RetrogeneDB ID: retro_mmul_17

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:84910149..84910623(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000029539
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: AP4S1
• Ensembl ID: ENSMMUG00000003123
• Aliases: None
• Description: None

Sequence

>retro_mmul_17
ATGATAAAATTTTTCCTCATGGTGAATAAACAAGGGCAGACTCAACTTTGTAAGTACTATGAACATGTAGATATTAATAA
GCGTACACTTCTGGAAACAGAAGTCATAAAGAGCTGTCTCTCTCGGTCCAATGAACAATGCCCTTTCACTGAATATAAGG
ATTTTCGGCTGATATATCGGCAGTGTGCAGCTCTCTTCATTGTGGTTGGAGTTGATGACACTGAGACAGAGATGGCTATT
TATGAATTCATTCATAATTTTGTGGAAGTTTTAGATGAGTATTTCAGCCGAGTGAGTGAATTAGATAAAATGTTTAATTT
GGATAAAGTACACATCATTTTGGATGAGACGGTGTTAAACGGCTGCGTTGTGGAAACTAACAGGGAAAGAATTCTTGCCC
CTCTACTAATTCTTTATGTCAGAAAGCTGAAAGGAAGTATCTTCCAGACAACATGGATTTATCGGAAATGCTAG

Alignment

ORF - retro_mmul_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.33 %
• Parental protein coverage: 70.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIKFFLMVNKQGQTRLSKYYEHVDINKRTLLETEVIKSCLSRSNEQCSFIEYKDFKLIYRQYAALFIVVG
          MIKFFLMVNKQGQT.L.KYYEHVDINKRTLLETEVIKSCLSRSNEQC.F.EYKDF.LIYRQ.AALFIVVG
Retrocopy MIKFFLMVNKQGQTQLCKYYEHVDINKRTLLETEVIKSCLSRSNEQCPFTEYKDFRLIYRQCAALFIVVG

Parental  VNDTENYASLDFFFFFFDGVLPCCQAVVHELDVSF
          V.DTE.......F...F..VL......V.ELD..F
Retrocopy VDDTETEMAIYEFIHNFVEVLDEYFSRVSELDKMF

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	2.58 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	1.67 RPM
SRP007412_cerebellum	0.32 RPM	2.20 RPM
SRP007412_heart	0.00 RPM	0.82 RPM
SRP007412_kidney	0.12 RPM	0.94 RPM
SRP007412_liver	0.00 RPM	0.20 RPM
SRP007412_testis	0.08 RPM	0.83 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_17 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_17 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_17 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3496
Pan troglodytes	retro_ptro_2368
Gorilla gorilla	retro_ggor_2363
Pongo abelii	retro_pabe_2889

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013301	4 retrocopies	retro_chof_2345, retro_chof_2677, retro_chof_393, retro_chof_820,
Callithrix jacchus	ENSCJAG00000005786	1 retrocopy	retro_cjac_2742,
Dipodomys ordii	ENSDORG00000009468	1 retrocopy	retro_dord_595,
Erinaceus europaeus	ENSEEUG00000013009	1 retrocopy	retro_eeur_301,
Myotis lucifugus	ENSMLUG00000011671	1 retrocopy	retro_mluc_1841,
Macaca mulatta	ENSMMUG00000003123	1 retrocopy	retro_mmul_17 ,
Macaca mulatta	ENSMMUG00000014055	1 retrocopy	retro_mmul_1716,
Monodelphis domestica	ENSMODG00000017579	1 retrocopy	retro_mdom_1774,
Ornithorhynchus anatinus	ENSOANG00000014031	1 retrocopy	retro_oana_60,
Pongo abelii	ENSPPYG00000005723	1 retrocopy	retro_pabe_2889,
Pteropus vampyrus	ENSPVAG00000017161	1 retrocopy	retro_pvam_1455,
Rattus norvegicus	ENSRNOG00000005765	1 retrocopy	retro_rnor_2200,
Ictidomys tridecemlineatus	ENSSTOG00000010759	1 retrocopy	retro_itri_1050,