RetrogeneDB ID: retro_mmus_3509

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:114021996..114022869(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082511
• 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_3509
ATGCCGAAGCCACACAGCAAAGCAGGGACTGCCTTCATTCAGACTCAGCAGATCCATGCAGCCATTATTGACACCTTCCT
GGAACATATGTGCCACCTGAACATTGACTCGGCACCCATCACAGCCTGCAACACTGACATCATTTGTACTGTTGGTCCTG
ATTTCTGATCTGTGGAGATGCTGAAGGAGATTATTAAGACTGGAATGATTGTGGCTCAACTGAATTTCTCTCATGGAACC
CATGAGTACCATGAAGAGACCATCAAGAATGTCTGTGCAGCCACAGAAAGTTTTACATCTGATACCATTCTCTACTATCG
CATTGCTGTGGCTCTGGACACAAAAGGACCTGAGATCCTGACTAGACTCATCAAGGGAAGCAGCACTGCAGAGATAGAGC
TGAGGAAGGGAGCCACTCTGAAGATCATCCTGGACAATGCCTATATGGAAATGTGTGACAAGAGCATCCTGCGGCTGGAC
TATAAGAACATTTGCAAGGTGATGGAGGTGGGCAGCAAGGTCTATGTGGATGATGGGCTCATCTCTCTGCAGGTGAAGGA
GAAAGGTGCTGACTACTTGGTGACATTGATTGAAAATCGTGGCTCCTTTTGTAGCAAGAAGGGCATGAACCTGTCCGGAG
CTGCTGTGGACCTCCCTACCATGTTAGAAAAGGACATCCAGGATTTGAAGTTTGGGGTGGAGGAGGATGTAGACATGGTG
TTTGCAAGTTTCATCTACAAGGCAGCAGACATGCATGAAGTTAGAAAGGCCCTGGGAGAGAAGAGCAAGAACATCAAGAT
CATCAGCAAAATCGAGAACTATGAAGGCACCTGCAGGTTTGATGGAATTTTGGAGGCCAGTGATGGGATCATG

Alignment

ORF - retro_mmus_3509 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.76 %
• Parental protein coverage: 54.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSAPITARNTGIICTIGPASRSVEMLKEMIKSGMN
          MPKPHS.AGTAFIQTQQ.HAA..DTFLEHMC.L.IDSAPITA.NT.IICT.GP...SVEMLKE.IK.GM.
Retrocopy MPKPHSKAGTAFIQTQQIHAAIIDTFLEHMCHLNIDSAPITACNTDIICTVGPDF*SVEMLKEIIKTGMI

Parental  VARLNFSHGTHEYHAETIKNVREATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATL
          VA.LNFSHGTHEYH.ETIKNV..ATESF.SD.ILY...AVALDTKGPEI.T.LIKGS.TAE.EL.KGATL
Retrocopy VAQLNFSHGTHEYHEETIKNVCAATESFTSDTILYYRIAVALDTKGPEILTRLIKGSSTAEIELRKGATL

Parental  KITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKEKGADFLVTEVENGGSLGSKKGVN
          KI.LDNAYME.CD..IL.LDYKNICKV.EVGSK.YVDDGLISLQVKEKGAD.LVT..EN.GS..SKKG.N
Retrocopy KIILDNAYMEMCDKSILRLDYKNICKVMEVGSKVYVDDGLISLQVKEKGADYLVTLIENRGSFCSKKGMN

Parental  LPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKAADVHEVRKVLGEKGKNIKIISKIENHEGVRRF
          L.GAAVDLP...EKDIQDLKFGVE.DVDMVFASFI.KAAD.HEVRK.LGEK.KNIKIISKIEN.EG..RF
Retrocopy LSGAAVDLPTMLEKDIQDLKFGVEEDVDMVFASFIYKAADMHEVRKALGEKSKNIKIISKIENYEGTCRF

Parental  DEILEASDGIM
          D.ILEASDGIM
Retrocopy DGILEASDGIM

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	0.02 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_3509 was not detected

EST

No EST(s) were mapped for retro_mmus_3509 retrocopy.

TSS

No TSS is located nearby retro_mmus_3509 retrocopy 5' end.

Lab

retro_mmus_3509 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3509 has 0 orthologous retrocopies within eutheria group .

---

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,