RetrogeneDB ID: retro_mmus_2065

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:100460459..100461753(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000094873
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pkm
• Ensembl ID: ENSMUSG00000032294
• Aliases: Pkm, AA414905, AL024370, AL024424, Pk-2, Pk-3, Pk3, Pkm2
• Description: pyruvate kinase, muscle [Source:MGI Symbol;Acc:MGI:97591]

Sequence

>retro_mmus_2065
CCGAAGCCACACAGCAAAGCAGGGACTGCCTTCATTCATACCTAGCAGCTCCATGTAGCCATGGCTGACACCTTCCTGGA
ACACATGTGCTGCCTGGACATTGACTCCGTGCCCATCAGGGCCTGCAACACTGGCATCATTTGTACCATTGGGCCTGCTT
CCCGATCTGTGGAGATGCTGAAGGAGATGATTAAGTCTAGAATGAATGTGGCTCAGTAGAATTTCTCTCATAGAACCCAT
GAGTACCATGCAGAGACCATTAAGAATGTCCGTGAAGCCACAGAAAGCTTTGCATCTGATTCCATTCTCTACCGTCCCAT
TGTGGTGGCTCTGGATACAAAGGGACCCGAGATCTGGACTGGACTCATCAAGGGTAGCGGCACTGAAGAGATGGAGCTGA
AGAGGGGAGCCACTCTGAAGATCACCCTGAACAAAGCTTTCATGAAGTGTGACGAGAGGATCCTGTGGCTGGACTACAAG
AACATCTGCAAGGTGGTGGAGGTGGGCAGCAAGATCTCCGTGGACGATGGGCTCATCTCACTGCAGGTGAAGGAGAAAGG
TGCTGGCTTCCTGGTGACAAAGGTGGAGAATGGTGCGTCCTTGGGCAGCAAGAAGTGTGTGATCCTGTCCGGCGCTGCTG
TGGATCTCCCCGCTGTGTCGGAAAAGGACATCCATGACCTAAAGTTTGGGGTGGAGCAGGATGTGGACATAGTGCTTGCA
TCTTTCATCCGCAAAGCAGCTGGTGTGCATGAAGTCAGGAAGGTCCTGGGAGAGAAGGGCAAGAACATCAATATCATCAG
CAAGATTGAGAACCATGAAGGTGTCCGCAGGTTTGATGAGATCTTGGAGGCCAGTGATGGGATGATGGTGGCTCGTGGTG
ACCTGGGCATTGAGATTCTTGCAGAGAAGGTCTTCCTGGCTCAGAAGACGATGAACGGAAGATGCAACCAAGCTGGGAAG
CTTGTCAAGTGTGCCACACAGATGCTGGAAAGCATAGTCAAGAATCCATGCCCCACTCATGCTGAAGGCAGTGATGTAGC
CAATGCAGTCCTGGATGGAGCAGACGGCATCGTGCTGTCCAGAGAAACTTCCAAGGGGGACTACCCTCCGGAGGGTGTTC
ACATGCAGCACCTGATTGCCCGAGAGGCAGAGGCTGTCATCTACCACTTACAGCTATTTGAGGAACTCCGCCGCCTGGCA
ACATTACCAGCGACCCCACAGAAGCTGCCACTGTGGGTACCGTGGAGGCCTCCTTCAATCCTGCAGTAGGGCCATTATCG
TGCTCACCAAGTCA

Alignment

ORF - retro_mmus_2065 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.29 %
• Parental protein coverage: 81.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSAPITARNTGIICTIGPASRSVEMLKEMIKSGMNV
          PKPHS.AGTAFI.T.QLH.AMADTFLEHMC.LDIDS.PI.A.NTGIICTIGPASRSVEMLKEMIKS.MNV
Retrocopy PKPHSKAGTAFIHT*QLHVAMADTFLEHMCCLDIDSVPIRACNTGIICTIGPASRSVEMLKEMIKSRMNV

Parental  ARLNFSHGTHEYHAETIKNVREATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATLK
          A..NFSH.THEYHAETIKNVREATESFASD.ILYRP..VALDTKGPEI.TGLIKGSGT.E.ELK.GATLK
Retrocopy AQ*NFSHRTHEYHAETIKNVREATESFASDSILYRPIVVALDTKGPEIWTGLIKGSGTEEMELKRGATLK

Parental  ITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKEKGADFLVTEVENGGSLGSKKGVNL
          ITL..A.M.KCDE.ILWLDYKNICKVVEVGSKI.VDDGLISLQVKEKGA.FLVT.VENG.SLGSKK.V.L
Retrocopy ITLNKAFM-KCDERILWLDYKNICKVVEVGSKISVDDGLISLQVKEKGAGFLVTKVENGASLGSKKCVIL

Parental  PGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKAADVHEVRKVLGEKGKNIKIISKIENHEGVRRFD
          .GAAVDLPAVSEKDI.DLKFGVEQDVD.V.ASFIRKAA.VHEVRKVLGEKGKNI.IISKIENHEGVRRFD
Retrocopy SGAAVDLPAVSEKDIHDLKFGVEQDVDIVLASFIRKAAGVHEVRKVLGEKGKNINIISKIENHEGVRRFD

Parental  EILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANA
          EILEASDG.MVARGDLGIEI.AEKVFLAQK.M.GRCN.AGK.V.CATQMLES..K.P.PT.AEGSDVANA
Retrocopy EILEASDGMMVARGDLGIEILAEKVFLAQKTMNGRCNQAGKLVKCATQMLESIVKNPCPTHAEGSDVANA

Parental  VLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLAP-ITSDPTEAAAVGAVEAS
          VLDGAD.I.LS.ET.KGDYP.E.V.MQHLIAREAEA.IYHLQLFEELRRLA..ITSDPTEAA.VG.VEAS
Retrocopy VLDGADGIVLSRETSKGDYPPEGVHMQHLIAREAEAVIYHLQLFEELRRLAT<ITSDPTEAATVGTVEAS

Parental  F-KCCSGAIIVLTKS
          F...CS.AIIVLTKS
Retrocopy F<QSCSRAIIVLTKS

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	0.00 RPM	753.97 RPM
SRP007412_cerebellum	0.00 RPM	976.07 RPM
SRP007412_heart	0.03 RPM	1282.44 RPM
SRP007412_kidney	0.00 RPM	505.13 RPM
SRP007412_liver	0.00 RPM	20.45 RPM
SRP007412_testis	0.00 RPM	322.64 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2065 was not detected

EST

No EST(s) were mapped for retro_mmus_2065 retrocopy.

TSS

No TSS is located nearby retro_mmus_2065 retrocopy 5' end.

Lab

retro_mmus_2065 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2065 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,