RetrogeneDB ID: retro_mmul_28

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:40840549..40841524(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000032474
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.2147
• Ensembl ID: ENSMMUG00000005007
• Aliases: None
• Description: None

Sequence

>retro_mmul_28
ATGGGGCCCTGGGGAGAGCCAGAGCTCCTGGTGTGGCACCCAGAGGCAGTAGCTTCAGAGCCTCCAGTGCCTGTGGGGCT
GGAGGTGAAGTTGGGGGCCCTGGTGCTGCTGCTGGTGCTCACCCTCCTCTGCAGCCTGGTGCCCATCTGTGTGCTGCGCC
AGCCAGGAGCTAACCATGAAGCCTCAGCTTTCCGCCAGAAAGCGCTGAGCCCAGTAAGCTGTTTTGCGGGGGGCGTCTTT
TTGGCCACCTGTCTCCTGGACCTGCTGCCTGACTACTTGGCTGCCATAGATGAGGCCCTGGCAGCCTTGCACGTGACGCT
CCAGTTCCCGCTGCAAGAGTTCATCCTGGCCATGGGCTTCTTCCTGGTCCTGGTGATGGAGCAGATCACACTGGCTTACA
AGGAGCAGTCAGGGCTGTCACCTCTTGAGGAAACAAGGGCTCTGCTGGGAACAGTGAATGGTGGGCCGCAGCATTGGCAT
AATGGGCCAGGGGTTCCACAGGCGAGTGGAACCCCAGCAAGCCCCTCAGCCTTGCGTGCCTGTGTACTGGTATTCTCCCT
GGCCCTCCACTCTGTGTTTGAGGGACTGGCGGTGGGGCTACAGCGAGACCGGGCTCGGGCGATGGAGCTGTGCCTGGCTT
TGCTGCTCCACAAGGGCATCCTGGCTGTCAGCCTGTCCCTGCGGCTGCTGCAGAGCCACCTTAGGGCACAGGTGGTGGCT
GGCTGTGGGATCCTCTTCTCATGCATGACACCTCTAGGCATCAGGCTGGGTGCAGCTCTGGCTGAGTCGGCAGGACCTCT
GCACCAGCTGGCTCAGTCTGTGCTAGAGGGCATGGCGGCTGGCACCTTTCTCTATATCACCTTTCTGGAAATCCTGCCCC
AGGAGCTGGCCAGTTCTGAACAAAGGATCCTCAAGGTCATCCTGCTCCTAGCAGACTTTGCCCTACTCACTGGCCTGCTC
TTCATCCAAATCTAG

Alignment

ORF - retro_mmul_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGPWGEPELLVWRPEAVASEPPVPVGLEVKLGALVLLLVLTLLCSLVPICVLRRPGANHEASASRQKALS
          MGPWGEPELLVW.PEAVASEPPVPVGLEVKLGALVLLLVLTLLCSLVPICVLR.PGANHEASA.RQKALS
Retrocopy MGPWGEPELLVWHPEAVASEPPVPVGLEVKLGALVLLLVLTLLCSLVPICVLRQPGANHEASAFRQKALS

Parental  LVSCFAGGVFLATCLLDLLPDYLAAIDEALAALHVTLQFPLQEFILAMGFFLVLVMEQITLAYKEQSGPS
          .VSCFAGGVFLATCLLDLLPDYLAAIDEALAALHVTLQFPLQEFILAMGFFLVLVMEQITLAYKEQSG.S
Retrocopy PVSCFAGGVFLATCLLDLLPDYLAAIDEALAALHVTLQFPLQEFILAMGFFLVLVMEQITLAYKEQSGLS

Parental  PLEETRALLGTVNGGPQHWHDGPGIPQASGAPASPSALRACVLVFSLALHSVFEGLAVGLQRDRARAMEL
          PLEETRALLGTVNGGPQHWH.GPG.PQASG.PASPSALRACVLVFSLALHSVFEGLAVGLQRDRARAMEL
Retrocopy PLEETRALLGTVNGGPQHWHNGPGVPQASGTPASPSALRACVLVFSLALHSVFEGLAVGLQRDRARAMEL

Parental  CLALLLHKGILAVSLSLRLLQSHLRAQVVAGCGILFSCMTPLGIGLGAALAESAGPLHQLAQSVLEGMAA
          CLALLLHKGILAVSLSLRLLQSHLRAQVVAGCGILFSCMTPLGI.LGAALAESAGPLHQLAQSVLEGMAA
Retrocopy CLALLLHKGILAVSLSLRLLQSHLRAQVVAGCGILFSCMTPLGIRLGAALAESAGPLHQLAQSVLEGMAA

Parental  GTFLYITFLEILPQELASSEQRILKVILLLAGFALLTGLLFIQI
          GTFLYITFLEILPQELASSEQRILKVILLLA.FALLTGLLFIQI
Retrocopy GTFLYITFLEILPQELASSEQRILKVILLLADFALLTGLLFIQI

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	7.84 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	15.07 RPM
SRP007412_cerebellum	0.13 RPM	6.46 RPM
SRP007412_heart	0.00 RPM	27.03 RPM
SRP007412_kidney	0.00 RPM	28.05 RPM
SRP007412_liver	1.43 RPM	38.99 RPM
SRP007412_testis	0.15 RPM	9.20 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_28 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_28 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_28 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010006	1 retrocopy	retro_cjac_1476,
Macropus eugenii	ENSMEUG00000006754	1 retrocopy	retro_meug_1551,
Microcebus murinus	ENSMICG00000010310	1 retrocopy	retro_mmur_162,
Myotis lucifugus	ENSMLUG00000013282	1 retrocopy	retro_mluc_2366,
Macaca mulatta	ENSMMUG00000005007	1 retrocopy	retro_mmul_28 ,
Mus musculus	ENSMUSG00000052310	1 retrocopy	retro_mmus_1899,
Oryctolagus cuniculus	ENSOCUG00000003045	1 retrocopy	retro_ocun_1792,