RetrogeneDB ID: retro_mmul_1077

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:84262657..84263582(+)
• 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_1077
ATGGCCGCGCCTCGAACCCCACGCGCTCTGGCGGCCGCCGCGCCCGCGTCTGGCAAGATCAAGCTGACGCTCCTGGGGAA
GGCGATCCTGGCAGGCGGCCTGGCGGGCAGCATCGAGATCTACATCACCTTCCCCACCCAGTATGTGAAGACGCAGGGCA
GCTGGACTAGCGCTCGCACCCGCTGCGGTACCAGAGCATCCGGGACCGGTGTGGTCGAGTGTCTGCAACCATGGCGTCCT
GGGCCTGTACCGCGGCCTCAGCTCCCTGCTCTACGGCTCCATCCCCAAGGTGGCCGCCAGGTTCGGAATGTTCTGGTTCC
TCAGCAACCACATGCGGGTTTCCCAGGGACGCTGGACAGCACGCGCGGGCTGCTGTGCTGCCTGGGCGCTGGAGTGGCTG
AGGCCGTGGTGATCATGTGCCCCATGAAGACCATCAATGTGAAGTTCAGCCGCCACACCTACCTAAACCCCCAGTACAGA
GGATTCTTCCGCGGGTTAGGAAGATTGTGCGGTAACAAGGGCTGAAGGGGATGTATCAGGGCCTCACAGTCACGGTGCTG
AAGCAGGGCTGGAATCAGGCCATCTGCTTCTTCGTCATGACATTCCCTGCACAGTTGGTACGGAGGGGACAACCCCAACA
AGCCTATGAACGTGCTGATCACTGGGGTCTTCGGAGCCATGGTGTGCACAGCCAGCGTCTTTGGAAACACTCCTCTGGAC
GTGATTAAGACCCGCAGGTAGGGCCTGGAGGCGCACAAATACCGGAACTCGATGGACTGCCTCTGGCAGATCCTGAGAAA
GGAGGAGCTCAAGGATTCTACAAGGGCATTGTCCCGCTCCGGGCCAGGTCAGCCTGGTTGTGGCCATAGTGTTTATCATC
TATGATGAGGTGGTGAAGCTGCTCAACGAAGTGTGGAAGACGGAC

Alignment

ORF - retro_mmul_1077 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.04 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MAAPRAPRALAAAAPASGKAKLTHPGKAILAGGLAGGIEICITFPTEYVKTQ-LQLDERSHPPRYRGIGD
          MAAPR.PRALAAAAPASGK.KLT..GKAILAGGLAG.IEI.ITFPT.YVKTQ..QLD.RSHP.RY..I.D
Retrocopy MAAPRTPRALAAAAPASGKIKLTLLGKAILAGGLAGSIEIYITFPTQYVKTQ<GQLD*RSHPLRYQSIRD

Parental  -CVRQTVRSHGVLGLYRGLSSLLYGSIPKAAVRFGMFEFLSNHMRDAQGR-LDSTRGLLCGLGAGVAEAV
          ..V...V..HGVLGLYRGLSSLLYGSIPK.A.RFGMF.FLSNHMR..QGR.LDSTRGLLC.LGAGVAEAV
Retrocopy <PVWSSVCNHGVLGLYRGLSSLLYGSIPKVAARFGMFWFLSNHMRVSQGR<LDSTRGLLCCLGAGVAEAV

Parental  VVVCPMETIKVKFIHDQTSPNPKYRGFFHG-VREIVREQGLKGTYQGLTATVLKQGSNQAIRFFVMT-SL
          V..CPM.TI.VKF....T..NP.YRGFF.G.VR.IVR.QGLKG.YQGLT.TVLKQG.NQAI.FFVMT.SL
Retrocopy VIMCPMKTINVKFSR-HTYLNPQYRGFFRG<VRKIVR*QGLKGMYQGLTVTVLKQGWNQAICFFVMT>SL

Parental  RNWYRGDNPNKPMNPLITGVFGAIAGAASVFGNTPLDVIKTRMQGLEAHKYRNTWDCGLQILRKEGLK-A
          ..WY.GDNPNKPMN.LITGVFGA....ASVFGNTPLDVIKTR..GLEAHKYRN..DC..QILRKE.LK..
Retrocopy HSWYGGDNPNKPMNVLITGVFGAMVCTASVFGNTPLDVIKTRR*GLEAHKYRNSMDCLWQILRKEELK<G

Parental  FYKGTV-PRLGRVCLDVAIVFIIYDEVVKLLNKVWKTD
          FYKG.V.P..G.V.L.VAIVFIIYDEVVKLLN.VWKTD
Retrocopy FYKGIV<PAPGQVSLVVAIVFIIYDEVVKLLNEVWKTD

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	0.16 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	3.24 RPM	32.94 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1077 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1077 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1077 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_804
Pan troglodytes	retro_ptro_560
Gorilla gorilla	retro_ggor_661
Pongo abelii	retro_pabe_719

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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,