RetrogeneDB ID: retro_mmul_343

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:157088754..157089495(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000012397
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.9925
• Ensembl ID: ENSMMUG00000016544
• Aliases: None
• Description: proteasome subunit alpha type-6 [Source:RefSeq peptide;Acc:NP_001180482]

Sequence

>retro_mmul_343
ATGTCCCGTGGTTCCAGCGCCGGTTTTGACCGCCACATTACTATTTTTTCACCCGAGGGTCGGCTCTACCAAATAGAATA
TGCTTTTAAGGCTATTAACCAGGGTGGCCTTACATCAGTAGCTGTCAGAGGGAAAGACTGTGCAGTAATTGTCACACAGA
AGAAAGTACCTGACAAATTATTGGATTCCAGCACAGTGACTCACTTATTCAAGATAACTGAAAACATTGGTTGTGTGATG
ACCGGAATGACAGCTGACAGCAGATCCCAGGTACAGAGGGCACGCTATGAGGCAGCTAACTGGAAATACAAGTATGGCTA
TGAGATTCCTGTGGACATGCTGTGTAAAAGAATTGCTGATATTTCTCAGGTCTACACACAGAATGCTGAAATGAGGCCTC
TTGGTTGTTGTATGATTTTAATTGGTATAGATGAAGAGCAAGGCCCTCAGGTATATAAGTGTGATCCTGCAGGTTACTAC
TGTGGGTTTAAAGCCACTGCAGCAGGAGTTAAACAAACTGAGTCAACCAGCTTCCTTGAAAAAAAAGTGAAGAAGAAATT
TGACTGGACATTTGAACAGACAGTGGAAACTGCAATTACATGCCTGTCTACTGTTCTGTCAATTGATTTCAAACCTTCAG
AAATAGAAGTTGGAGTAGTGACAGTTGAAAATCCTAAATTCAGGATTCTTACGGAAGCAGAGATTGATGCTCACCTTGTT
GCTCTAGCAGAGAGAGACTAA

Alignment

ORF - retro_mmul_343 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTVTHLF
          MSRGSSAGFDRHITIFSPEGRLYQ.EYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTVTHLF
Retrocopy MSRGSSAGFDRHITIFSPEGRLYQIEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTVTHLF

Parental  KITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMIL
          KITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMIL
Retrocopy KITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMIL

Parental  IGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCLSTVLSIDF
          IGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCLSTVLSIDF
Retrocopy IGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCLSTVLSIDF

Parental  KPSEIEVGVVTVENPKFRILTEAEIDAHLVALAERD
          KPSEIEVGVVTVENPKFRILTEAEIDAHLVALAERD
Retrocopy KPSEIEVGVVTVENPKFRILTEAEIDAHLVALAERD

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	14.57 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	22.69 RPM
SRP007412_cerebellum	0.13 RPM	12.27 RPM
SRP007412_heart	0.06 RPM	12.78 RPM
SRP007412_kidney	0.00 RPM	12.32 RPM
SRP007412_liver	0.00 RPM	12.75 RPM
SRP007412_testis	0.08 RPM	27.67 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_343 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_343 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_343 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013409	2 retrocopies	retro_cfam_1581, retro_cfam_743,
Echinops telfairi	ENSETEG00000004892	1 retrocopy	retro_etel_1775,
Felis catus	ENSFCAG00000026276	1 retrocopy	retro_fcat_973,
Homo sapiens	ENSG00000100902	2 retrocopies	retro_hsap_1228, retro_hsap_4923,
Macropus eugenii	ENSMEUG00000016537	1 retrocopy	retro_meug_1217,
Microcebus murinus	ENSMICG00000000083	4 retrocopies	retro_mmur_104, retro_mmur_165, retro_mmur_752, retro_mmur_80,
Myotis lucifugus	ENSMLUG00000010228	1 retrocopy	retro_mluc_822,
Macaca mulatta	ENSMMUG00000016544	1 retrocopy	retro_mmul_343 ,
Mustela putorius furo	ENSMPUG00000016288	1 retrocopy	retro_mputfur_1089,
Mus musculus	ENSMUSG00000021024	1 retrocopy	retro_mmus_654,
Otolemur garnettii	ENSOGAG00000008492	10 retrocopies	retro_ogar_1273, retro_ogar_1397, retro_ogar_1928, retro_ogar_1950, retro_ogar_2021, retro_ogar_2073, retro_ogar_2274, retro_ogar_2488, retro_ogar_2521, retro_ogar_3089,
Pan troglodytes	ENSPTRG00000006264	2 retrocopies	retro_ptro_3297, retro_ptro_844,
Rattus norvegicus	ENSRNOG00000007114	4 retrocopies	retro_rnor_1724, retro_rnor_1960, retro_rnor_854, retro_rnor_924,
Ictidomys tridecemlineatus	ENSSTOG00000011774	1 retrocopy	retro_itri_1713,
Tupaia belangeri	ENSTBEG00000011241	17 retrocopies	retro_tbel_1304, retro_tbel_1415, retro_tbel_1789, retro_tbel_2028, retro_tbel_2466, retro_tbel_2519, retro_tbel_3227, retro_tbel_3280, retro_tbel_3535, retro_tbel_4181, retro_tbel_4183, retro_tbel_4357, retro_tbel_4465, retro_tbel_4495, retro_tbel_509, retro_tbel_602, retro_tbel_725,