RetrogeneDB ID: retro_mmus_2636

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:22724577..22726168(-)
• Located in intron of: ENSMUSG00000097207

Retrocopy information

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

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_2636
ATGCCGAAGCCACACAGTGAAGCGGGGACTGCCTTCATTCAGACCCAGCAGCTCCATGCAGCCATGGCTGACACCTTCCT
GGAACACATGTGCCGCCTGGACATTGACTCTCCCCCCATCACGGCCCGCAACACTGGCATCATTTGTACCATTGGGCCTG
CTTCCCGATCTGTGGAGATGCTGAAGGAGATGATCAAGTCTGGAATGAATGTGGCTCGGCTGAATTTCTCTCATGGAACT
CATGAGTACCATGCAGAGACCATCAAGAATGTTCGTGAAGCCACAGAAAGCTTTGCATCTGATCCCATTCTCTACCGTCC
TGTTGCGGTGGCTCTGGATACAAAGGGACCTGAGATCCGGACTGGACTCATCAAGGGCAGCAGTACCGCTGAGGTGGAGC
TGAAGAAGGGAGCCACTCCGAAGAGCACCCTGGACAACGCTTACATGGAGAAGTGTGACGAGAACATCCTGTGGCTGGAT
ACAAGAACATCTGCAAGGTGGTGGAGGTGGGCAGCAAGATCTATGTGGACGATGGGCTCATCTCACTGCAGGTGAAGGAG
AAAGGCGCTGACTTCCTGGTGACGGAGGTGGAGAATGGTGGCCCCTTGGGCAGCAAGAAGGGCATGAACCTGCCGGGCGC
TGCTGTGGATCTCCCCGCTGTGTCGGAAAAGGACATCCAGGACCTGAAGTTTGGGGTGGAGCAGGATGTGGACATGGTGT
TTGCATCTTTCATCCGCAAGGCAACCGATGTGCATGAAGTCAGGAAGGTGCTGGGAGAGAAGGGCAAGAACATCAACATC
ATCAGCAAAATCGAGAACCATGAAGGCGTCCGCAGGTTTGATGAGATCTTGGAGGCCAGTGATGGGATCATGGTGGCTCG
TGGTGACCTGGACATTGAGATTCCTGCAGAGAAGGTCTTCCTGGCTCAGAAGATGATGATCGGGCGATGCAACCGAGCTG
GGAAGCCTGTCATCTGTGCCACACAGATGCTGGAGAGCATGATCAAGAAGTCACGCCCCACCCGTGCTGAAGGCAGTGAT
GTGGCCAATGCAGTCCTGGATGGAGCAGACTGCATCATGCTGTCTGGAGAAACAGCCAAGGGGGACTACCCTCTGGAGGC
TGTACGCATGCAGCACCTGATTGCCCGAGAGCAGAGGCTGCCATCTACCACTTGCAGCTATTTGAGGAATTCCGCCGCCT
GGCGCCCATTACCAGCGACCCCACAGAAGCTGCTGCCGTGGGTGCCGTGGAGGCCTCCTTCAAGTGCTGCAGTGGGGCCA
TTATCGTGCTCACCAAGTCTGGCAGGAGTGCTCACCAAGTGGCCAGGTACCGCCCTCGGGCTCCTATCATTGCCGTGACT
CGAAATCCCCAGACTGCTCGCCAGGCCCATCTGTACCGTGGCATCTTCCCTGTGCTGTGTAAGGATGCCTTACTGAATGC
CTGGGCTGAGGATGTCGACCTTCGTGTAAACTTGGCCATGGATGTTGGCAAGGCCCGAGGCTTCTTCAAGAAGGGAAATG
TGGTCATTGTGCTGACCGGGTGGCGCCCTGGCTCTGGATTCACCAACACCATGCGTGTAGTGCCTGTACCT

Alignment

ORF - retro_mmus_2636 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.19 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSAPITARNTGIICTIGPASRSVEMLKEMIKSGMN
          MPKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDS.PITARNTGIICTIGPASRSVEMLKEMIKSGMN
Retrocopy MPKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVEMLKEMIKSGMN

Parental  VARLNFSHGTHEYHAETIKNVREATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATL
          VARLNFSHGTHEYHAETIKNVREATESFASDPILYRPVAVALDTKGPEIRTGLIKGS.TAEVELKKGAT.
Retrocopy VARLNFSHGTHEYHAETIKNVREATESFASDPILYRPVAVALDTKGPEIRTGLIKGSSTAEVELKKGATP

Parental  KITLDNAYMEKCDENILWLD-YKNICKVVEVGSKIYVDDGLISLQVKEKGADFLVTEVENGGSLGSKKGV
          K.TLDNAYMEKCDENILWLD.YKNICKVVEVGSKIYVDDGLISLQVKEKGADFLVTEVENGG.LGSKKG.
Retrocopy KSTLDNAYMEKCDENILWLD<YKNICKVVEVGSKIYVDDGLISLQVKEKGADFLVTEVENGGPLGSKKGM

Parental  NLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKAADVHEVRKVLGEKGKNIKIISKIENHEGVRR
          NLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKA.DVHEVRKVLGEKGKNI.IISKIENHEGVRR
Retrocopy NLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKATDVHEVRKVLGEKGKNINIISKIENHEGVRR

Parental  FDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVA
          FDEILEASDGIMVARGDL.IEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKK.RPTRAEGSDVA
Retrocopy FDEILEASDGIMVARGDLDIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKSRPTRAEGSDVA

Parental  NAVLDGADCIMLSGETAKGDYPLEAVRMQHLIARE-AEAAIYHLQLFEELRRLAPITSDPTEAAAVGAVE
          NAVLDGADCIMLSGETAKGDYPLEAVRMQHLIARE.AEAAIYHLQLFEE.RRLAPITSDPTEAAAVGAVE
Retrocopy NAVLDGADCIMLSGETAKGDYPLEAVRMQHLIARE<AEAAIYHLQLFEEFRRLAPITSDPTEAAAVGAVE

Parental  ASFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDAVLNAWAEDVDL
          ASFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDA.LNAWAEDVDL
Retrocopy ASFKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDALLNAWAEDVDL

Parental  RVNLAMDVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP
          RVNLAMDVGKARGFFKKG.VVIVLTGWRPGSGFTNTMRVVPVP
Retrocopy RVNLAMDVGKARGFFKKGNVVIVLTGWRPGSGFTNTMRVVPVP

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	0.91 RPM	753.97 RPM
SRP007412_cerebellum	0.69 RPM	976.07 RPM
SRP007412_heart	2.09 RPM	1282.44 RPM
SRP007412_kidney	0.83 RPM	505.13 RPM
SRP007412_liver	0.03 RPM	20.45 RPM
SRP007412_testis	0.78 RPM	322.64 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2636 was not detected

EST

No EST(s) were mapped for retro_mmus_2636 retrocopy.

TSS

No TSS is located nearby retro_mmus_2636 retrocopy 5' end.

Lab

retro_mmus_2636 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2636 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,