RetrogeneDB ID: retro_pabe_429

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:113678335..113679304(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PKM2
• Ensembl ID: ENSPPYG00000006613
• Aliases: PKM2, PKM
• Description: pyruvate kinase isozyme M1 [Source:RefSeq peptide;Acc:NP_001127083]

Sequence

>retro_pabe_429
ATGTCGAAGCCCCATAGTGAAGCTGGGACTGCCTTCATTCAGACCCAGCAGCTACATGCAGCCATGGCTGACACATTCTT
GGAGCACATGTGCCACCTGGACATTCACACACCACCCATCACAGCCTGGAACACTGGCATCATCTGTACCATTAGCCTAG
CTTCCTGATCGGTGGAGATGTTGAAGGAGATGATTAAGTCTGGAATGAATGTGGCTTGTCTGAACTTCTCTCATGGAACT
CATGAGTACCACGTGGAGACCATCAAGAGCATGTGCACAGCCACGGAAAGCTTCGCTGCTGACCCCATCCTCTACCGTCC
TGTTGTTTTGGCTCTGGATACTAAAGGACCTGAGATCCGAACTGGGCTCATCAAGGGCAGCAGCACCATAGAGGTGGGGC
TGAAGATGGGAGCCACTCTCAAAATCATGCTGGATAACGCCTACATGAAAAAGTGTGACGAGAACATCCTGTGGCTGGAC
TACAAGAGCATCTGCAAGGTGATGGAAGTGGGCAGCAAGATCTACGTGGATGATGGGCTTATTTCTCTCCAGGTAAAGCA
GAAAGGTGCTGACTTCCTGGTGACGGAGGTGGAAAATGGTGGTTCCTCGGGCAGCAAGAAGGGTGTGAACCTTCCTGGGG
CTGCTGTGCACTTGCCTGCTGTGTCAGAGGACATCCAGGACCTGAAGTTTGGGGTCGAGCAGGATGTCGATATGGTGTTT
GCGTCGTTCATCCGCAAGGCATCTGATGTCCATGAAGTTAGGGAGGCCCTGGGAGAGAAGGGAAAGAACATCAAGATAAT
CAACAAAATCGAGAATCATGTGGGGGTTCGGAGGTTTGATGAAATCCTAGAGGCCAGTGATGGGATCATGGTGGCTCGTG
GTGATCTAGGCATTGAGATTCCTGCAGAGAAGTTCTTCCTTGCTCAGAAGGTGATGATTGGGCGTTGCAGCTGAGCTGGG
AAGCCTATC

Alignment

ORF - retro_pabe_429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.58 %
• Parental protein coverage: 61.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMN
          MSKPHSEAGTAFIQTQQLHAAMADTFLEHMC.LDI..PPITA.NTGIICTI..AS.SVE.LKEMIKSGMN
Retrocopy MSKPHSEAGTAFIQTQQLHAAMADTFLEHMCHLDIHTPPITAWNTGIICTISLAS*SVEMLKEMIKSGMN

Parental  VARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATL
          VA.LNFSHGTHEYH.ETIK...TATESFA.DPILYRPV..ALDTKGPEIRTGLIKGS.T.EV.LK.GATL
Retrocopy VACLNFSHGTHEYHVETIKSMCTATESFAADPILYRPVVLALDTKGPEIRTGLIKGSSTIEVGLKMGATL

Parental  KITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLLTEVENGGSLGSKKGVN
          KI.LDNAYM.KCDENILWLDYK.ICKV.EVGSKIYVDDGLISLQVKQKGADFL.TEVENGGS.GSKKGVN
Retrocopy KIMLDNAYMKKCDENILWLDYKSICKVMEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSSGSKKGVN

Parental  LPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRF
          LPGAAV.LPAVSE.DIQDLKFGVEQDVDMVFASFIRKASDVHEVR..LGEKGKNIKII.KIENH.GVRRF
Retrocopy LPGAAVHLPAVSE-DIQDLKFGVEQDVDMVFASFIRKASDVHEVREALGEKGKNIKIINKIENHVGVRRF

Parental  DEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPV
          DEILEASDGIMVARGDLGIEIPAEK.FLAQK.MIGRC..AGKP.
Retrocopy DEILEASDGIMVARGDLGIEIPAEKFFLAQKVMIGRCS*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	0.06 RPM	1056.99 RPM
SRP007412_cerebellum	0.12 RPM	584.42 RPM
SRP007412_heart	0.03 RPM	414.49 RPM
SRP007412_kidney	0.13 RPM	391.89 RPM
SRP007412_liver	0.00 RPM	70.17 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_429 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_429 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_429 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 26 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,
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,
Pongo abelii	ENSPPYG00000006613	3 retrocopies	retro_pabe_2834, retro_pabe_3645, retro_pabe_429 ,
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,