RetrogeneDB ID: retro_mmul_1958

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:91911354..91911630(-)
• Located in intron of: ENSMMUG00000011062

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.16850
• Ensembl ID: ENSMMUG00000019544
• Aliases: None
• Description: 60S ribosomal protein L37a [Source:RefSeq peptide;Acc:NP_001252654]

Sequence

>retro_mmul_1958
ATGGCCAAACGTACCAAGAAAGTCGGGATCGTCGGTAAATACGGGACGCGCTATGGGGCCTCCCTCCGGAAAATGGTGAA
GAAAATTGAAATCAGCCAGCACGCCAAGTACACTTGCTCTTTCTGTGGCAAAACCAAGATGAAGAGATGAGCTGTGGGGA
TCTGGCACTGTGGTTCCTGCATGAAGACAGTGGCCGGCGGTGCCTGGACATACAATACCACTTCCGCTGTCACGGTAAAG
TCCGCCATCAGAAGACTGAAGGAGTTGAAAGACCAG

Alignment

ORF - retro_mmul_1958 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.91 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKRTKKVGIVGKYGTRYGASLRKMVKKIEISQHAKYTCSFCGKTKMKRRAVGIWHCGSCMKTVAGGAWT
          MAKRTKKVGIVGKYGTRYGASLRKMVKKIEISQHAKYTCSFCGKTKMKR.AVGIWHCGSCMKTVAGGAWT
Retrocopy MAKRTKKVGIVGKYGTRYGASLRKMVKKIEISQHAKYTCSFCGKTKMKR*AVGIWHCGSCMKTVAGGAWT

Parental  YNTTSAVTVKSAIRRLKELKDQ
          YNTTSAVTVKSAIRRLKELKDQ
Retrocopy YNTTSAVTVKSAIRRLKELKDQ

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	0.22 RPM	18.15 RPM
SRP007412_brain_prefrontal_cortex	6.27 RPM	95.20 RPM
SRP007412_cerebellum	0.19 RPM	22.79 RPM
SRP007412_heart	0.47 RPM	35.86 RPM
SRP007412_kidney	0.00 RPM	24.76 RPM
SRP007412_liver	0.08 RPM	51.18 RPM
SRP007412_testis	1.47 RPM	24.58 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1958 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1958 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1958 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 78 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000014352	34 retrocopies	retro_etel_1002, retro_etel_1038, retro_etel_1090, retro_etel_1098, retro_etel_1205, retro_etel_121, retro_etel_1359, retro_etel_1426, retro_etel_1448, retro_etel_164, retro_etel_1862, retro_etel_1873, retro_etel_1977, retro_etel_2035, retro_etel_2036, retro_etel_2105, retro_etel_2215, retro_etel_238, retro_etel_277, retro_etel_304, retro_etel_305, retro_etel_307, retro_etel_364, retro_etel_441, retro_etel_478, retro_etel_634, retro_etel_728, retro_etel_742, retro_etel_784, retro_etel_812, retro_etel_817, retro_etel_829, retro_etel_866, retro_etel_907,
Gorilla gorilla	ENSGGOG00000014827	5 retrocopies	retro_ggor_1546, retro_ggor_2393, retro_ggor_2538, retro_ggor_2636, retro_ggor_633,
Latimeria chalumnae	ENSLACG00000011578	1 retrocopy	retro_lcha_71,
Macaca mulatta	ENSMMUG00000019544	11 retrocopies	retro_mmul_1123, retro_mmul_1639, retro_mmul_1667, retro_mmul_1811, retro_mmul_1892, retro_mmul_1942, retro_mmul_1958 , retro_mmul_2468, retro_mmul_456, retro_mmul_590, retro_mmul_844,
Monodelphis domestica	ENSMODG00000025485	9 retrocopies	retro_mdom_1106, retro_mdom_1555, retro_mdom_1848, retro_mdom_1934, retro_mdom_350, retro_mdom_521, retro_mdom_771, retro_mdom_805, retro_mdom_975,
Procavia capensis	ENSPCAG00000006891	5 retrocopies	retro_pcap_185, retro_pcap_28, retro_pcap_343, retro_pcap_414, retro_pcap_423,
Petromyzon marinus	ENSPMAG00000000001	1 retrocopy	retro_pmar_11,
Pongo abelii	ENSPPYG00000025878	1 retrocopy	retro_pabe_62,
Tarsius syrichta	ENSTSYG00000004258	11 retrocopies	retro_tsyr_1122, retro_tsyr_1704, retro_tsyr_1707, retro_tsyr_1831, retro_tsyr_1999, retro_tsyr_213, retro_tsyr_278, retro_tsyr_316, retro_tsyr_321, retro_tsyr_800, retro_tsyr_815,