RetrogeneDB ID: retro_mmus_854

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:31018516..31019821(+)
• Located in intron of: None

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_854
TCTTGTCCATCTGATCCCATTCTCTAACATCCTGTTGCGGTGGCTCTGGATACAAAGGGACCTGAGATCTGGAATGGGCT
CACCAAGGGCAGCGGCACTGCAGAGGTGGAGCTGAAGAAGGTAGCCACTCCGAAGACCACCCTGGACAACGATTACATGG
AGAAGTGTGACGAGAGGATCCTGTGGCTGGACTACAAGAACATCTGCAAGGTGGTGGAGGTGGGCAGCAAGATCTACGTG
GACGATGGGCTCATCTCACTGCAGGTGAAGGAGAAAGGTGCTGACTTCCTAGTGACCGAAGTGGAGAATGGTGGCTCCTT
GGACAGCAAGAAGGGCGTGAACCTGCCCGGCGCTGCTGTGGATCTCCCCGCTGTGTTGGAAAAGGACATCTAGGACCTGA
AGTTTGGGGTGGAGCAGGATGTGGACATGGTGTTTGCATCTTTCATCTGCAAGGCAGCCGACGTGCATGAAGTCAGGAAG
GTCCTAGGAGAGAAGGGCAAGAACATCAAGATCATCAGCAAAATCGAGAACTATGAAGGTGTCCGCAGGTTTGATGAGAT
CTTGGAGGCCAGTGATGGGATCATGGTGGCTCGTGGTGACCTGGGCATTGTGATTCCTGCAGAGAAGGTCTTCCTAGCTC
AGGAGATGAAGATCGGACGATGCAACTGAGCTGGGAAGCCTGTCATCTGTGCCACGCAGATGCTGGAGAGCATGATCAAG
AAGCCACTCCCCACCCGTGCTGAAGGCAGTGATGTGGCCAACGCAGTCCTGGATGGAGCAGACTGCTTCATGCTGTCTGG
AGAAACCGCCAAGGGGGACGACCCTCTGGAGGCTGTTCTCATGCAGCACCTGACTGCCCGAGAGGCAGAGGCTGCCATCT
ACCACTTGCAGCTATTCGAGGAACTCCTCTACTTGGCGCCCATTACCACCGACCCCACAGAAGCTGCTGCCGTGGGCGCC
ATGAAGGCCTCCTTCAAGTGCTGCAGTGGGGCCATTATCGTGCTCTCCAAGTCTGGCAGGAGTGCTCACCAAGTGGCCAG
GTACCGCCCTCGGGCTCCCATCATTGCTGTGACGTGCAATCCCCAGACTGCTCGCCAGGCCCATCTGTACCGTGGCATCT
TCCCTGTGCTGTGTAAGGATGCCGTACTGAATGCCTGGGCTGAGGATGTTGACCTTCGTGTAAACTTGGCCATGGATGTT
GGCAAGGCCCGAGGCTTCTTCAAGAAGGGATATGTGGTCATTGTGCTGACCGGGTGGCGCCCTGGCTCTGGATTCACCAA
CACCATGCGTGTAGTGCCTGTACCT

Alignment

ORF - retro_mmus_854 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.18 %
• Parental protein coverage: 81.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICK
          S..SDPIL..PVAVALDTKGPEI..GL.KGSGTAEVELKK.AT.K.TLDN.YMEKCDE.ILWLDYKNICK
Retrocopy SCPSDPIL*HPVAVALDTKGPEIWNGLTKGSGTAEVELKKVATPKTTLDNDYMEKCDERILWLDYKNICK

Parental  VVEVGSKIYVDDGLISLQVKEKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQD
          VVEVGSKIYVDDGLISLQVKEKGADFLVTEVENGGSL.SKKGVNLPGAAVDLPAV.EKDI.DLKFGVEQD
Retrocopy VVEVGSKIYVDDGLISLQVKEKGADFLVTEVENGGSLDSKKGVNLPGAAVDLPAVLEKDI*DLKFGVEQD

Parental  VDMVFASFIRKAADVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKV
          VDMVFASFI.KAADVHEVRKVLGEKGKNIKIISKIEN.EGVRRFDEILEASDGIMVARGDLGI.IPAEKV
Retrocopy VDMVFASFICKAADVHEVRKVLGEKGKNIKIISKIENYEGVRRFDEILEASDGIMVARGDLGIVIPAEKV

Parental  FLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVR
          FLAQ.M.IGRCN.AGKPVICATQMLESMIKKP.PTRAEGSDVANAVLDGADC.MLSGETAKGD.PLEAV.
Retrocopy FLAQEMKIGRCN*AGKPVICATQMLESMIKKPLPTRAEGSDVANAVLDGADCFMLSGETAKGDDPLEAVL

Parental  MQHLIAREAEAAIYHLQLFEELRRLAPITSDPTEAAAVGAVEASFKCCSGAIIVLTKSGRSAHQVARYRP
          MQHL.AREAEAAIYHLQLFEEL..LAPIT.DPTEAAAVGA..ASFKCCSGAIIVL.KSGRSAHQVARYRP
Retrocopy MQHLTAREAEAAIYHLQLFEELLYLAPITTDPTEAAAVGAMKASFKCCSGAIIVLSKSGRSAHQVARYRP

Parental  RAPIIAVTRNPQTARQAHLYRGIFPVLCKDAVLNAWAEDVDLRVNLAMDVGKARGFFKKGDVVIVLTGWR
          RAPIIAVT.NPQTARQAHLYRGIFPVLCKDAVLNAWAEDVDLRVNLAMDVGKARGFFKKG.VVIVLTGWR
Retrocopy RAPIIAVTCNPQTARQAHLYRGIFPVLCKDAVLNAWAEDVDLRVNLAMDVGKARGFFKKGYVVIVLTGWR

Parental  PGSGFTNTMRVVPVP
          PGSGFTNTMRVVPVP
Retrocopy PGSGFTNTMRVVPVP

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	0.14 RPM	753.97 RPM
SRP007412_cerebellum	0.39 RPM	976.07 RPM
SRP007412_heart	0.50 RPM	1282.44 RPM
SRP007412_kidney	0.33 RPM	505.13 RPM
SRP007412_liver	0.00 RPM	20.45 RPM
SRP007412_testis	0.18 RPM	322.64 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_854 was not detected

EST

No EST(s) were mapped for retro_mmus_854 retrocopy.

TSS

No TSS is located nearby retro_mmus_854 retrocopy 5' end.

Lab

retro_mmus_854 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_854 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,