RetrogeneDB ID: retro_mmul_1132

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:132128989..132129492(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.18827
• Ensembl ID: ENSMMUG00000019392
• Aliases: None
• Description: protein tyrosine phosphatase type IVA 3 [Source:RefSeq peptide;Acc:NP_001180623]

Sequence

>retro_mmul_1132
GCCATAATGAACCATCCAGCCCCTGTCGAGATCTCCTGTGAGAACATGCGTTTTCTTACAACTCACAACCCCCCAACCAA
TGCTACTCTCAACAAGTTCCCAGAGGAACTTAAGAAGTATGGAGTGACGACTTTGGTTCGAGTCTGTGATGCTACATATG
ATAAACCTCCAGTTGAAAAAGAAGGAATCCATGTTCTTGATTGGCCATTTGATGATGGAGCTCCACCCCCTAATCAGATA
GCAGATGATTGGTTAAACCTGTTATAAACCGAATTTCATGAAGAGCCAGGCTGCTGTGTTGCAGTGCCTTCTGCTGTGGG
ATTGGGAAGGGCATCTGTGCTGGTTGCACTTGCTTTGATTGAATGTGGAATGAAGTACGAAGACGCAGTTCAGTTTATAA
GACAAAAGGGGAGCATTCAATTCCAAACAGCTGCTTTACTTGGGAGAAATACTGACCTAAGATGCGATTACGCTTCAGAG
ATACCCATGGGCATTGCTGTGTT

Alignment

ORF - retro_mmul_1132 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.39 %
• Parental protein coverage: 98.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ARMNRPAPVEVSYKHMRFLITHNP-TNATLSTFIEDLKKYGATTVVRVCEVTYDKTPLEKDGITVVDWPF
          A.MN.PAPVE.S...MRFL.THNP.TNATL..F.E.LKKYG.TT.VRVC..TYDK.P.EK.GI.V.DWPF
Retrocopy AIMNHPAPVEISCENMRFLTTHNPPTNATLNKFPEELKKYGVTTLVRVCDATYDKPPVEKEGIHVLDWPF

Parental  DDGAPPPGKVVEDWLSLVKAKFCEAPGSCVAVHCVAGLGRAPVLVALALIESGMKYEDAIQFIRQKRRGA
          DDGAPPP.....DWL.L....F.E.PG.CVAV....GLGRA.VLVALALIE.GMKYEDA.QFIRQK..G.
Retrocopy DDGAPPPNQIADDWLNLL*TEFHEEPGCCVAVPSAVGLGRASVLVALALIECGMKYEDAVQFIRQK--GS

Parental  I-NSKQLTYL-EKYRPKQRLRFKDPHTHKTRCCV
          I.NSKQL.YL.EKY.PK.RLRF.D.H.H...CCV
Retrocopy I>NSKQLLYL>EKY*PKMRLRFRDTHGH---CCV

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	1.68 RPM	0.78 RPM
SRP007412_brain_prefrontal_cortex	2.70 RPM	2.86 RPM
SRP007412_cerebellum	1.23 RPM	0.39 RPM
SRP007412_heart	1.94 RPM	54.17 RPM
SRP007412_kidney	3.17 RPM	1.29 RPM
SRP007412_liver	1.23 RPM	2.89 RPM
SRP007412_testis	21.64 RPM	5.99 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1132 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1132 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1132 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_944
Pan troglodytes	retro_ptro_654
Gorilla gorilla	retro_ggor_763
Pongo abelii	retro_pabe_808

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046467	1 retrocopy	retro_btau_380,
Gorilla gorilla	ENSGGOG00000010609	1 retrocopy	retro_ggor_843,
Microcebus murinus	ENSMICG00000006858	4 retrocopies	retro_mmur_269, retro_mmur_349, retro_mmur_642, retro_mmur_889,
Macaca mulatta	ENSMMUG00000002777	1 retrocopy	retro_mmul_1720,
Macaca mulatta	ENSMMUG00000012930	1 retrocopy	retro_mmul_1235,
Macaca mulatta	ENSMMUG00000019392	1 retrocopy	retro_mmul_1132 ,