RetrogeneDB ID: retro_mmul_1058

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:37484330..37484814(+)
• Located in intron of: ENSMMUG00000021647

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.3907
• Ensembl ID: ENSMMUG00000005633
• Aliases: None
• Description: methylmalonic aciduria (cobalamin deficiency) cblD type, with homocystinuria [Source:RefSeq peptide;Acc:NP_001252571]

Sequence

>retro_mmul_1058
CTGCTTCACAGAAGAAAAGCCTGGTTTCTAGCAGAAACTTCATCAAGTGAAAGACACGAGTTTGTGATGACACAATATGT
GAATGAATTTCAGGGTAATGATGCACCTGTTGAACAAGAAATTAACAGTGCAGAAACTTAACTTTGAAAGTGCCAGAGTA
GGGTGTGCAATACAAACATGTCCAGAATTGCGGCGAAAAGATTTTGAATCACTGTTTCCAGAAGTAGCTAATAGCAAAGT
AATCATTCTGACTGTAACACAGAAAGCTAAGAATGATATGACTGTTTAGAGTGAAGAAGTAGAAACTGAAAGAGAAGTGC
TCTTAGAAAAGTTCATCAATGCTGCTGAGGAAATTTGCTGTGCTCTTTTAGCTGAGGGATATTGGGCTGACTTTACTGAC
CCATCATTTGGTTTGGCATTTTTTGGACCATATACAAACAACACTCTTTTCGAAACCCTTGAATGCTAACAACATTTAGG
ATTC

Alignment

ORF - retro_mmul_1058 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.1 %
• Parental protein coverage: 54.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LVHKTLPDVLAEPLSSERHEFVMAQYVNEFQGNDAPVEQEINSAET-YFESARVECAIQTCPELLRKDFE
          L.H......LAE..SSERHEFVM.QYVNEFQGNDAPVEQEINSAET..FESARV.CAIQTCPEL.RKDFE
Retrocopy LLHRRKAWFLAETSSSERHEFVMTQYVNEFQGNDAPVEQEINSAET>NFESARVGCAIQTCPELRRKDFE

Parental  SLFPEVANSKLLILTVTQKTKNDMTVWSEEVEIEREVLLEKFINGAKEICYALRAEGYWADFIDPSSGLA
          SLFPEVANSK..ILTVTQK.KNDMTV.SEEVE.EREVLLEKFIN.A.EIC.AL.AEGYWADF.DPS.GLA
Retrocopy SLFPEVANSKVIILTVTQKAKNDMTV*SEEVETEREVLLEKFINAAEEICCALLAEGYWADFTDPSFGLA

Parental  FFGPYTNNTLFETDERYRHLGF
          FFGPYTNNTLFET.E...HLGF
Retrocopy FFGPYTNNTLFETLEC*QHLGF

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	28.68 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	18.72 RPM
SRP007412_cerebellum	0.00 RPM	25.44 RPM
SRP007412_heart	0.12 RPM	30.86 RPM
SRP007412_kidney	0.12 RPM	33.68 RPM
SRP007412_liver	0.24 RPM	37.88 RPM
SRP007412_testis	0.04 RPM	69.77 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1058 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1058 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1058 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_865
Pan troglodytes	retro_ptro_599
Gorilla gorilla	retro_ggor_704

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003086	2 retrocopies	retro_cjac_4082, retro_cjac_4101,
Cavia porcellus	ENSCPOG00000007690	1 retrocopy	retro_cpor_30,
Homo sapiens	ENSG00000168288	2 retrocopies	retro_hsap_4716, retro_hsap_865,
Gorilla gorilla	ENSGGOG00000027348	1 retrocopy	retro_ggor_704,
Macaca mulatta	ENSMMUG00000005633	1 retrocopy	retro_mmul_1058 ,
Monodelphis domestica	ENSMODG00000003566	2 retrocopies	retro_mdom_1749, retro_mdom_620,
Mustela putorius furo	ENSMPUG00000000323	1 retrocopy	retro_mputfur_1253,
Nomascus leucogenys	ENSNLEG00000010795	2 retrocopies	retro_nleu_1988, retro_nleu_426,
Otolemur garnettii	ENSOGAG00000034385	4 retrocopies	retro_ogar_3266, retro_ogar_356, retro_ogar_688, retro_ogar_813,
Pan troglodytes	ENSPTRG00000012525	1 retrocopy	retro_ptro_599,
Ictidomys tridecemlineatus	ENSSTOG00000021576	1 retrocopy	retro_itri_1809,
Tarsius syrichta	ENSTSYG00000009075	1 retrocopy	retro_tsyr_1690,