RetrogeneDB ID: retro_ggor_2650

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 8:30067146..30068330(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000022968
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAP2K1
• Ensembl ID: ENSGGOG00000003687
• Aliases: None
• Description: None

Sequence

>retro_ggor_2650
ATGCCCAGGAAGACGCCGACGCCCATCCAGCTGACCCCAGCCCCTGACGGCTCCAGCCGTGGTTAACGGGACCAGCTCTG
CGGAAACCAACTTGGAGGCCTTGCAGAAGAAGCTGGAAGAGCTAGAGCTTGACAAGCAGCAGCGAAAGCGCCTTGAGGCC
TTTCTTACCCAGAAACAGAAGGTGGGAGAACTAAAGGATGACGACTTTGAGAAGATCAGTGAGCTGGGGGCTGGCAATGG
CGGTGTGGTGTTCAAGGCCTCCCACAAGCCTTCTGGCCTGGTCATGGCCAGAAAGCTAATTCATCTGGAGATCAAACCTG
CAATCCGGAACCAGATCATAAGGGAGCTGCAGGTTCTTCATGAGTGCAACTCTCCCTACATCGTGGGCTTCTGTGGTGCA
TTCTACAGCGAGAGGCGAGATCAGTATCTGCAGGTAGCACATGGATGGAGATTCCCTGGATCAAGTCCTGAAGAAAGCGG
GAAGAATTCCTGAACAAATTTTAGAAAAAGTTAGCATTGCTGTAATAAAAGGCCTGACATATCTGAGGGAGAAGCACAAG
ATCATGCACATAGATGTCCAGCCCTCCCACATCATAGTCAGCTCCCGTGGGGAGATCAAGCTCTGTAACTTTGGGGTCAG
TGGGCAGCTCATCAACTCCATGGCCAACTCCTTCATGGGCCCAAGGTCCTACATGTCGCCAGAAAGATTCCAGGGGACTC
ATTACTCTGTGCAGTCAGACATCTGGAGCATGGGACTCTCTCTGGTAGAGATGGCAGTTGGGAGGTATCCCAACCCTTCT
CCAGATGCCAAGGAGCTTGAGCTGATGTTTGGGTGCCAGGTGGAGGGAGATGCGGCTGAGACCCCACCCAGGCCAAGGAC
CCCAGGGAGGCCTCTTAGCTCATATGGAATGGACAGCCGACCTCCCATGGCAATTTTTGAGTTGTTGGATTACATAGTCA
ACGAGCCTCCTCCAAAACTGCCCAGTGGAGTGTTCAGTCTGGAATTTCAAGATTTTGTGAATAAATGCCTAATTAAAAAC
CCCGTAGAGAGAGCAGATTTGAAGCAACTCATGGTTCATGCTTTTATCAAGAGATCTGATGCTGAGGAAGTGGATTTTGC
GGGTTGGCTCTGCTCCACCATCGGGCTTAACCAGCCCAGCACACCAACCCATGCTGCTGGCGTC

Alignment

ORF - retro_ggor_2650 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKKKPTPIQLNPAPDGS-AVNGTSSA-ETNLEALQKKLEELELDEQQRKRLEAFLTQKQKVGELKDDDF
          MP.K.PTPIQL.PAPDGS.AV....S..ETNLEALQKKLEELELD.QQRKRLEAFLTQKQKVGELKDDDF
Retrocopy MPRKTPTPIQLTPAPDGS>AVVNGTSSAETNLEALQKKLEELELDKQQRKRLEAFLTQKQKVGELKDDDF

Parental  EKISELGAGNGGVVFKVSHKPSGLVMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGFYGAFYSD-G
          EKISELGAGNGGVVFK.SHKPSGLVMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGF.GAFYS..G
Retrocopy EKISELGAGNGGVVFKASHKPSGLVMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGFCGAFYSE>G

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

Parental  DFGVSGQLIDSMANSFVGTRSYMSPERLQGTHYSVQSDIWSMGLSLVEMAVGRYPIPPPDAKELELMFGC
          .FGVSGQLI.SMANSF.G.RSYMSPER.QGTHYSVQSDIWSMGLSLVEMAVGRYP.P.PDAKELELMFGC
Retrocopy NFGVSGQLINSMANSFMGPRSYMSPERFQGTHYSVQSDIWSMGLSLVEMAVGRYPNPSPDAKELELMFGC

Parental  QVEGDAAETPPRPRTPGRPLSSYGMDSRPPMAIFELLDYIVNEPPPKLPSGVFSLEFQDFVNKCLIKNPA
          QVEGDAAETPPRPRTPGRPLSSYGMDSRPPMAIFELLDYIVNEPPPKLPSGVFSLEFQDFVNKCLIKNP.
Retrocopy QVEGDAAETPPRPRTPGRPLSSYGMDSRPPMAIFELLDYIVNEPPPKLPSGVFSLEFQDFVNKCLIKNPV

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	0.19 RPM	168.22 RPM
SRP007412_cerebellum	0.08 RPM	58.78 RPM
SRP007412_heart	0.00 RPM	9.69 RPM
SRP007412_kidney	0.00 RPM	23.72 RPM
SRP007412_liver	0.00 RPM	16.09 RPM
SRP007412_testis	0.21 RPM	30.56 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2650 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2650 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2676
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 ,
Gorilla gorilla	ENSGGOG00000008832	1 retrocopy	retro_ggor_115,
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,