RetrogeneDB ID: retro_ptro_2676

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:26410560..26411744(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAP2K1
• Ensembl ID: ENSPTRG00000007193
• Aliases: MAP2K1, MEK
• Description: Pan troglodytes mitogen-activated protein kinase kinase 1 (MAP2K1), mRNA. [Source:RefSeq mRNA;Acc:NM_001009071]

Sequence

>retro_ptro_2676
ATGCCCAAGAAGACGCCGACGCCCATCCAGCTGACCCCAGCCCCCGACGGCTCCAGCCGTGGTTAACGGGACCAGCTCTG
CGGAAACCAATTTGGAGGCCTTGCAGAAGAAGCTGGAAGAGCTAGAGCTTGACGAGCAGCAGCGAAAGCACCTTGAGGCC
TTTCTTACCCAGAAATAGAAGGTGGGAGAACTAAAGGATGACGACTTTGAGAAGATCAGTGAGTTGGGGGCTGGCAATGG
CGGTGTGGTGTTCAAGGCTTCCCACAAGCCTTCTGGCCTGGTCGTGGCCAGAAAGCTAATTCATCTGGAGATCAAACCTG
CAATCCGGAACCAGATCATAAGGGAGCTGCAGGTTCTTCATGAGTGCAACTCTCCGTACATCGTGGGCTTCTGTGGTGCA
TTCTACAGTGAGAGGCGAGATCAGTATCTGCAGGTAGCACATGGATGGAGATTCCCTGGATCAAGTCCTGAAGAAAGCGG
GAAGAATTCCTGAACAAATTTTAGAAAAAGTTAGCATTGCTGTAATAAAAGGCCTGACATATCTGAGGGAGAAGCACAAG
ATCATGCACATAGATGTCCAGCCCTCCCACATCATAGTCAGGTCCCGTGGGGAGATCAAGCTCTGTAACTTTGGGGTCAG
TGGGCAGCTCATCGACTCCATGGCCAACTCCTTCATGGGCCCAAGGTCCTACATGTCGCCAGAAAGATTCCAGGGGACTC
ATTACTCTGTGCAGTCAGACATCTGGAGCATGGGACTCTCTCCGGTAGAGATGGCAGTTGGGAGGTATCCCATCCCTTCT
CCAGATGCCAAGGAGCTGGAGCTGATGTTTGGGTGCCAGGTGGAGGGAGATGCGGCTGAGACCCCACCCAGGCCAAGGAC
CCCAGGGAGGCCTCTTAGCTCATATGGAATGGACAGCCGACCTCCCGTGGCAATTTTTGAGTTGTTGGATTACATAGTCA
ACGAGCCTCCTCCAAAACTGCCCAGTGGAGTGTTCAGTCTGGAATTTCAAGATTTTGTGAATAAATGCCTAATTAAAAAC
CCCGTAGAGAGAGCAGATTTGAAGCAACTCATGGTTCATGCTTTTATCAAGAGATCTGATGCTGAGGAAGTGGATTTTGC
GGGTTGGCTCTGCTCCACCATCGGGCTTAACCAGCCCAGCACACCAACCCATGCTGCTGGCGTC

Alignment

ORF - retro_ptro_2676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKKKPTPIQLNPA-PDGSAV-NGTSSAETNLEALQKKLEELELDEQQRKRLEAFLTQKQKVGELKDDDF
          MPKK.PTPIQL.PA.P...AV.NGTSSAETNLEALQKKLEELELDEQQRK.LEAFLTQK.KVGELKDDDF
Retrocopy MPKKTPTPIQLTPA>PTAPAVVNGTSSAETNLEALQKKLEELELDEQQRKHLEAFLTQK*KVGELKDDDF

Parental  EKISELGAGNGGVVFKVSHKPSGLVMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGFYGAFYSD-G
          EKISELGAGNGGVVFK.SHKPSGLV.ARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGF.GAFYS..G
Retrocopy EKISELGAGNGGVVFKASHKPSGLVVARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGFCGAFYSE>G

Parental  EISICMEHMDGGSLDQVLKKAGRIPEQILGKVSIAVIKGLTYLREKHKIMHRDVKPSNILVNSRGEIKLC
          EISIC..HMDG.SLDQVLKKAGRIPEQIL.KVSIAVIKGLTYLREKHKIMH.DV.PS.I.V.SRGEIKLC
Retrocopy EISICR*HMDGDSLDQVLKKAGRIPEQILEKVSIAVIKGLTYLREKHKIMHIDVQPSHIIVRSRGEIKLC

Parental  DFGVSGQLIDSMANSFVGTRSYMSPERLQGTHYSVQSDIWSMGLSLVEMAVGRYPIPPPDAKELELMFGC
          .FGVSGQLIDSMANSF.G.RSYMSPER.QGTHYSVQSDIWSMGLS.VEMAVGRYPIP.PDAKELELMFGC
Retrocopy NFGVSGQLIDSMANSFMGPRSYMSPERFQGTHYSVQSDIWSMGLSPVEMAVGRYPIPSPDAKELELMFGC

Parental  QVEGDAAETPPRPRTPGRPLSSYGMDSRPPMAIFELLDYIVNEPPPKLPSGVFSLEFQDFVNKCLIKNPA
          QVEGDAAETPPRPRTPGRPLSSYGMDSRPP.AIFELLDYIVNEPPPKLPSGVFSLEFQDFVNKCLIKNP.
Retrocopy QVEGDAAETPPRPRTPGRPLSSYGMDSRPPVAIFELLDYIVNEPPPKLPSGVFSLEFQDFVNKCLIKNPV

Parental  ERADLKQLMVHAFIKRSDAEEVDFAGWLCSTIGLNQPSTPTHAAGV
          ERADLKQLMVHAFIKRSDAEEVDFAGWLCSTIGLNQPSTPTHAAGV
Retrocopy ERADLKQLMVHAFIKRSDAEEVDFAGWLCSTIGLNQPSTPTHAAGV

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_prefrontal_cortex	0.09 RPM	116.31 RPM
SRP007412_cerebellum	0.04 RPM	89.73 RPM
SRP007412_heart	0.09 RPM	34.28 RPM
SRP007412_kidney	0.21 RPM	34.34 RPM
SRP007412_liver	0.03 RPM	32.54 RPM
SRP007412_testis	0.32 RPM	26.35 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2676 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2676 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2676 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2650
Pongo abelii	retro_pabe_3249
Macaca mulatta	retro_mmul_2285

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033983	1 retrocopy	retro_btau_1416,
Cavia porcellus	ENSCPOG00000003053	1 retrocopy	retro_cpor_483,
Gorilla gorilla	ENSGGOG00000003687	1 retrocopy	retro_ggor_2650,
Macaca mulatta	ENSMMUG00000016840	1 retrocopy	retro_mmul_2285,
Otolemur garnettii	ENSOGAG00000015876	1 retrocopy	retro_ogar_1598,
Ochotona princeps	ENSOPRG00000007770	1 retrocopy	retro_opri_846,
Pongo abelii	ENSPPYG00000006576	2 retrocopies	retro_pabe_3092, retro_pabe_3249,
Pan troglodytes	ENSPTRG00000007193	1 retrocopy	retro_ptro_2676 ,
Pan troglodytes	ENSPTRG00000010294	1 retrocopy	retro_ptro_2566,