RetrogeneDB ID: retro_mmul_659

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099213996158:4..850(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IVD
• Ensembl ID: ENSMMUG00000014462
• Aliases: None
• Description: None

Sequence

>retro_mmul_659
GTCGCACCGCTGGCCGCCGAGGCCGATGCCAGCAACCAGTTCCCGCTGGCCCTGTGGCCGAAGCTGGGCGAACAGGGCCT
GCTCGGCCTCACCGTGGAAGAAGAATACGGCGGCACCGGCATGGGTTACCTGGCCCATGTGGTGGCGATGGAAGAAATCT
CGCGTGCCTCCGGCGGCATCGGCCTGTCCTATGGCGCGCACTCCAACCTGTGCGTGAACCAGCTGCGCAAGAACGGCAAC
GAAGAACAGAAGCAGCGCTTCCTGCCCGGCCTGCGCAACGGCAGCCTGGTCGGCGCGCTGGCGATGAGCGAGCCGGGTGC
CGGTTCGGACGTGGTGTCGATGAAGCTGCGCGCCGACAAGCGCGGTGACCGCTACGTGCTCAACGGCAACAAGATGTGGA
TCACCAACGGCCCGGACGCCGACGTGCTGGTGGTCTATGCCAAGACCGACATGGAAGCGGGTGCCAAGGGCATCACCGCG
TTCCTGGTCGAGAAGGGCATGAAGGGCTTCTCCACCGCGCAGAAGCTGGACAAGCTGGGCATGCGCTCCTCGCCCACCTG
CGAGCTGGTGTTCCAGGACTGCGAGATTCCCGAAGAAAACGTGCTGGGCCAGGTCGGTGGTGGCGTGCGCGTGTTGATGT
CCGGCCTGGATTACGAGCGCGTGGTCCTTTCTGGTGGCCCGCTGGGCCTGATGGCCGCGGCCATGGACGTGGTGATGCCG
TACGTGCATGAGCGCCACCAGTTCGGCGAACCGATCGGCAGCTTCCAGCTGATCCTGGCCGAGATCGCCGACATGTACGT
GGGCCTGGGCGCGTGCCGCGCCTACGTCTATGCCGTCGCGCGCGCC

Alignment

ORF - retro_mmul_659 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.69 %
• Parental protein coverage: 67.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAPKAQEIDCSNEFKNLREFWKQLGNLGVLGITAPVQYGGSGLGYLEHVLVMEEISRASGAVGLSYGAHS
          .AP.A.E.D.SN.F......W..LG..G.LG.T....YGG.G.GYL.HV..MEEISRASG..GLSYGAHS
Retrocopy VAPLAAEADASNQFP--LALWPKLGEQGLLGLTVEEEYGGTGMGYLAHVVAMEEISRASGGIGLSYGAHS

Parental  NLCVNQLVRNGNEAQKEKYLPKLTSGEYIGALAMSEPNSGSDVVSMKLKAEKKGDHYVLNGNKSWITNGP
          NLCVNQL..NGNE.QK...LP.L..G...GALAMSEP..GSDVVSMKL.A.K.GD.YVLNGNK.WITNGP
Retrocopy NLCVNQLRKNGNEEQKQRFLPGLRNGSLVGALAMSEPGAGSDVVSMKLRADKRGDRYVLNGNKMWITNGP

Parental  DADVLIVYAKTDLAATPASRGITAFIVEKGMPGFSTSKKLDKLGMRGSDTCELIFEDCKVPAANILGHEN
          DADVL.VYAKTD..A.....GITAF.VEKGM.GFST..KLDKLGMR.S.TCEL.F.DC..P..N.LG...
Retrocopy DADVLVVYAKTDMEA--GAKGITAFLVEKGMKGFSTAQKLDKLGMRSSPTCELVFQDCEIPEENVLGQVG

Parental  KGVYVLMSGLDLERLVLAGGPLGLMQAVLDHTIPYLHVREAFGQKIGHFQLMQGKMADMYTRLMACRQYV
          .GV.VLMSGLD.ER.VL.GGPLGLM.A..D...PY.H.R..FG..IG.FQL.....ADMY..L.ACR.YV
Retrocopy GGVRVLMSGLDYERVVLSGGPLGLMAAAMDVVMPYVHERHQFGEPIGSFQLILAEIADMYVGLGACRAYV

Parental  YNVAKA
          Y.VA.A
Retrocopy YAVARA

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	18.71 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	42.68 RPM
SRP007412_cerebellum	0.00 RPM	27.38 RPM
SRP007412_heart	0.00 RPM	45.46 RPM
SRP007412_kidney	0.00 RPM	170.07 RPM
SRP007412_liver	0.00 RPM	181.45 RPM
SRP007412_testis	0.00 RPM	19.79 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_659 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_659 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_659 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000014462	1 retrocopy	retro_mmul_659 ,
Xenopus tropicalis	ENSXETG00000016078	1 retrocopy	retro_xtro_43,