RetrogeneDB ID: retro_mmul_1943

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:46060308..46061182(-)
• Located in intron of: ENSMMUG00000030337

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A14
• Ensembl ID: ENSMMUG00000008386
• Aliases: None
• Description: brain mitochondrial carrier protein 1 precursor [Source:RefSeq peptide;Acc:NP_001244545]

Sequence

>retro_mmul_1943
AGCCAAGAGATGCCTGATCTGAATTGGAAACCCTTTGTATATGGCGGCCTTGCCTCTATCATTGCTGAGTTTGGAACATT
CCCCATGGACCTTACCAAAACACACTTCAGGTAGGTTCAAGGCCAAAGCATTGATGTCTGTTTCAAAGAAATAAAATATA
GACGGATGTTTCAAGCTTTGTTTTGGATCTACAAAGAGGAAGGTGTATTGGCTCTGTATTAAGGAATTGCTTCTGTTTGC
GAAGACAAGCATCATATGGCACCATTAAAATTGGGATTTACCAAAGCTTGAAGCAATTATTTGTAGAACGTTTAGAAGAT
GAAACTCTTTCAATTAACATGATCTGTGGGGTGGTGTCAGGAGTGGTATTTTCCAATATAGCCAATCCCACCGATGTTCT
AAAGATTCGAATGCAGGCTCAAGGAAGTCTGTTCCAAGGGAACATGATTGGCAGCTTCATTGATATGTACCAACAGAAAG
GCACCAGGGCTCTGTGGAGGGGTGTGGTTCCAACTGTTGAGCATGCTGCCATCGTTGTGGGAGTAGAGCTACAGTCTATG
ATATTACTAAGAAGTATTTAATATTGTCAGGAATGATGGAAGACACAACTTTAACTTGCTTTGTTTCCAGCTTTACGTGT
AGTTTAGCTGGAGCTCTTGCCTCTAATCCGGGTGATGTGGTAGGCACTCGTATGATGAACCAGAGGGCAATCGTGGGATA
TGTGGATCTCTGTAAGTGTACTTTGGATGGTATTTTAAAGATGTGGAAACATGAGGGCTTTTTTGCACTCTATAAAGGAT
TTTGGCCAAAGTGGCTTCGGCTTGGACCCTGGAACATTATTTTTTAAATTACATATGAGCAGCTCAAGAGGCTT

Alignment

ORF - retro_mmul_1943 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.01 %
• Parental protein coverage: 89.54 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SHEMSGLNWKPFVYGGLASIVAEFGTFPVDLTKTRLQ-VQGQSIDARFKEIKYRGMFHALFRICKEEGVL
          S.EM..LNWKPFVYGGLASI.AEFGTFP.DLTKT....VQGQSID..FKEIKYR.MF.ALF.I.KEEGVL
Retrocopy SQEMPDLNWKPFVYGGLASIIAEFGTFPMDLTKTHFR*VQGQSIDVCFKEIKYRRMFQALFWIYKEEGVL

Parental  ALYSGIAPA-LLRQASYGTIKIGIYQSLKRLFVERLEDETLLINMICGVVSGVISSTIANPTDVLKIRMQ
          ALY.GIA...L.RQASYGTIKIGIYQSLK.LFVERLEDETL.INMICGVVSGV..S.IANPTDVLKIRMQ
Retrocopy ALY*GIASV<LRRQASYGTIKIGIYQSLKQLFVERLEDETLSINMICGVVSGVVFSNIANPTDVLKIRMQ

Parental  AQGSLFQGSMIGSFIDIYQQEGTRGLWRGVVPTAQRAAIVVGVELP-VYDITKKHLILSGMMGDTILTHF
          AQGSLFQG.MIGSFID.YQQ.GTR.LWRGVVPT...AAIVVGVEL..VYDITKK.LILSGMM.DT.LT.F
Retrocopy AQGSLFQGNMIGSFIDMYQQKGTRALWRGVVPTVEHAAIVVGVELQ<VYDITKKYLILSGMMEDTTLTCF

Parental  VSSFTCGLAGALASNPVDVVRTRMMNQRAIVGHVDLYKGTVDGILKMWKHEGFFALYKGFWPNWLRLGPW
          VSSFTC.LAGALASNP.DVV.TRMMNQRAIVG.VDL.K.T.DGILKMWKHEGFFALYKGFWP.WLRLGPW
Retrocopy VSSFTCSLAGALASNPGDVVGTRMMNQRAIVGYVDLCKCTLDGILKMWKHEGFFALYKGFWPKWLRLGPW

Parental  NIIFFITYEQLKRL
          NIIF.ITYEQLKRL
Retrocopy NIIF*ITYEQLKRL

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	14.23 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	12.30 RPM
SRP007412_cerebellum	0.26 RPM	11.04 RPM
SRP007412_heart	0.00 RPM	3.00 RPM
SRP007412_kidney	0.00 RPM	2.23 RPM
SRP007412_liver	0.00 RPM	0.67 RPM
SRP007412_testis	0.11 RPM	2.75 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1943 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1943 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1943 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_2257

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016263	1 retrocopy	retro_btau_1362,
Canis familiaris	ENSCAFG00000018766	1 retrocopy	retro_cfam_1359,
Callithrix jacchus	ENSCJAG00000002456	1 retrocopy	retro_cjac_2257,
Homo sapiens	ENSG00000102078	1 retrocopy	retro_hsap_2954,
Macaca mulatta	ENSMMUG00000008386	1 retrocopy	retro_mmul_1943 ,
Nomascus leucogenys	ENSNLEG00000015318	1 retrocopy	retro_nleu_1638,
Pongo abelii	ENSPPYG00000020715	2 retrocopies	retro_pabe_2450, retro_pabe_3595,
Pan troglodytes	ENSPTRG00000022268	1 retrocopy	retro_ptro_2048,
Tursiops truncatus	ENSTTRG00000016206	2 retrocopies	retro_ttru_1159, retro_ttru_1570,