RetrogeneDB ID: retro_mmul_1559

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 20:45637158..45638441(+)
• Located in intron of: ENSMMUG00000004717

Retrocopy information

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

Parental gene information

• Parental gene symbol: ELK1
• Ensembl ID: ENSMMUG00000019420
• Aliases: None
• Description: ETS domain-containing protein Elk-1 [Source:RefSeq peptide;Acc:NP_001244117]

Sequence

>retro_mmul_1559
ATGGACCCATCTGTGACGCTGTGGCAGTTTCTGCTGCAGCTGCTGAGAGAGCAACGCAATGGCCACATCATCTCCTGGAC
TTCACGGGATGGTGGTGAATTCAAGCTGGTGGATGCAGAGGAGGTGGCCCGGCTGTGGGGGCTACGTAAGAACAAGACCA
ACATGAATTACGACAAGCTCAGCCGGGCCTTGTGGTACTACTATGACAAGAACATCATCTGCAAGGTGAGCGGCCAGAAG
TTCGTCTACAAGTTTGTGTCCTATCCTGAGGTCGCAGGGTGCTCCACTGAGGACTGCCCGCCCCAGCCAGATGTGTCTGT
TACCTCCGCCATGCCAAATGTGGCCCCTGCTGCTGTACATGCCGCCCCAGGGGACACTGCCTCTGGAAAGCCAGGCACAC
CCAAGGGTGCAGGAATGGCAGGCCCGGGTGGTTTGGCATGCAGCAGCCGGAACGAGTACATGCGCTCGGGCCTCTATTCC
ACCTTCACCATCCAGTCTCTGCAGCCACAGCCACCCCCTCATCCTCAGCCTGCTGTGGTGCTCCCCAATGCAGCTCCTGC
AGGAGCAGCAGCGCCCTCCTCGGGGAGCAGGAGCACCAGTCCAAGCCCCTTGGAGGCCTGCCTGGAGGCTGAGGAGGCCG
GCTTGCCTCTGCAGGTCATCCTGACCCCACCCGAGGCCCCAAACCTGAAATCGCAGGAGCTGAATATGGAGCCAGGTTTG
GGCCGGGCTTTGCCCGCAGAAGTGAAAGTGGAAGGGCCCAAGAAGAGTTGGAAGTTGCCGGGGAGAGAGGGTTTGTGCCG
GAAACTACCAAGGCCGAGCCAGAAGTCCCTCCATAGGAGGGCGTGCCAGCCCGGCTGCCCGCGGTTGTTATGGACACCGC
AGGGCAGGCGGGCGACCACACGGCTTCCAGCCCTGAGATCTCCCAGCCGCAGAAGGGCCGGAAGCCCCGGGACCTAGAGC
TTCCACTCAGCCCGAGCCTGCTAGGTGGGCCAGGACTCGAACAGACCCCAGGATCGGGAACTGGCTCCGGCCTCCAGGCG
CCTGGGGCGGCGCTAACTCCGTCCCTACTTCCTACGTATACATTGACCCCGGTGCTGCTGACACCCAGCTCGCTGCCTCC
CAGCATTCACTTCTGGAGCACCCTGAGTCCCACTGCGCCCCGTAGTCCGGCCAAGCTCTCCTTCCAGTTTCCGTCCGGTG
GCAGCGCCCAGGTGCACATCCCTTCCATCAGCGTGGCTGGCCTCTCGACCCCCGTGGTGCTCTCCCCAGGGCCCCAGAAG
CCA

Alignment

ORF - retro_mmul_1559 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.64 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDPSVTLWQFLLQLLREQGNGHIISWTSRDGGEFKLVDAEEVARLWGLRKNKTNMNYDKLSRALRYYYDK
          MDPSVTLWQFLLQLLREQ.NGHIISWTSRDGGEFKLVDAEEVARLWGLRKNKTNMNYDKLSRAL.YYYDK
Retrocopy MDPSVTLWQFLLQLLREQRNGHIISWTSRDGGEFKLVDAEEVARLWGLRKNKTNMNYDKLSRALWYYYDK

Parental  NIIRKVSGQKFVYKFVSYPEVAGCSTEDCPPQPEVSVTSAMPNVAPAAVHATPGDTASGKPGTPKGAGMA
          NII.KVSGQKFVYKFVSYPEVAGCSTEDCPPQP.VSVTSAMPNVAPAAVHA.PGDTASGKPGTPKGAGMA
Retrocopy NIICKVSGQKFVYKFVSYPEVAGCSTEDCPPQPDVSVTSAMPNVAPAAVHAAPGDTASGKPGTPKGAGMA

Parental  GPGGLARSSRNEYMRSGLYSTFTIQSLQPQPPPHPRPAVVLPNAAPAGAAAPPSGSRSTSPSPLEACLEA
          GPGGLA.SSRNEYMRSGLYSTFTIQSLQPQPPPHP.PAVVLPNAAPAGAAAP.SGSRSTSPSPLEACLEA
Retrocopy GPGGLACSSRNEYMRSGLYSTFTIQSLQPQPPPHPQPAVVLPNAAPAGAAAPSSGSRSTSPSPLEACLEA

Parental  EEAGLPLQVILTPPEAPNLKSEELNVEPGLGRALPPEVKVEGPK-EELEVARERGFVPETTKAEPEVPPQ
          EEAGLPLQVILTPPEAPNLKS.ELN.EPGLGRALP.EVKVEGPK.EELEVA.ERGFVPETTKAEPEVPP.
Retrocopy EEAGLPLQVILTPPEAPNLKSQELNMEPGLGRALPAEVKVEGPK<EELEVAGERGFVPETTKAEPEVPP*

Parental  EGVPARLPAVVMDTAGQAGGHVASSPEISQPQKGRKPRDLELPLSPSLLGGPGPERTPGSGTGSGLQAPG
          EGVPARLPAVVMDTAGQAG.H.ASSPEISQPQKGRKPRDLELPLSPSLLGGPG.E.TPGSGTGSGLQAPG
Retrocopy EGVPARLPAVVMDTAGQAGDHTASSPEISQPQKGRKPRDLELPLSPSLLGGPGLEQTPGSGTGSGLQAPG

Parental  PALTPSLLPTHTLTPVLLTPSSLPPSIHFWSTLSPIAPRSPAKLSFQFPSSGSAQVHIPSISVDGLSTPV
          .ALTPSLLPT.TLTPVLLTPSSLPPSIHFWSTLSP.APRSPAKLSFQFPS.GSAQVHIPSISV.GLSTPV
Retrocopy AALTPSLLPTYTLTPVLLTPSSLPPSIHFWSTLSPTAPRSPAKLSFQFPSGGSAQVHIPSISVAGLSTPV

Parental  VLSPGPQKP
          VLSPGPQKP
Retrocopy VLSPGPQKP

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	0.11 RPM	15.46 RPM
SRP007412_brain_prefrontal_cortex	3.17 RPM	55.85 RPM
SRP007412_cerebellum	0.90 RPM	15.56 RPM
SRP007412_heart	0.24 RPM	5.12 RPM
SRP007412_kidney	0.12 RPM	4.69 RPM
SRP007412_liver	0.67 RPM	10.17 RPM
SRP007412_testis	0.38 RPM	17.49 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1559 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1559 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1559 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000126767	2 retrocopies	retro_hsap_1465, retro_hsap_1466,
Gorilla gorilla	ENSGGOG00000008714	1 retrocopy	retro_ggor_1126,
Macaca mulatta	ENSMMUG00000019420	2 retrocopies	retro_mmul_1559 , retro_mmul_2276,