RetrogeneDB ID: retro_mmul_1683

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:61429385..61430080(-)
• 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_1683
CGTGCACATTGTCGCAGCCACGGCGTCCCGGGCATGCACCGCCGCCTCGGCTCCCTGCTTTGCTGCTCCATCCCCAAGGC
GGCTTTGGGTTCCGAATGTCCCAGTTCCTCAGCAGCCAGAGGCGGGAAGCCCAGGGACGGCTTTACAGCAGCGCAGGCTG
CGGTGCCGCTGGGGCGCCGGCGTGGCGGAGGCAGTGGTGGTCGTGTGTCCCATGGACACCATTAAGGTGAAGATCATCCA
CGGCCAGACCCCTCCAGACCTCCAGTGCAGAGGAGTGTCCCACCGGGTTAGGGAGATGTGCGGAAACAAGGGGAACTCAC
CGGGGCTTCCAGCGCAGAAGCAGGGCTGGAACCAGGCCGTGCGCCTCTTCTCCTGACCCCCCTGCACAGCTGGTACCGAG
GGGACAACCGAGCAAGCCCATGAACTGGCTGGTCGCTGGGGCATTCGGAGCCATTGTGGGCGCAGCCAGTGTCTTGGGAA
ACGCTCCCATGCACGGGATCAAGACCCGGATGCGGGGCCTGGAGAAGCACAAACGCTGAACACACGGGACTGCCGCTGCA
GATCCTGAGGAAGAGGGGCTCAAGGCCTTCTACGACGGCACTGTCCCCCGCCTGGGCCGGGTCTGCCTGGATATGACCAC
AGTGTTTATCCTCTGCCATGAGGTGGAAAGCTGCTCAACAGTGTGGAAGACGGAC

Alignment

ORF - retro_mmul_1683 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.94 %
• Parental protein coverage: 77.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  RQTVRSHGVLGLYRGLSSLLYGSIPKAAVR-FGMFEFLSNHMRDAQGRLDSTRG-LLCGLGAGVAEAVVV
          R...RSHGV.G..R.L.SLL..SIPKAA...F.M..FLS...R.AQGRL.S..G.L.C..GAGVAEAVVV
Retrocopy RAHCRSHGVPGMHRRLGSLLCCSIPKAALG<FRMSQFLSSQRREAQGRLYSSAG<LRCRWGAGVAEAVVV

Parental  VCPMETIKVKFIHDQTSPNPKYRGFFHGVREIVREQGLKGTYQGLTATVLKQGSNQAIRFF-VMTSLRNW
          VCPM.TIKVK.IH.QT.P....RG..H.VRE.....G.KG...GL.A...KQG.NQA.R.F...T.L..W
Retrocopy VCPMDTIKVKIIHGQTPPDLQCRGVSHRVREMC---GNKGNSPGLPAQ--KQGWNQAVRLF<LLTPLHSW

Parental  YRGDN-PNKPMNPLITGVFGAIAGAASVFGNTPLDVIKTRMQGLEAHK-YRNTWDC-GLQILRK-EGLKA
          YRGDN.P.KPMN.L..G.FGAI.GAASV.GN.P...IKTRM.GLE.HK...NT.DC..LQILRK.EGLKA
Retrocopy YRGDN<PSKPMNWLVAGAFGAIVGAASVLGNAPMHGIKTRMRGLEKHK<TLNTRDC<PLQILRK<EGLKA

Parental  FYKGTVPRLGRVCLDVAIVFIIYDEVVKLLNKVWKTD
          FY.GTVPRLGRVCLD...VFI...E.V.....VWKTD
Retrocopy FYDGTVPRLGRVCLDMTTVFILCHE-VESCSTVWKTD

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	0.11 RPM	9.64 RPM
SRP007412_brain_prefrontal_cortex	0.56 RPM	28.72 RPM
SRP007412_cerebellum	0.39 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	0.08 RPM	32.94 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1683 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1683 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1683 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,