RetrogeneDB ID: retro_rnor_2703

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:98057305..98058337(+)
• 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_2703
CAGATCCAACAGCTCGATGCAGTCATGGCTGACACCTTCCTGGAACACACGCGCTGCCTGGACGTTGACTCCACACCCAT
CATGGCCCGCAACACTGGCATCATTTGTACCAATGGCGCTGCCCCCGATCTGTGGAGATGCTGAAGAAGATGTTTAAGTC
TGGGATGAATGTGGCTCGGCTGAATTTCTCTCATGGAACCCATGAGTACCATGCAGAGACCATCAAGAATGCCCGTGCAG
CCACAGAAAGCTTTGCATCTGATCCCATTCTCTACCGTCCCATTGTGGTGGCTGTGGACACAAAGGGACCTGAGATCCGG
ACGGCACTCATCAAGGGCAGCAGCCCTGAAGAGGTGGAGATGAAGAAGGGAGCCACGCTGAAGATCACCCTGGACAACGC
CTACATGGAGAACTGTGACAAGAGCATCCTGTGGCTGGACTATAAGAACATCTGCAAGGTGGTGGAGGTGGGTAGCAAGA
TCTACTTGGACAATGGGCTCATCTCTCTGCAGGCGAAGGAGAAAGGAACTGACTACCTGGTGACAGAGGTGGAGAATGGT
GGCTCCTCGGGCAGCAAGAAGGGCATGAACCTGCCCGGTGCTGCTGTGGACCTCCCTGCCATGTCAGAAAAGGACATCCA
GGATCTGAAGTTTGGGGTGGAGCGGGACGTGGACATGGTGTTTGCGTCTTTCATCTGCAAGGCAGCCGACGTGCATGAGG
TTAGGAAGGGTCCTGGGAGAGAAGGGCAAGAGCATCAAGGTCATCAGCAAAATCGAGAACCATGAAGGTGTCCATTAGTT
TGATGAGATTTTGGGGTCCAGTGATGGGATCATGGTGGCTCGTGGTGACCTGAGCATTGAGATTCCTGCAGAGAAGGTCT
TCCAGGTTCAGAAGATGATGATCCGACGATGCAACCAAGCTGGGAAGTCTGTCCTCTGTGCCACACAGATGCTGGAGAGC
GTGATCAAGAAGCCACGCCCCACCTGTGCTGAAGGCAGTGACGTGGCCAATGCAGTCCTAGATGGAGCAGAC

Alignment

ORF - retro_rnor_2703 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.97 %
• Parental protein coverage: 64.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QTQQLHAAMADTFLEHMCRLDIDSAPITARNTGIICTIGPAS-RSVEMLKEMIKSGMNVARLNFSHGTHE
          Q.QQL.A.MADTFLEH...LD.DS.PI.ARNTGIICT.G.A..RSVEMLK.M.KSGMNVARLNFSHGTHE
Retrocopy QIQQLDAVMADTFLEHTRCLDVDSTPIMARNTGIICTNGAAP<RSVEMLKKMFKSGMNVARLNFSHGTHE

Parental  YHAETIKNVRAATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATLKITLDNAYMEKC
          YHAETIKN.RAATESFASDPILYRP..VA.DTKGPEIRT.LIKGS...EVE.KKGATLKITLDNAYME.C
Retrocopy YHAETIKNARAATESFASDPILYRPIVVAVDTKGPEIRTALIKGSSPEEVEMKKGATLKITLDNAYMENC

Parental  DENILWLDYKNICKVVEVGSKIYVDDGLISLQVKEKGADYLVTEVENGGSLGSKKGVNLPGAAVDLPAVS
          D..ILWLDYKNICKVVEVGSKIY.D.GLISLQ.KEKG.DYLVTEVENGGS.GSKKG.NLPGAAVDLPA.S
Retrocopy DKSILWLDYKNICKVVEVGSKIYLDNGLISLQAKEKGTDYLVTEVENGGSSGSKKGMNLPGAAVDLPAMS

Parental  EKDIQDLKFGVEQDVDMVFASFIRKAADVHEVRK-VLGEKGKNIKIISKIENHEGVRRFDEILEASDGIM
          EKDIQDLKFGVE.DVDMVFASFI.KAADVHEVRK.VLGEKGK.IK.ISKIENHEGV..FDEIL..SDGIM
Retrocopy EKDIQDLKFGVERDVDMVFASFICKAADVHEVRK>VLGEKGKSIKVISKIENHEGVH*FDEILGSSDGIM

Parental  VARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGAD
          VARGDL.IEIPAEKVF..QKMMI.RCN.AGK.V.CATQMLES.IKKPRPT.AEGSDVANAVLDGAD
Retrocopy VARGDLSIEIPAEKVFQVQKMMIRRCNQAGKSVLCATQMLESVIKKPRPTCAEGSDVANAVLDGAD

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	0.79 RPM	402.69 RPM
SRP017611_kidney	0.00 RPM	89.60 RPM
SRP017611_liver	0.40 RPM	3.56 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2703 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2703 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2703 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,