RetrogeneDB ID: retro_mmul_1241

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 16:61062519..61063002(+)
• Located in intron of: ENSMMUG00000005637

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.12791
• Ensembl ID: ENSMMUG00000013735
• Aliases: None
• Description: dynactin subunit 6 [Source:RefSeq peptide;Acc:NP_001244351]

Sequence

>retro_mmul_1241
GGAGCTCAGTCAGTGATCCATCCTAAAGCACGAATTATTGCGGAAGCCGGGCCAATAGTGATTGGCAAAGGGAACCTAAT
AGAAGAACAGGCCCTTATCATAAATGCTCCCTCGGATAATATCACTCCTGACACTGAGGATCCAGAACCAAAACCTATGA
TCATTGGCACCAATAATGTGCTTGAAGTTGGTTGTCATTCCCAAGCCATGAAAATGGGAGACAATAATGTCATTGAATTA
AAAGCATATGTAGGCAGAAATGGAATATTGACAAGTGGCTGCCTCACTGGGGCTTGCTGTAACCTAGATACTTTTAAAGT
CATCCCTGAGAATATGGTGATCTATGGTGCAGACTGCCTTCGTCGGGTGCAGGCTGAGCGACCGCAGCCCCGGACACTAC
AGCTGGATTTCTTGATGAAAATCTTGCCAAATTACCACCACCTAAAGAAGACTATGAAAGGAAGCTCAGCTCCAGTAAAG
AAC

Alignment

ORF - retro_mmul_1241 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.82 %
• Parental protein coverage: 84.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPRTVIHPKARIIAEAGPIVIGEGNLIEEQALIINAYPDNITPDTEDPEPKPMIIGTNNVFEVGCYSQAM
          G...VIHPKARIIAEAGPIVIG.GNLIEEQALIINA..DNITPDTEDPEPKPMIIGTNNV.EVGC.SQAM
Retrocopy GAQSVIHPKARIIAEAGPIVIGKGNLIEEQALIINAPSDNITPDTEDPEPKPMIIGTNNVLEVGCHSQAM

Parental  KMGDNNVIESKAYVGRNVILTSGCIIGACCNLNTFEVIPENTVIYGADCLRRVQTERPQPQTLQLDFLMK
          KMGDNNVIE.KAYVGRN.ILTSGC..GACCNL.TF.VIPEN.VIYGADCLRRVQ.ERPQP.TLQLDFLMK
Retrocopy KMGDNNVIELKAYVGRNGILTSGCLTGACCNLDTFKVIPENMVIYGADCLRRVQAERPQPRTLQLDFLMK

Parental  ILPNYHHLKKTMKGSSTPVKN
          ILPNYHHLKKTMKGSS.PVKN
Retrocopy ILPNYHHLKKTMKGSSAPVKN

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	38.43 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	24.12 RPM
SRP007412_cerebellum	0.06 RPM	33.84 RPM
SRP007412_heart	0.06 RPM	42.22 RPM
SRP007412_kidney	0.00 RPM	25.23 RPM
SRP007412_liver	0.00 RPM	12.03 RPM
SRP007412_testis	0.11 RPM	12.59 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1241 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1241 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1241 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1780
Pan troglodytes	retro_ptro_1191
Gorilla gorilla	retro_ggor_2236

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001497	1 retrocopy	retro_amel_1860,
Canis familiaris	ENSCAFG00000006518	1 retrocopy	retro_cfam_2154,
Choloepus hoffmanni	ENSCHOG00000002554	3 retrocopies	retro_chof_1387, retro_chof_390, retro_chof_71,
Cavia porcellus	ENSCPOG00000011021	2 retrocopies	retro_cpor_1437, retro_cpor_706,
Echinops telfairi	ENSETEG00000012307	2 retrocopies	retro_etel_1571, retro_etel_1652,
Felis catus	ENSFCAG00000000133	1 retrocopy	retro_fcat_113,
Homo sapiens	ENSG00000104671	1 retrocopy	retro_hsap_1780,
Gorilla gorilla	ENSGGOG00000013074	1 retrocopy	retro_ggor_2236,
Myotis lucifugus	ENSMLUG00000028330	2 retrocopies	retro_mluc_1616, retro_mluc_2026,
Macaca mulatta	ENSMMUG00000013735	1 retrocopy	retro_mmul_1241 ,
Monodelphis domestica	ENSMODG00000019010	1 retrocopy	retro_mdom_1260,
Nomascus leucogenys	ENSNLEG00000011906	2 retrocopies	retro_nleu_1311, retro_nleu_2969,
Oryctolagus cuniculus	ENSOCUG00000010968	1 retrocopy	retro_ocun_917,
Ochotona princeps	ENSOPRG00000005061	1 retrocopy	retro_opri_950,
Pan troglodytes	ENSPTRG00000020134	1 retrocopy	retro_ptro_1191,
Tarsius syrichta	ENSTSYG00000013306	1 retrocopy	retro_tsyr_893,
Tursiops truncatus	ENSTTRG00000012439	1 retrocopy	retro_ttru_780,