RetrogeneDB ID: retro_mmul_938

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:12433413..12433878(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000031468
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.3739
• Ensembl ID: ENSMMUG00000007918
• Aliases: ZNHIT3, TRIP-3, TRIP3
• Description: zinc finger HIT domain-containing protein 3 [Source:RefSeq peptide;Acc:NP_001182347]

Sequence

>retro_mmul_938
ATGGCGTCACTGAGATGTAGCACCGTCGTCTGCGTGATCTGCTTGGAGAAGCCCAAATACCGCTGTCCGGCCTGCCGCGT
GCCCTACTGCTCTGTAGCCTGCTTCCGGAAGCACAAAGAACAGTGCAACCCTGAAGCTCGTCCTGTTGAGAAAAAAATAA
GATCAGCTCTTCCTACCAAAACCATAAAGCCTTTGGAAAACAAAGATGATGATGACTCTATAGCTGATTTTCTCAATAGT
GATGAGGAAGAAGACAGAGTTTCTTTGCAGAATTTAAAGAATTTAAGGGAATCTGCAACATTAAGAAGCTTATTGCTCAA
TCCACACCTCAGGCAGTTGATGGTCAACCTCGATCAGGGGGAAGACAAAGCAAAGCTCATGAGAGCCTACATGCAAGAGC
CCTTGTTTGTGGAGTTTGCAGACTGCTGTTTAGGAATTGTGGAGCCATCCCAGAATGAGGATTCT

Alignment

ORF - retro_mmul_938 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASLRCSTVVCVICLEKPKYRCPACRVPYCSVACFRKHKEQCNPEARPVEKKIRSALPTKTIKPVENKDD
          MASLRCSTVVCVICLEKPKYRCPACRVPYCSVACFRKHKEQCNPEARPVEKKIRSALPTKTIKP.ENKDD
Retrocopy MASLRCSTVVCVICLEKPKYRCPACRVPYCSVACFRKHKEQCNPEARPVEKKIRSALPTKTIKPLENKDD

Parental  DDSIADFLNSDEEEDRVSLQNLKNLGKSATLRSLLLNPHLRQLMVNLDQGEDKAKLMRAYMQEPLFVEFA
          DDSIADFLNSDEEEDRVSLQNLKNL..SATLRSLLLNPHLRQLMVNLDQGEDKAKLMRAYMQEPLFVEFA
Retrocopy DDSIADFLNSDEEEDRVSLQNLKNLRESATLRSLLLNPHLRQLMVNLDQGEDKAKLMRAYMQEPLFVEFA

Parental  DCCLGIVEPSQNEDS
          DCCLGIVEPSQNEDS
Retrocopy DCCLGIVEPSQNEDS

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	0.45 RPM	3.92 RPM
SRP007412_brain_prefrontal_cortex	2.06 RPM	3.49 RPM
SRP007412_cerebellum	0.26 RPM	2.71 RPM
SRP007412_heart	0.12 RPM	2.18 RPM
SRP007412_kidney	0.00 RPM	2.46 RPM
SRP007412_liver	0.12 RPM	0.67 RPM
SRP007412_testis	1.73 RPM	4.07 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_938 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_938 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_938 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
Bos taurus	ENSBTAG00000012672	1 retrocopy	retro_btau_1218,
Dasypus novemcinctus	ENSDNOG00000011745	1 retrocopy	retro_dnov_1037,
Echinops telfairi	ENSETEG00000018407	1 retrocopy	retro_etel_1415,
Myotis lucifugus	ENSMLUG00000013155	1 retrocopy	retro_mluc_1100,
Macaca mulatta	ENSMMUG00000007918	1 retrocopy	retro_mmul_938 ,