RetrogeneDB ID: retro_mmul_1556

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 20:33558132..33558729(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A1
• Ensembl ID: ENSMMUG00000005431
• Aliases: None
• Description: tricarboxylate transport protein, mitochondrial [Source:RefSeq peptide;Acc:NP_001253635]

Sequence

>retro_mmul_1556
AGCCATGGCGTCCTGGGCCTGGACAGCAGCCTCAGCTCTCTGCCCTCCCGCTCCATTTCCGAGGCAGCGTCAGGTTCGGG
AAGTTCGAATTCCTCGGCACCCAGATGTGGGATGCCCATGGACTGCTGAACAGCAGGTTCGGGCTGCTGCGTGGCCTGGG
CTCCAGCGTGGTCGAGGCCGTGGTGGTCGTCCGTCCCATGGAGACCATCAAAGTGAAATTCATCCACCGCCAGACTTCCC
CAAACCCCAAGAACAAATAATTCTTTGGGGTTAGGGGGATTGTGCGGGAACAAGGGCTGAGGGGACATACCAGGACCTCG
CGGCCACTGTGCTGAAGCAGGGCTGGAACCAGGCCATTGCTTCTTCGTCCTGACCTCCCTGCAGCAACTGGTGCCAAAGG
GATAAGCCCATGAACCCGCTGATCACTGGGGTCTTCTGAGCCACTGCGGGCGCAGCCCACGTCTTGGGAAACGCCCCTCT
GGACGGGATCCAGACTCATATGCGGGGCCTGGAAGTGCACAAACACCGGAACCCGGGACTCCGGCTGCAGATCCCGAGGA
AGGAGGGGCTCAAGGCCGTCACAAGGGCACTATCCCC

Alignment

ORF - retro_mmul_1556 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.1 %
• Parental protein coverage: 65.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SHGVLGLYRGLSSLLYGSIPKAA-VRFGMFEFLSNHMRDAQGRLDSTRGLLCGLGAGVAEAVVVVCPMET
          SHGVLGL...LSSL...SI..AA.VRFG.FEFL...M.DA.G.L.S..GLL.GLG..V.EAVVVV.PMET
Retrocopy SHGVLGLDSSLSSLPSRSISEAA<VRFGKFEFLGTQMWDAHGLLNSRFGLLRGLGSSVVEAVVVVRPMET

Parental  IKVKFIHDQTSPNPKYRGFFHGVREIVREQGLK-GTYQGLTATVLKQGSNQAIR-FFVMTSLR-NWYRGD
          IKVKFIH.QTSPNPK...FF.GVR.IVREQGL..GTYQ.L.ATVLKQG.NQAI..FFV.TSL..NW...D
Retrocopy IKVKFIHRQTSPNPKNK*FF-GVRGIVREQGLR<GTYQDLAATVLKQGWNQAIA<FFVLTSLQ>NWCQRD

Parental  NPNKPMNPLITGVFGAIAGAASVFGNTPLDVIKTRMQGLEAHKYRNTWDCGLQILRKEGLKAF-YKGTVP
          ...KPMNPLITGVF.A.AGAA.V.GN.PLD.I.T.M.GLE.HK.RN.....LQI.RKEGLKA...KGT.P
Retrocopy ---KPMNPLITGVF*ATAGAAHVLGNAPLDGIQTHMRGLEVHKHRNP-GLRLQIPRKEGLKAV<HKGTIP

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	9.64 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	28.72 RPM
SRP007412_cerebellum	0.00 RPM	11.75 RPM
SRP007412_heart	0.00 RPM	15.43 RPM
SRP007412_kidney	0.00 RPM	170.89 RPM
SRP007412_liver	0.00 RPM	328.07 RPM
SRP007412_testis	0.00 RPM	32.94 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1556 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1556 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1556 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000100075	2 retrocopies	retro_hsap_1632, retro_hsap_804,
Gorilla gorilla	ENSGGOG00000006198	2 retrocopies	retro_ggor_1230, retro_ggor_661,
Macaca mulatta	ENSMMUG00000005431	4 retrocopies	retro_mmul_1077, retro_mmul_1556 , retro_mmul_1683, retro_mmul_485,
Nomascus leucogenys	ENSNLEG00000005215	2 retrocopies	retro_nleu_2866, retro_nleu_408,
Ochotona princeps	ENSOPRG00000011649	1 retrocopy	retro_opri_1053,
Pongo abelii	ENSPPYG00000029785	9 retrocopies	retro_pabe_1346, retro_pabe_1414, retro_pabe_1529, retro_pabe_1671, retro_pabe_3125, retro_pabe_3217, retro_pabe_334, retro_pabe_3564, retro_pabe_719,
Pan troglodytes	ENSPTRG00000014057	3 retrocopies	retro_ptro_1139, retro_ptro_1364, retro_ptro_560,
Tursiops truncatus	ENSTTRG00000006845	1 retrocopy	retro_ttru_228,