RetrogeneDB ID: retro_rnor_831

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 11:47653320..47654304(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mapk3
• Ensembl ID: ENSRNOG00000019601
• Aliases: Mapk3, ERK1, ERT2, Erk-1, Esrk1, MAPK1, MNK1, Prkm3, p44, p44erk1, p44mapk
• Description: Mitogen-activated protein kinase 3 [Source:UniProtKB/Swiss-Prot;Acc:P21708]

Sequence

>retro_rnor_831
CCCAGGGGAACTGCTGGGGTCGTCCTGGTGGTCCCCCGGGAGGTGGAGGGGCAGCCATTCGACGTGGGCCCATGTTACAC
ACAGCTGCAGTACATCGGCGAAGATGCGGACATGGTCAGCTCAGCTTATGACCACGTGCGCAAGACCAGAGTGGCTATCA
AGAAGATTAGCCCCTTCGAGCATCAAACCTACTGTCAGCCCACGTTGAGAGAAACCCAGATCTTGCTGCGATTCCGCCAT
GAGAATGTCATAGGCATCCGAGACATCCTCAGAGCACCCACCCTGGAAGCTATGAGAGATGTTTACATTGTTCAGGACCT
CATGGATACAGACCTGTACAAGCTGCTTAAGAGCCAACAGCTGAGCAATGACCACATCTGCTTCTTCCTCTACCAGATCC
TCCGGGGCCTCAAGTACATACACTCGGCCAATGTGCTGCACCGGGACCTGAAGCCCTCCAATCTGCTTATCAACACCACC
TGAGACCTTAAGATCTGTGATTTTGGCCTGGCCCGGATTGCTGACCCTGAGCACGACCACACTGGCTTTCTGACCGAGTA
TGTGGCCACACGCTGGTACCGAGCCCCAGAGATCATGCTTAACTCCAAGGGCTACACCAAATCCATTGATGTCTGGTCTG
TGGGCTGCATTCTGGCTGAGATGCTCTCCAACCGGCCTATCTTCCTCGGCAAGCACTACCTGGACCAGCTCAACCACATT
CTAGGTATACTGGGTTCCCCATCCCAGGAGGACCTAAATTGTGTCATTAACATGAAGGCCCGAAACTAATTATAGTCTCT
GCCCTCTAAAACCAAGGTGGCTTGGGCCAAGCTTTTTCCCAAATCTGACTCCAAAGCTCTTGACCTGCTGGACCAGATGT
TAACCTTTAACCCAAACAAGCGCATCACAGTAGAGGAAGCACTGACTCACCCTTACCTGGAACAGTACTATGATCCGACA
GATGAACCAGTGGCTGAGGAGCCA

Alignment

ORF - retro_rnor_831 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.67 %
• Parental protein coverage: 87.37 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PRGTAGVVPVVPGEVEVVKGQPFDVGPRYTQLQYIGEGAYGMVSSAYDHVRKTRVAIKKISPFEHQTYCQ
          PRGTAGVV.VVP.EVE...GQPFDVGP.YTQLQYIGE.A..MVSSAYDHVRKTRVAIKKISPFEHQTYCQ
Retrocopy PRGTAGVVLVVPREVE---GQPFDVGPCYTQLQYIGEDA-DMVSSAYDHVRKTRVAIKKISPFEHQTYCQ

Parental  RTLREIQILLRFRHENVIGIRDILRAPTLEAMRDVYIVQDLMETDLYKLLKSQQLSNDHICYFLYQILRG
          .TLRE.QILLRFRHENVIGIRDILRAPTLEAMRDVYIVQDLM.TDLYKLLKSQQLSNDHIC.FLYQILRG
Retrocopy PTLRETQILLRFRHENVIGIRDILRAPTLEAMRDVYIVQDLMDTDLYKLLKSQQLSNDHICFFLYQILRG

Parental  LKYIHSANVLHRDLKPSNLLINTTCDLKICDFGLARIADPEHDHTGFLTEYVATRWYRAPEIMLNSKGYT
          LKYIHSANVLHRDLKPSNLLINTT.DLKICDFGLARIADPEHDHTGFLTEYVATRWYRAPEIMLNSKGYT
Retrocopy LKYIHSANVLHRDLKPSNLLINTT*DLKICDFGLARIADPEHDHTGFLTEYVATRWYRAPEIMLNSKGYT

Parental  KSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINMKARNYLQSLPSKTKVAWA
          KSID.WSVGCILAEMLSNRPIF.GKHYLDQLNHILGILGSPSQEDLNC.INMKARN.L.SLPSKTKVAWA
Retrocopy KSIDVWSVGCILAEMLSNRPIFLGKHYLDQLNHILGILGSPSQEDLNCVINMKARN*L*SLPSKTKVAWA

Parental  KLFPKSDSKALDLLDRMLTFNPNKRITVEEALAHPYLEQYYDPTDEPVAEEP
          KLFPKSDSKALDLLD.MLTFNPNKRITVEEAL.HPYLEQYYDPTDEPVAEEP
Retrocopy KLFPKSDSKALDLLDQMLTFNPNKRITVEEALTHPYLEQYYDPTDEPVAEEP

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	0.14 RPM	103.03 RPM
SRP017611_kidney	0.07 RPM	68.32 RPM
SRP017611_liver	0.00 RPM	21.31 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_831 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_831 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_831 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017108	1 retrocopy	retro_cfam_1254,
Dasypus novemcinctus	ENSDNOG00000002191	1 retrocopy	retro_dnov_1241,
Loxodonta africana	ENSLAFG00000017904	1 retrocopy	retro_lafr_1022,
Myotis lucifugus	ENSMLUG00000011284	1 retrocopy	retro_mluc_1697,
Mus musculus	ENSMUSG00000063065	1 retrocopy	retro_mmus_2694,
Pongo abelii	ENSPPYG00000007239	1 retrocopy	retro_pabe_1440,
Rattus norvegicus	ENSRNOG00000008704	1 retrocopy	retro_rnor_952,
Rattus norvegicus	ENSRNOG00000019601	1 retrocopy	retro_rnor_831 ,