RetrogeneDB ID: retro_rnor_515

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:200648795..200649897(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000015130
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_515
ATGCCGAAGCCACACAGCGAAGCAGGGACTGCCTTCATTCAGACCCAGCAGCTCCATGTAGCCATGGCTGACACCTTCCT
GGAACACATGTGCCGCCTAGACATTGACTCCGCACCCATCACGGCCCACAACACTGGCATCATTTGTACCATTGGTCCTG
CTTCCCGATTTGTGGAGATGCTAAAGAGATGATTAAGTCTGGGATGAATGTGGCTCGGCTGAATTTCTCTCATGGAACCC
ATGAGTACCATGCAGAGACCATCAAGAATGTCCGTGCAGCCACAGAAAGCTTTGCATCTGATCCCTTTCTCTACTGTCCC
ATTGCGGTGGCTCTGGACACAAAGGGACCGGAGATCCGAACTGGACTCATCAAAGGCAGCGGCACTGCAGAGGTGGAGCT
GAAGAAGGGAGCCACTCTGAAGATCACCCGGACAACGCCTACATGGAGAAGTGCGACGAGAACAGCCTGTGGTTGGACTA
TAAGAACATCTGCAAGGTGGTGGAGGTGGGCAGCAAGATCTGCGTGGACGATGGGCTCGTCTCTCTGCAGGCGAAGGAGA
AAGGTGCTGACTACCTGGTGACAGAGGTGGAGAATGGTGACTCCTTGGGCAGCAAGAAGGGCGTGAACCTGCCCGGTGCT
GCTGTGGACATCCCTGCCGTGTTAGAAAAGGACATCCAGGACCTGAAGTTTGTGGTGGAACAGGACGTGGACATGGTGTT
TGCGTCTTTCATCCTCAAGGTGGCTGACGTGCATGAGGTTAGGAAGATCCTGGGAGAGAAGGGCAAGAACATCAAGATCA
TCAGCAAAATCGAGAACCATGAAGGTGTCCGCAGGTTTGATGAAGTTTTGGAGGCCAGTGATGGGATCATGGTAGCTCGT
GGTGACCTGGGCATTGAGATTCCTGCAGAGAAGTTCTTCTTGGCTCAGAAGATGATGATCGGACGATACAACCGAGCTGG
GAAACTGGTCGTCTGCGCCACACAGATGCTGGAGAGCATGGTCAAGAAGCCACGCTCCACCCGTGCTGAAGGCAGTGACG
TGGCCAATGCAGTCCTAGATGGAGCAGACTGCATCATGCTGTCTGAAGAAACAGCCAAAGGA

Alignment

ORF - retro_rnor_515 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.16 %
• Parental protein coverage: 69.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKPDSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSAPITARNTGIICTIGPASRSVEMLK-EMIKSGM
          MPKP.SEAGTAFIQTQQLH.AMADTFLEHMCRLDIDSAPITA.NTGIICTIGPASR.VEMLK.EMIKSGM
Retrocopy MPKPHSEAGTAFIQTQQLHVAMADTFLEHMCRLDIDSAPITAHNTGIICTIGPASRFVEMLK<EMIKSGM

Parental  NVARLNFSHGTHEYHAETIKNVRAATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGAT
          NVARLNFSHGTHEYHAETIKNVRAATESFASDP.LY.P.AVALDTKGPEIRTGLIKGSGTAEVELKKGAT
Retrocopy NVARLNFSHGTHEYHAETIKNVRAATESFASDPFLYCPIAVALDTKGPEIRTGLIKGSGTAEVELKKGAT

Parental  LKITL-DNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKEKGADYLVTEVENGGSLGSKKG
          LKIT..DNAYMEKCDEN.LWLDYKNICKVVEVGSKI.VDDGL.SLQ.KEKGADYLVTEVENG.SLGSKKG
Retrocopy LKITR<DNAYMEKCDENSLWLDYKNICKVVEVGSKICVDDGLVSLQAKEKGADYLVTEVENGDSLGSKKG

Parental  VNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKAADVHEVRKVLGEKGKNIKIISKIENHEGVR
          VNLPGAAVD.PAV.EKDIQDLKF.VEQDVDMVFASFI.K.ADVHEVRK.LGEKGKNIKIISKIENHEGVR
Retrocopy VNLPGAAVDIPAVLEKDIQDLKFVVEQDVDMVFASFILKVADVHEVRKILGEKGKNIKIISKIENHEGVR

Parental  RFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDV
          RFDE.LEASDGIMVARGDLGIEIPAEK.FLAQKMMIGR.NRAGK.V.CATQMLESM.KKPR.TRAEGSDV
Retrocopy RFDEVLEASDGIMVARGDLGIEIPAEKFFLAQKMMIGRYNRAGKLVVCATQMLESMVKKPRSTRAEGSDV

Parental  ANAVLDGADCIMLSGETAKG
          ANAVLDGADCIMLS.ETAKG
Retrocopy ANAVLDGADCIMLSEETAKG

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	0.00 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_515 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_515 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_515 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,