RetrogeneDB ID: retro_rnor_2253

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:137972104..137972918(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pkm
• Ensembl ID: ENSRNOG00000011329
• Aliases: Pkm, PKM12, Pk3, Pkm2
• Description: Pyruvate kinase isozymes M1/M2 [Source:UniProtKB/Swiss-Prot;Acc:P11980]

Sequence

>retro_rnor_2253
ATGCCGCAGGCACACAGCGAAGCAGGGACTGCCTTCATTCAGACCCAACAGCTCCATGCAGCCAGAGCTGACACCTCCCT
GGAACATGTGTGCTGCCTGGACATGGACTCCACTCCCATCACGGCCCAGAACACTGGCATCATGTGTACCATTGACCCTG
CTTCCCGATCTGTGGAGATGCTGAAGGAGATGATTAAGTCTGGGATGAATGTGGCTCCGTTGAATTTCTCTCATGGAACT
CATGAGTACCAGGCAGAGACCATCAAGAATGTCCGTGTAGCCACAGAAAGCTTGGCATCTGGTCGCATTCTCTACTGTCC
CATTGCAGTGGCTCTGGACATAAAGGGACCGGAGATCAGAACTGGACTCACCAAGGGCAGACGCACCGCAGAGGTGGAGC
TGAAGAAGGGAGCCACTCTGAAGATCACCTGGACAATGCCTATGTGGAGAAGTGCGACAAAATCATCCGGTGGCTGGACT
GTAAGAACATCTGCAAGTTGATGGAGGCGGGCAGCAAGATCTACGTGGACGAAGGGTTCATCTCGCTGAGGTCAAAGAGA
AAGGTGCTGACTACCTGGTGTCAGAGATGGAGAATGGTGGCTCCTTGGGCAGCAAGAAGGGTGTGAACCTGCCTGGAGTT
GCTGCGGACCTGCCTGCCATGTCAGAAAAGGACGTCTAGGACCTGAAGTTTGGGGTGGAGCAGGGTGTGGACCTGGTGTT
TGCATCTTTCATCTGCAAGGCAGCTGATGTGCATGAAGTTTGGAAGGTCCTGGGAGAGAAGGGCAAGAACATCAAGATCA
TCAGCAAAATTGAG

Alignment

ORF - retro_rnor_2253 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.48 %
• Parental protein coverage: 51.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKPDSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSAPITARNTGIICTIGPASRSVEMLKEMIKSGMN
          MP...SEAGTAFIQTQQLHAA.ADT.LEH.C.LD.DS.PITA.NTGI.CTI.PASRSVEMLKEMIKSGMN
Retrocopy MPQAHSEAGTAFIQTQQLHAARADTSLEHVCCLDMDSTPITAQNTGIMCTIDPASRSVEMLKEMIKSGMN

Parental  VARLNFSHGTHEYHAETIKNVRAATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATL
          VA.LNFSHGTHEY.AETIKNVR.ATES.AS..ILY.P.AVALD.KGPEIRTGL.KG..TAEVELKKGATL
Retrocopy VAPLNFSHGTHEYQAETIKNVRVATESLASGRILYCPIAVALDIKGPEIRTGLTKGRRTAEVELKKGATL

Parental  KIT-LDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISL-QVKEKGADYLVTEVENGGSLGSKKG
          KIT.LDNAY.EKCD..I.WLD.KNICK..E.GSKIYVD.G.ISL..VKEKGADYLV.E.ENGGSLGSKKG
Retrocopy KIT<LDNAYVEKCDKIIRWLDCKNICKLMEAGSKIYVDEGFISL<EVKEKGADYLVSEMENGGSLGSKKG

Parental  VNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKAADVHEVRKVLGEKGKNIKIISKIE
          VNLPG.A.DLPA.SEKD..DLKFGVEQ.VD.VFASFI.KAADVHEV.KVLGEKGKNIKIISKIE
Retrocopy VNLPGVAADLPAMSEKDV*DLKFGVEQGVDLVFASFICKAADVHEVWKVLGEKGKNIKIISKIE

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
SRP017611_brain	0.00 RPM	402.69 RPM
SRP017611_kidney	0.49 RPM	89.60 RPM
SRP017611_liver	0.00 RPM	3.56 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2253 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2253 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2253 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 33 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,
Homo sapiens	ENSG00000067225	2 retrocopies	retro_hsap_210, retro_hsap_3418,
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,
Nomascus leucogenys	ENSNLEG00000013869	3 retrocopies	retro_nleu_1859, retro_nleu_2319, retro_nleu_2716,
Pongo abelii	ENSPPYG00000006613	3 retrocopies	retro_pabe_2834, retro_pabe_3645, retro_pabe_429,
Pan troglodytes	ENSPTRG00000007246	2 retrocopies	retro_ptro_2322, retro_ptro_335,
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,