RetrogeneDB ID: retro_mmul_2200

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:163230939..163231720(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000015430
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.4247
• Ensembl ID: ENSMMUG00000008691
• Aliases: None
• Description: voltage-dependent anion-selective channel protein 2 [Source:RefSeq peptide;Acc:NP_001244353]

Sequence

>retro_mmul_2200
ATGTGTAACACCCCAACTTACTGTGACCTGGGAAAGGCTGCTAAGGATGTCTTCAGCAAAGGATATGGCTTTGGCATGGT
GGAGATAGACCTGAAAACCAAGTCTTGTAGTGGAATGGAATTTTCTACGTCTGGTCACGCTTACACTGATACAGGGAAAG
CATCAGGCAACCTAGACACCGAATGTAAGGTCTGTAACTATGGACTCACCTTCACCCAAAAACGGAACACACACAATACT
CTTGGGACAGAAATCTCTGGAGAATAAGTTGGCTGAAGGGTTGAAACTGAGTTTTGATACCATATTGGTACCGAACACGG
GAAAGAAGAGTGAGAAATTGAAGGCCTCCTATAAATGGGATTGTTTTAGTGTTGGCAGTGACGTTGATATAGATTTTTCT
GGATCAACCGTCTATGGCTGGGCTGTGTTGGTCTTTGAAGGGTGGCTTGTCGGCTGTCAGATGAGTTTTGACACAGCCAA
ATCCAAACTGTCACAGAATAATTTCGCCCCGGGTTACGAGGCTGCAGACTTCCAGCTGCACATACATGTGAAGGATGGCA
CTGAATTTGGAGGTTCTATCTACCAGAAGGTTAATGAGATTGAAATGCCAATAAACCTTGCTTGGACGGGTGGAAGTAAC
AACACCCGTTTTGGCATTGCTGCTAAGTACAAGCTGGACTGTAGAACTTCTCTTTCTGCTAAAGCAAATAATGACAGCCT
GATTGGACTGGGTTCTACTCAGACCCTTCGACCCGGAGTCAAGTTGACCCTTTATCAGCTT

Alignment

ORF - retro_mmul_2200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.5 %
• Parental protein coverage: 89.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MCIPPSYADLGKAARDIFNKGFGFGLVKLDVKTKSCSGVEFSTSGSSNTDTGKVTGTLETKYKWCEYGLT
          MC..P.Y.DLGKAA.D.F.KG.GFG.V..D.KTKSCSG.EFSTSG...TDTGK..G.L.T..K.C.YGLT
Retrocopy MCNTPTYCDLGKAAKDVFSKGYGFGMVEIDLKTKSCSGMEFSTSGHAYTDTGKASGNLDTECKVCNYGLT

Parental  FTEKWNTDNT-LGTEIAIEDQICQGLKLTFDTTFSPNTGKKSGKIKSSYKRECINLGCDVDFDFAGPAIH
          FT.K.NT.NT.LG.....E.....GLKL.FDT...PNTGKKS.K.K.SYK..C...G.DVD.DF.G....
Retrocopy FTQKRNTHNT>LGQK-SLENKLAEGLKLSFDTILVPNTGKKSEKLKASYKWDCFSVGSDVDIDFSGSTVY

Parental  GSAVFGYEGWLAGYQMTFDSAKSKLTRNNFAVGYRTGDFQLHTNVNDGTEFGGSIYQKVCEDLDTSVNLA
          G.AV...EGWL.G.QM.FD.AKSKL..NNFA.GY...DFQLH..V.DGTEFGGSIYQKV........NLA
Retrocopy GWAVLVFEGWLVGCQMSFDTAKSKLSQNNFAPGYEAADFQLHIHVKDGTEFGGSIYQKV-NEIEMPINLA

Parental  WTSGTNCTRFGIAAKYQLDPTASISAKVNNSSLIGVGYTQTLRPGVKLTLSAL
          WT.G.N.TRFGIAAKY.LD...S.SAK.NN.SLIG.G.TQTLRPGVKLTL..L
Retrocopy WTGGSNNTRFGIAAKYKLDCRTSLSAKANNDSLIGLGSTQTLRPGVKLTLYQL

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	131.10 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	92.58 RPM
SRP007412_cerebellum	0.13 RPM	119.08 RPM
SRP007412_heart	0.18 RPM	238.55 RPM
SRP007412_kidney	0.12 RPM	152.93 RPM
SRP007412_liver	0.04 RPM	47.58 RPM
SRP007412_testis	0.08 RPM	115.42 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2200 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2200 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2200 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1375
Pan troglodytes	retro_ptro_945
Gorilla gorilla	retro_ggor_1071
Pongo abelii	retro_pabe_1145

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000012995	1 retrocopy	retro_meug_30,
Microcebus murinus	ENSMICG00000017815	1 retrocopy	retro_mmur_191,
Macaca mulatta	ENSMMUG00000008691	1 retrocopy	retro_mmul_2200 ,
Macaca mulatta	ENSMMUG00000016235	6 retrocopies	retro_mmul_1023, retro_mmul_1070, retro_mmul_1305, retro_mmul_1851, retro_mmul_2417, retro_mmul_2613,
Rattus norvegicus	ENSRNOG00000013505	1 retrocopy	retro_rnor_2652,
Tupaia belangeri	ENSTBEG00000001946	4 retrocopies	retro_tbel_1504, retro_tbel_1541, retro_tbel_1885, retro_tbel_4597,
Tarsius syrichta	ENSTSYG00000004764	1 retrocopy	retro_tsyr_14,
Tursiops truncatus	ENSTTRG00000000371	3 retrocopies	retro_ttru_116, retro_ttru_1172, retro_ttru_776,
Vicugna pacos	ENSVPAG00000008068	1 retrocopy	retro_vpac_156,