RetrogeneDB ID: retro_pabe_3249

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:29978458..29979642(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAP2K1
• Ensembl ID: ENSPPYG00000006576
• Aliases: None
• Description: mitogen-activated protein kinase kinase 1 [Source:HGNC Symbol;Acc:6840]

Sequence

>retro_pabe_3249
ATGCCCAAGAGGACGCCGACGCCCATCCAGCTGACCCCGGCCGCCGACGGCTCCAGCCGTGGTTAACGGGACCAGCTCTG
CGGAAACCAACTTGGAGGCCTTACAGAAGAAGCTGGAAGAGCTAGAGCTTGACAAGCAGCAGTGAAAGCACCTTGAGGCC
TTTCTTACCCAGAAACAGAAGGTGGGAGAACTAAAGGATAACGACTTTGAGAAGATCAGTGAGCTGGGGCCTGGCAATGG
CGGTGTGGTGTTCAAGGCCTCCCACAAGCCTTCTGGCCTGGTCATGGCCAGAAAGCTAATTCATCTGGAGATCAAACCTG
CAATCCGGAACCTGATCATGAGGGAGCTGCAGGTTCTTCATGAGTGCAACTCTCCATACATCGTGGGCTTCTGTGGTGCA
TTCTACAGCGAGAGGCGAGATCAGTATCTGCATGTAGCACATGGATGGAGATTCCCTGGATCAAGTCCTGAAGAAAGCCG
GAAGAATTCCTGAACAAATTTTAGAAAAAGTTAGCATTGCTGTAATTAAAGGCCTGACATATCTGAGGGAGAAGCACAAG
ATCATGCACATAGATGTCCAGCCCTCCCACATCATAGTCAGCTCCCGTGGGGAGATCAAGCTCTGTAACTTTGGGGTCAG
CGGGCAGCTCGTCGACTCCATGGCCAACTCCTTCGTGGGCCCAAGGTCCTACATGTCGCCAGAAAGATTCCAGGGGACTC
ATTACTCTGTGCAGTCACACATCTGGAGCATGGGACTCGCTCTGGTAGAGATGGCAGTTGGGAGGTATCCCATCCCTTCT
CCAGATGCCAAGGAGCTGGAGCTGATGTTTGGGTGCCAGGTGGAGGGAGATGCGGCTGAGACCCCACCCAGGCCAAGGAC
CCCAGGGAGGCCTCTTAGCTCATATGCAATGGACAGCCGACCTCCCATGACAATTTTTGAGTTGTTGGATTGCATAGTCA
ACGAGCCTCCTCCAAAACTGCCCAGTGGAGTGTTCAGTCTGGAATTTCAAGATTTTGTGAATAAATGCCTAATTAAAAAC
CCCGTAGAGAGAGCAGATTGGAAGCAACTCATGGTTTATGCTTTTATCAAGAGATCTGATGCTGAGGAAGTGGATTTTGC
GGGTTGGCTCTGCTCCACCATCGGGCTTAACCAGCCCAGCACAGCAACCCATGCTGCTGGCGTC

Alignment

ORF - retro_pabe_3249 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.94 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKKKPTPIQLNPA-PDGSAV-NGTSSAETNLEALQKKLEELELDEQQRKRLEAFLTQKQKVGELKDDDF
          MPK..PTPIQL.PA.P...AV.NGTSSAETNLEALQKKLEELELD.QQ.K.LEAFLTQKQKVGELKD.DF
Retrocopy MPKRTPTPIQLTPA>PTAPAVVNGTSSAETNLEALQKKLEELELDKQQ*KHLEAFLTQKQKVGELKDNDF

Parental  EKISELGAGNGGVVFKVSHKPSGLVMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGFYGAFYSD-G
          EKISELG.GNGGVVFK.SHKPSGLVMARKLIHLEIKPAIRN.I.RELQVLHECNSPYIVGF.GAFYS..G
Retrocopy EKISELGPGNGGVVFKASHKPSGLVMARKLIHLEIKPAIRNLIMRELQVLHECNSPYIVGFCGAFYSE>G

Parental  EISICMEHMDGGSLDQVLKKAGRIPEQILGKVSIAVIKGLTYLREKHKIMHRDVKPSNILVNSRGEIKLC
          EISICM.HMDG.SLDQVLKKAGRIPEQIL.KVSIAVIKGLTYLREKHKIMH.DV.PS.I.V.SRGEIKLC
Retrocopy EISICM*HMDGDSLDQVLKKAGRIPEQILEKVSIAVIKGLTYLREKHKIMHIDVQPSHIIVSSRGEIKLC

Parental  DFGVSGQLIDSMANSFVGTRSYMSPERLQGTHYSVQSDIWSMGLSLVEMAVGRYPIPPPDAKELELMFGC
          .FGVSGQL.DSMANSFVG.RSYMSPER.QGTHYSVQS.IWSMGL.LVEMAVGRYPIP.PDAKELELMFGC
Retrocopy NFGVSGQLVDSMANSFVGPRSYMSPERFQGTHYSVQSHIWSMGLALVEMAVGRYPIPSPDAKELELMFGC

Parental  QVEGDAAELTPPRPRTPGRPLSSYGMDSRKPPMAIFELLDYIVNEPPPKLPSGVFSLEFQDFVNKCLIKN
          QVEGDAAE.TPPRPRTPGRPLSSY.MDSR.PPM.IFELLD.IVNEPPPKLPSGVFSLEFQDFVNKCLIKN
Retrocopy QVEGDAAE-TPPRPRTPGRPLSSYAMDSR-PPMTIFELLDCIVNEPPPKLPSGVFSLEFQDFVNKCLIKN

Parental  PAERADLKQLMVHAFIKRSDAEEVDFAGWLCSTIGLNQPSTPTHAVGV
          P.ERAD.KQLMV.AFIKRSDAEEVDFAGWLCSTIGLNQPST.THA.GV
Retrocopy PVERADWKQLMVYAFIKRSDAEEVDFAGWLCSTIGLNQPSTATHAAGV

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	37.49 RPM	106.93 RPM
SRP007412_cerebellum	15.93 RPM	47.42 RPM
SRP007412_heart	3.91 RPM	12.07 RPM
SRP007412_kidney	6.33 RPM	13.03 RPM
SRP007412_liver	4.71 RPM	11.38 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3249 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3249 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3249 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2676
Gorilla gorilla	retro_ggor_2650
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 ,
Pongo abelii	ENSPPYG00000007993	1 retrocopy	retro_pabe_3775,
Pan troglodytes	ENSPTRG00000007193	1 retrocopy	retro_ptro_2676,