RetrogeneDB ID: retro_mmul_952

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:56401243..56401699(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM9B
• Ensembl ID: ENSMMUG00000001998
• Aliases: None
• Description: None

Sequence

>retro_mmul_952
ATGGCGACCCTGTGGGGAGGCCTTCCTCGACTTGGCTCTTTGCTCAGCCTGTAGTGCCTGGCGCTGTCCGTGCTGCTGCT
GGCGCAGCTGTCAGACGCCGCCAGGAATTTCGAGGATGTCAGATGTAAATATATCTGCCCTCCCTATAAAGAAAATTCTG
GACATATTTATAATAAGAACATATCTCAGAAAGAGTGTGATTGCCTTCATGTTGTGGAGCCTATGCCTGTGCAGGGGCCT
GATGTAGAAGCATACTGTCTACTCTGTGAATGCAAATACAAAGAGAGAAGCTCTGTCACAATCAAGTTTACCATTATAAT
TTCTCTCTCCATTTTGGGCCTTCTACTTCAGTACATGGTATATCTTACTCTGGTTGAGCCCACACCGAAGAGGCGCCTCT
TTGGACACTCATAGTTGATACAGAGTGATGATGATATTGGGGATCACCAGCCTTTT

Alignment

ORF - retro_mmul_952 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.03 %
• Parental protein coverage: 76.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATLWGGLLRLGSLLSLSCLALSVLLLAQLSDAAKNFEDVRCKCICPPYKENSGHIYNKNISQKDWKLLY
          MATLWGGL.RLGSLLSL.CLALSVLLLAQLSDAA.NFEDVRCK.ICPPYKENSGHIYNKNISQK....L.
Retrocopy MATLWGGLPRLGSLLSL*CLALSVLLLAQLSDAARNFEDVRCKYICPPYKENSGHIYNKNISQKECDCLH

Parental  MIQECTQTGPYVIRPWLLVKISLETVEILTVLVTIIIYLSILGLLLLYMVYLTLVEPILKRRLFGHSQLI
          ........GP.V....LL...........T...TIII.LSILGLLL.YMVYLTLVEP..KRRLFGHS.LI
Retrocopy VVEPMPVQGPDVEAYCLLCECKYKERSSVTIKFTIIISLSILGLLLQYMVYLTLVEPTPKRRLFGHS*LI

Parental  QSDDDIGDHQPF
          QSDDDIGDHQPF
Retrocopy QSDDDIGDHQPF

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	0.34 RPM	13.22 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	14.44 RPM
SRP007412_cerebellum	0.39 RPM	11.82 RPM
SRP007412_heart	0.12 RPM	6.36 RPM
SRP007412_kidney	0.23 RPM	13.15 RPM
SRP007412_liver	0.08 RPM	7.09 RPM
SRP007412_testis	0.08 RPM	6.86 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_952 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_952 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_952 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000014721	1 retrocopy	retro_mluc_291,
Macaca mulatta	ENSMMUG00000001998	1 retrocopy	retro_mmul_952 ,