RetrogeneDB ID: retro_mmus_1678

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:92717935..92718873(-)
• 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_1678
AATGGGTTGATTTCACTACAGGTGACAGAGAAAGGTGCTGAGTACTTTGTGACAGAAGTGGAGAATGGTGACTCATTGTG
CAGCAAGAAAAAGGAAACCTTGCCCGGAGATGCTGTGGATTTCCTTGCCCTGTCATAAAAGGACATCCAGGATCTGATAT
TTGGGATACAGGAGGGTATAGACATGATATTTGGGTATTTTATCAGCAAGGTAGCTGATGTGCATGAAAGTCCTGGGAAA
GATGGGTAAGAATATCAAGATCATCAGCAAAATCGAGAACCATGAAAGTGTCTGCAGGTTTAATAAGATTTTGGAGGCCA
GTGATGGGTTCATAGTGGCTCATTGTGACCTGGGTATTGAAATTCCTGCTGGGAAGGTATTTCTGGTTCAGAAGATGATA
ATCAGACAATGCAACCAAAGTAGGAAAGAAGCCTGTACTCTTCACCACACAGAAGCTGGAGAACAAGATCAAGAAGCCAT
GCCCCACCCATGCTGAAGGCAGTGATATGGCCAATGCAGTCGTAGATGGAGAAGACTGTATCATTCTATGGGAAGAAACA
ACCAAAGGGACTACCTTCTAGAAACTGTTCACATGCTCACTTGAGTGCCTGAGAGGTAAAGGCTGCCATATCCCCTTGCA
GTTATTCTAAGAGCTCAGACATTTGGCACCCATTACCAGAGACCCCATAGAAGCTGCCCCTGTGAGCATTGTGAAGGCTT
CCTTCAAGTGCTGCAGTGGAGCAATTATTGTACACACCAATGGCAGAAATGTTCATTAAGTGGCCAAGTACCACCCTCAT
TCTCCTATCAATGCTGTGATACACAATCCAAAGGTGGCTCAAGAGACCTATCTGTGCAGTGGCATTTTTCCTGTGCTGTG
TAATGATAATGTACAGGATGCCTGGGCAAAGGATGTTGACCTTCATGTAAACTTGGCA

Alignment

ORF - retro_mmus_1678 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.8 %
• Parental protein coverage: 59.51 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DGLISLQVKEKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRK
          .GLISLQV.EKGA...VTEVENG.SL.SKK...LPG.AVD..A.S.KDIQDL.FG.....DM.F..FI.K
Retrocopy NGLISLQVTEKGAEYFVTEVENGDSLCSKKKETLPGDAVDFLALS*KDIQDLIFGIQEGIDMIFGYFISK

Parental  AADVHE-VRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGR
          .ADVHE.V....G...K.I..I...E....V.RF..ILEASDG..VA..DLGIEIPA.KVFL.QKM.I..
Retrocopy VADVHE>VLGKMGKNIKIISKIENHES---VCRFNKILEASDGFIVAHCDLGIEIPAGKVFLVQKMIIRQ

Parental  CN-RAGK-PVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKG-DYPLEAVRM-QHLIA
          CN...GK.PV...TQ.LE..IKKP.PT.AEGSD.ANAV.DG.DCI.L..ET.KG.DY.LE.V.M..HL.A
Retrocopy CN>KVGKKPVLFTTQKLENKIKKPCPTHAEGSDMANAVVDGEDCIILWEETTKG<DYLLETVHM<AHLSA

Parental  REAEAAI-YHLQLFEELRRLAPITSDPTEAAAVGAVEASFKCCSGAIIVLTKSGRSAHQVARYRPRAPII
          .E..AAI...LQLF.ELR.LAPIT.DP.EAA.V..V.ASFKCCSGAIIV.T..GR..H.VA.Y.P..PI.
Retrocopy *EVKAAI<IPLQLF*ELRHLAPITRDPIEAAPVSIVKASFKCCSGAIIVHT-NGRNVH*VAKYHPHSPIN

Parental  AVTRNPQTARQAHLYRGIFPVLCKDAVLNAWAEDVDLRVNLA
          AV..NP..A....L..GIFPVLC.D.V..AWA.DVDL.VNLA
Retrocopy AVIHNPKVAQETYLCSGIFPVLCNDNVQDAWAKDVDLHVNLA

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	0.00 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 actvity near the 5' end of retro_mmus_1678 was not detected

EST

No EST(s) were mapped for retro_mmus_1678 retrocopy.

TSS

No TSS is located nearby retro_mmus_1678 retrocopy 5' end.

Lab

retro_mmus_1678 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1678 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,