RetrogeneDB ID: retro_mmul_197

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:86165149..86165923(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000020716
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: EEF1D
• Ensembl ID: ENSMMUG00000001645
• Aliases: None
• Description: None

Sequence

>retro_mmul_197
ATGGCTACAAACTTCCTAGTACATGAGAAGATCTGGTTTGACAACTTCAAATATGACGATGCAGAAAGGAGATTCTACGA
GCAGATGAACGGGCCTGTGGCCGGTGCCTCCCGCCAGACCTCAGGCCCCGGGGCCTCCAGCGGCCCCAGCGGAGACCACA
GCGAGCTTGTCGTCCGGATCGCCAGTTTGGAAGTGGAGAACCAGAGCCTGCGTGGCGTGGTACAGGAGCTGCAGCAGGCC
ATCTCCAAGCTGGAGGCCCGGCTGAACGTGCTGGAGAAGAGCTCGCCTGGCCACCGGGCCACGGCCCCGCAGACCCAGCA
CGTGTCTCCCATGCGCCAAGTGGAGCCCCCGGCCAAGAAGCCAGCCACACCAGCAGAGGATGACGAGGATGATGACACTG
ACCTGTTTGGCAGCGACAATGAGGAGGAGGACAAGGAGGCGGCACAGCTGCGGGAGGAGCGGCTGCGGCAGTACGCGGAG
AAGAAGGCCAAGAAGCCTGCACTGGTGGCCAAGTCCTCCATCCTGCTGGATGTCAAGCCTTGGGACGATGAGACGGACAT
GGCCCAGCTGGAGGCCTGTGTGCGATCTATCCAGCTGGACGGGCTGGTCTGGGGGGCTTCCAAGCTGGTGCCCGTGGGCT
ACGGTATCTGGAAGCTACAGATTCAGTGTGTGGTGGAGGACGACAAGGTGGGGACAGACTTGCTGGAGGAGGAGATCACC
AAGTTTGAGGAGCACGTGCAGAGTGTCGATATCGCAGCTTTCAACAAGATTTGA

Alignment

ORF - retro_mmul_197 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.83 %
• Parental protein coverage: 89.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATNFLVHEKIWFDKFKYDDAERRFYEQMNGPVAGASRQTSGPGASSGPSGDHSELVVRIASLEVENQSL
          MATNFLVHEKIWFD.FKYDDAERRFYEQMNGPVAGASRQTSGPGASSGPSGDHSELVVRIASLEVENQSL
Retrocopy MATNFLVHEKIWFDNFKYDDAERRFYEQMNGPVAGASRQTSGPGASSGPSGDHSELVVRIASLEVENQSL

Parental  RGVVQELQQAISKLEARLNVLEKSSPGHRATAPQTQHVSPMRQVEPPAKKPATPAEDDEDDDIDLFGSDN
          RGVVQELQQAISKLEARLNVLEKSSPGHRATAPQTQHVSPMRQVEPPAKKPATPAEDDEDDD.DLFGSDN
Retrocopy RGVVQELQQAISKLEARLNVLEKSSPGHRATAPQTQHVSPMRQVEPPAKKPATPAEDDEDDDTDLFGSDN

Parental  EEEDKEAAQLREERLRQYAEKKAKKPALVAKSSILLDVKPWDDETDMAQLEACVRSIQLDGLVWGASKLV
          EEEDKEAAQLREERLRQYAEKKAKKPALVAKSSILLDVKPWDDETDMAQLEACVRSIQLDGLVWGASKLV
Retrocopy EEEDKEAAQLREERLRQYAEKKAKKPALVAKSSILLDVKPWDDETDMAQLEACVRSIQLDGLVWGASKLV

Parental  PVGYGIRKLQIQCVVEDDKVGTDLLEEEITKFEEHVQSVDIAAFNKI
          PVGYGI.KLQIQCVVEDDKVGTDLLEEEITKFEEHVQSVDIAAFNKI
Retrocopy PVGYGIWKLQIQCVVEDDKVGTDLLEEEITKFEEHVQSVDIAAFNKI

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	0.56 RPM	17.93 RPM
SRP007412_brain_prefrontal_cortex	0.56 RPM	56.40 RPM
SRP007412_cerebellum	1.16 RPM	19.37 RPM
SRP007412_heart	4.77 RPM	101.28 RPM
SRP007412_kidney	3.40 RPM	52.11 RPM
SRP007412_liver	4.12 RPM	113.76 RPM
SRP007412_testis	0.60 RPM	109.50 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_197 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_197 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_197 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Danio rerio	ENSDARG00000008109	1 retrocopy	retro_drer_26,
Macaca mulatta	ENSMMUG00000001054	6 retrocopies	retro_mmul_1456, retro_mmul_1767, retro_mmul_1881, retro_mmul_2140, retro_mmul_894, retro_mmul_969,
Macaca mulatta	ENSMMUG00000001645	4 retrocopies	retro_mmul_1795, retro_mmul_197 , retro_mmul_733, retro_mmul_747,