RetrogeneDB ID: retro_mmul_1972

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:117054821..117055535(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4860
• Ensembl ID: ENSMMUG00000007775
• Aliases: None
• Description: survival of motor neuron-related-splicing factor 30 [Source:RefSeq peptide;Acc:NP_001253685]

Sequence

>retro_mmul_1972
ATGTCAGAGGATTTAGCAAAGCAGCTGGCAAGCTACAAAGCTCAGCTCCAGCAAGTTGAAGCTGCGTTATCTGGAAATGG
AGAAAATGAAGATTGGCTAAAATTGAAGAAAGATTTATAAGAAGTTATAGAACTAACCAAAGACCTTCTGTCAACTCAAC
CTTCTGAGACGCTTGCAAGTTCAGACAGTTTTGCTTCTACTCAACCTACTCATTCATGGAAAGTAGGAGACAAGTGTATG
GCAATCTGGAGTGAAGATGGACAGTGTTATGAAGCGGAGACTGAAGAGATAGATGAAGAAAATGGCACCGCTGCAATCAC
CTTTGCTGGTTATGGCAATGCTGAAGCGACTCCACCCTTGAACCTCAAGCCTGTAGAATAAGGAGGGAAGGCAAAGGAGG
ACAGTGGCAACAAACCCATGTCAAAAAAAGAAATGATTGCCCAGCAGCGTGAATATAAAAGGAAGAAAGCTTTGAAAAAA
GCTCAGAGAATAAAAGAACTTGAGCAGGAAAGAGAGGACCAGAAAGTGAAATGGCAACAATTCAACAACAGAGCCTATTC
CAAAAACAAAAAAGGCCAGGTAAAGAGGAATATTTTTGCATCATCTGAGAGTGTGACTGGCAAAGTTGGAGTAGGAACAT
TTGGAATTGCCGATAAACCTATGACACAATATCAAGATACCTCTAAATACAATGGCAGGCATTTGATGCCTCAA

Alignment

ORF - retro_mmul_1972 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.96 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSEDLAKQLASYKAQLQQVEAALSGNGENEDLLKLKKDLQEVIELTKDLLSTQPSETLASSDSFASTQPT
          MSEDLAKQLASYKAQLQQVEAALSGNGENED.LKLKKDL.EVIELTKDLLSTQPSETLASSDSFASTQPT
Retrocopy MSEDLAKQLASYKAQLQQVEAALSGNGENEDWLKLKKDL*EVIELTKDLLSTQPSETLASSDSFASTQPT

Parental  HSWKVGDKCMAIWSEDGQCYEAEIEEIDEENGTAAITFAGYGNAEVTPLLNLKPVEEGRKAKEDSGNKPM
          HSWKVGDKCMAIWSEDGQCYEAE.EEIDEENGTAAITFAGYGNAE.TP.LNLKPVE.G.KAKEDSGNKPM
Retrocopy HSWKVGDKCMAIWSEDGQCYEAETEEIDEENGTAAITFAGYGNAEATPPLNLKPVE*GGKAKEDSGNKPM

Parental  SKKEMIAQQREYKKKKALKKAQRIKELEQEREDQKVKWQQFNNRAYSKNKKGQVKRSIFASPESVTGKVG
          SKKEMIAQQREYK.KKALKKAQRIKELEQEREDQKVKWQQFNNRAYSKNKKGQVKR.IFAS.ESVTGKVG
Retrocopy SKKEMIAQQREYKRKKALKKAQRIKELEQEREDQKVKWQQFNNRAYSKNKKGQVKRNIFASSESVTGKVG

Parental  VGTCGIADKPMTQYQDTSKYNVRHLMPQ
          VGT.GIADKPMTQYQDTSKYN.RHLMPQ
Retrocopy VGTFGIADKPMTQYQDTSKYNGRHLMPQ

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	8.40 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	5.32 RPM
SRP007412_cerebellum	0.00 RPM	8.98 RPM
SRP007412_heart	0.00 RPM	5.30 RPM
SRP007412_kidney	0.00 RPM	5.05 RPM
SRP007412_liver	0.00 RPM	2.61 RPM
SRP007412_testis	0.00 RPM	6.22 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1972 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1972 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1972 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006335	1 retrocopy	retro_cpor_408,
Macaca mulatta	ENSMMUG00000007775	2 retrocopies	retro_mmul_1972 , retro_mmul_2419,
Mus musculus	ENSMUSG00000025024	1 retrocopy	retro_mmus_2685,
Tarsius syrichta	ENSTSYG00000006636	1 retrocopy	retro_tsyr_965,