGACTACAAGAACATCTGCAAGGTGATGGAAGTGGGCAGCAAGATCTAGGTGGATGATGG
GCTTATTTCTCTCCAGGTAAAGCAGAAAGGTGCTGACTTCCTGGTGACGGAGGTGGAAAATGGTGGTTCCTCGGGCAGCA
AGAAGGGTGTGAACCTTCCTGGGGCTGCTGTGGACTTGCCTGCTGTGTCAGAGGACATCCAGGACCTGAATTTTGGGGTC
GAGCAGGATGTCGATATGGTGTTTGCGTCGTTCATCCGCAAGGCATCTGATGTCCATGAAGTTAGGGAGGCCCTGGGAGA
GAAGGGAAAGAACATCAAGATAATCAACACAATCGAGAATCATGTGGGGGTTCGGAGGTTTGATGAAATCCTAGAGGCCA
GTGATGGGATCATGGTGGCTCATGGTAATCTAGGCATTGAGATTCCTGCAGAGAAGGTCTTCCTTGCTCAGAAGATGATG
ATTGGGTGTTGCAGCTGAGCTGGGAAGCCTATC

Alignment

ORF - retro_ggor_281 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.75 %
• Parental protein coverage: 54.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ENQRTSAAMSKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLK
          ...RTSAAMSKPHSEAGTAFIQTQQLHAAMADTFLEHMC.LDI..PPI...NTGIICTI.PAS.SVE.LK
Retrocopy QHWRTSAAMSKPHSEAGTAFIQTQQLHAAMADTFLEHMCHLDIHTPPIPGWNTGIICTISPASQSVEMLK

Parental  EMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEV
          EM.KSGMNVA.LNFSHGTHEYH.ETIKN..TATESFA.DPILYRPVA..LDTKGPEIRTGLIKGS.T.EV
Retrocopy EMTKSGMNVACLNFSHGTHEYHMETIKNMCTATESFAADPILYRPVALGLDTKGPEIRTGLIKGSSTMEV

Parental  ELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGS
          .LK.GATLKI.LDN.YM.KCDEN.LWLDYKNICKV.EVGSKI.VDDGLISLQVKQKGADFLVTEVENGGS
Retrocopy GLKMGATLKIMLDNTYMKKCDENNLWLDYKNICKVMEVGSKI*VDDGLISLQVKQKGADFLVTEVENGGS

Parental  LGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIE
          .GSKKGVNLPGAAVDLPAVSE.DIQDL.FGVEQDVDMVFASFIRKASDVHEVR..LGEKGKNIKII..IE
Retrocopy SGSKKGVNLPGAAVDLPAVSE-DIQDLNFGVEQDVDMVFASFIRKASDVHEVREALGEKGKNIKIINTIE

Parental  NHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPV
          NH.GVRRFDEILEASDGIMVA.G.LGIEIPAEKVFLAQKMMIG.C..AGKP.
Retrocopy NHVGVRRFDEILEASDGIMVAHGNLGIEIPAEKVFLAQKMMIGCCS*AGKPI

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	0.14 RPM	1001.47 RPM
SRP007412_cerebellum	0.08 RPM	575.29 RPM
SRP007412_heart	0.00 RPM	301.53 RPM
SRP007412_kidney	0.00 RPM	306.67 RPM
SRP007412_liver	0.00 RPM	34.50 RPM
SRP007412_testis	0.10 RPM	323.96 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_281 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_281 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 33 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,
Mus musculus	ENSMUSG00000032294	8 retrocopies	retro_mmus_1402, retro_mmus_1678, retro_mmus_1754, retro_mmus_2065, retro_mmus_2066, retro_mmus_2636, retro_mmus_3509, retro_mmus_854,
Nomascus leucogenys	ENSNLEG00000013869	3 retrocopies	retro_nleu_1859, retro_nleu_2319, retro_nleu_2716,
Pongo abelii	ENSPPYG00000006613	3 retrocopies	retro_pabe_2834, retro_pabe_3645, retro_pabe_429,
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,