RetrogeneDB ID: retro_mmul_851

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:26600616..26601351(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000007050
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.4849
• Ensembl ID: ENSMMUG00000009590
• Aliases: EIF4A3, DDX48
• Description: eukaryotic initiation factor 4A-III [Source:RefSeq peptide;Acc:NP_001253345]

Sequence

>retro_mmul_851
GTTTTTGATATGATTCGTCACGGAAGCTTAAGGACATGTGCCATCAAAATGTTGGTTTTGGATGAAGCTGATGAAATGTT
GAATAAAGGTTTCAAAGAGCAGATCTATGACGTATACAGGTACCTGCCTCCAGCCACACAGGTGGTTCTCATCAGTGCCA
CGCTGCCACACGAGATCCTGGAGATGACCAACAAGTTCATGACCGACCCAATCCACATCTTGGCGAAACGTGATGAATTG
ACTCTGGAAGGCATCAAGCAATTTTTTGTGGCAGTGGAGAGGGAAGAGTGGAAATTTGACACTCTGTGTGACCTCTACGA
CACACTGACCATCACTCAGGCGGTCATCTTCTGCAACACCAAAAGAAAGGTGGACTGGCTGACAGAAAAAATGAGAGAAG
CCAACTTCACTGTGTCCTCAATGCACGGAGACATGCCCCAGAAAGAGCGGGAGTCCATCATGAAGGAGTTCCGGTCGGGC
GCCAGGCGAGTGCTTATTTCTACAGACGTCTGGGCCAGGGGGTTGGATGTCCCTCATGTGTCCCTCATCATCAACTATGA
TCTCCCCAATAACAGAGAATTGTACATACACAAAATTGGGAGATCAGGTCGATACGGCCGGAAGGGTGTCGCCATTAACC
TTGTAAAGAACAATGACATCCGCATCCTCAGAGATACTGAGCAGTACTATTCCACTCAGATTGATGAGATGCCTATGAAC
GTTGCTGATCTGATC

Alignment

ORF - retro_mmul_851 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.51 %
• Parental protein coverage: 59.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDP
          VFDMIR..SLRT.AIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDP
Retrocopy VFDMIRHGSLRTCAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDP

Parental  IRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSS
          I.IL.KRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSS
Retrocopy IHILAKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSS

Parental  MHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGV
          MHGDMPQKERESIMKEFRSGA.RVLISTDVWARGLDVP.VSLIINYDLPNNRELYIH.IGRSGRYGRKGV
Retrocopy MHGDMPQKERESIMKEFRSGARRVLISTDVWARGLDVPHVSLIINYDLPNNRELYIHKIGRSGRYGRKGV

Parental  AINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI
          AIN.VKN.DIRILRD.EQYYSTQIDEMPMNVADLI
Retrocopy AINLVKNNDIRILRDTEQYYSTQIDEMPMNVADLI

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	19.61 RPM
SRP007412_brain_prefrontal_cortex	0.32 RPM	29.99 RPM
SRP007412_cerebellum	0.00 RPM	22.67 RPM
SRP007412_heart	0.00 RPM	21.32 RPM
SRP007412_kidney	0.00 RPM	31.69 RPM
SRP007412_liver	0.00 RPM	25.18 RPM
SRP007412_testis	0.04 RPM	54.17 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_851 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_851 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_851 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000009136	2 retrocopies	retro_mmur_444, retro_mmur_50,
Myotis lucifugus	ENSMLUG00000009585	1 retrocopy	retro_mluc_65,
Macaca mulatta	ENSMMUG00000003702	2 retrocopies	retro_mmul_1055, retro_mmul_2450,
Macaca mulatta	ENSMMUG00000009590	1 retrocopy	retro_mmul_851 ,
Macaca mulatta	ENSMMUG00000013499	1 retrocopy	retro_mmul_1280,
Monodelphis domestica	ENSMODG00000002190	1 retrocopy	retro_mdom_202,
Ornithorhynchus anatinus	ENSOANG00000000334	1 retrocopy	retro_oana_47,
Otolemur garnettii	ENSOGAG00000007495	1 retrocopy	retro_ogar_212,