RetrogeneDB ID: retro_mmul_627

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:33279759..33280463(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000012755
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DKKL1
• Ensembl ID: ENSMMUG00000014794
• Aliases: None
• Description: None

Sequence

>retro_mmul_627
ATGGGAGAAACTTCCTCCCCTGCCCCCACAATGCGGCATCCGCTGGTCCTGCTGCTGCTCCTCTCTGCCCTGGTGACTCC
CTCCACTGCAGCCTCTATCCACGACGCTGATGCCCAAGAGAGCTCCTTGGGTCTTACAGGCCTCCAGAGCCTACTCCAAG
GCTTCAGCCGACTTTTCCTGAAAGATGACCTGCTTCAGGGCATAGACAGCTTCTTCTCTGCCCCCATGGATTTCCGGGGC
CTCCCTAGGAACTACTACCAAGAGGAGAACCAGGAGCACCAGCTGGGAAACAACACCCTCTCCAGCCACCTCCAGATTGA
CAAGGTGACCGACAACAAGACGGGAGAGGTGCTGATCTCCGAGAAGGTGGTGGCATCCATCCAGCCGCGGAGGGGAGCTT
CCAAGGTAACCGGAAGGTACCCAGGATGGAGGAGAAGGAGGCCCTGGTGTCCATCCGGAAGGCCATGGACAGCTTCCACA
TGGAGCTCCATCCCCGGGTGGCCTTCTGGATCATGACGCTGCCACGGCGGAGGTCCCACCACAATGTCCTGGAGGGCGGC
CGCTGGCTCAGTGAGAAGCCACACCACCTGCAGGCCGTCCAGGATGGGCTTAGTGAGGGAACCCACGAGGTCTTCCTAAA
AGAGGGGACCCAGGGCTCCTCCCACTCCTGGCTGTCCCCCTGAAAGACCCACTTACTGTACATC

Alignment

ORF - retro_mmul_627 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.47 %
• Parental protein coverage: 97.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGEASPSAPTMRHRLVLLLLLSALVTPSTAAPIHDADAQESSLGLTGLQSLLQGFSRLFLKGNLLRGIDS
          MGE.S..APTMRH.LVLLLLLSALVTPSTAA.IHDADAQESSLGLTGLQSLLQGFSRLFLK..LL.GIDS
Retrocopy MGETSSPAPTMRHPLVLLLLLSALVTPSTAASIHDADAQESSLGLTGLQSLLQGFSRLFLKDDLLQGIDS

Parental  FFSAPMDFRGLPRNYHKEENQEHQLGNNTLSSHLQIDKMTDNKTGEVLISENMVASIQP-AEGSFEGDLK
          FFSAPMDFRGLPRNY..EENQEHQLGNNTLSSHLQIDK.TDNKTGEVLISE..VASIQP.AEGSF.G..K
Retrocopy FFSAPMDFRGLPRNYYQEENQEHQLGNNTLSSHLQIDKVTDNKTGEVLISEKVVASIQP<AEGSFQGNRK

Parental  VPRMEEKEALVPIQKAMDSFHAELHPRVAFWIIKLPRRRSHQDALEGGHWLSEKRHRLQAIRDGLRKGTH
          VPRMEEKEALV.I.KAMDSFH.ELHPRVAFWI..LPRRRSH...LEGG.WLSEK.H.LQA..DGL..GTH
Retrocopy VPRMEEKEALVSIRKAMDSFHMELHPRVAFWIMTLPRRRSHHNVLEGGRWLSEKPHHLQAVQDGLSEGTH

Parental  EDVLEEGTESSSHSRLSPRKTHLLYI
          E..L.EGT..SSHS.LSP.KTHLLYI
Retrocopy EVFLKEGTQGSSHSWLSP*KTHLLYI

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	0.00 RPM	0.00 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.08 RPM
SRP007412_cerebellum	0.00 RPM	0.06 RPM
SRP007412_heart	0.00 RPM	0.29 RPM
SRP007412_kidney	0.00 RPM	0.23 RPM
SRP007412_liver	0.00 RPM	0.04 RPM
SRP007412_testis	0.11 RPM	342.86 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_627 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_627 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_627 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000102	1 retrocopy	retro_cjac_1433,
Homo sapiens	ENSG00000104901	1 retrocopy	retro_hsap_2421,
Gorilla gorilla	ENSGGOG00000016382	1 retrocopy	retro_ggor_1506,
Macaca mulatta	ENSMMUG00000014794	1 retrocopy	retro_mmul_627 ,
Pan troglodytes	ENSPTRG00000011292	1 retrocopy	retro_ptro_1395,