RetrogeneDB ID: retro_mmul_2045

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:142462817..142463604(+)
• Located in intron of: ENSMMUG00000018386

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOOL
• Ensembl ID: ENSMMUG00000004335
• Aliases: None
• Description: None

Sequence

>retro_mmul_2045
GGAAAACTGACAATCATGCCTGCAGGTCTGATACATGCATCTGTAAGTGTACATGCAGCCAAAGCAGAGGAATCCAAAAA
GCAGCTAGTGATACCAGAGCAAGTCCCCATATATACTGCACCACCGCTCCCGTCTAAATATGTTGAAGAGCAGCCTGGTC
ATTTACAAATGGGCTTTGCTTCCATCTGCACTGCAACTGGTCATTATACTGGCTGGTGCAAGGGTGTTTATGTCTTTGGG
AAAAATGGGATAATTGATACGGTAGAATTTGGAAAAGATGCTCATGTCTATCTGAAGAATCCTCCTCAAGATTTTCTTCC
AAAAATGGGAGTTATTACGGTTTCAGGATTGGTGGGCTTGGTTTCAGCGAGAAAAGGTTCTAAGTGTAAGAAAATTACTT
ATCCTCTGGGACTGACTACTTTATGAGCAACTGTTTGCTACCCAGTTTGGTCAGTAATAATTGCTAAGGTAACAGGGGAA
AAGGTATATGCTACAAACCAGCACATTTTTGGAGCAGTTAAATCATTGTGGACAAAAGCAGCAGAAACGAGTCACTCCCT
AAACCTAAAGAAAAAAAGCTAAGCTAGGATCCTCCGCCGAAATAGAAGTACCTGCAAAAACAACTCACGTCTTGAAACAC
GCAGTGCCCTTGCCAACAGAACTCAGCTTAGAAGCAAAGACCAAATCAGAATCCAACTCAGGTGCTACACAATTCATGCC
TGACCCCAAGTTCATGGATTGTGGGTGGTCCCACCCAGAAGATATAGATAAGTACAGCACTGGAAGC

Alignment

ORF - retro_mmul_2045 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.4 %
• Parental protein coverage: 97.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GKLTTMPAGLIYASVSVHAVKEEESKKQLVKPEQLPIYTAPPLQSKYVEEQPGHLQMGFASIRTATGCYI
          GKLT.MPAGLI.ASVSVHA.K.EESKKQLV.PEQ.PIYTAPPL.SKYVEEQPGHLQMGFASI.TATG.Y.
Retrocopy GKLTIMPAGLIHASVSVHAAKAEESKKQLVIPEQVPIYTAPPLPSKYVEEQPGHLQMGFASICTATGHYT

Parental  GWCKGVYVFVKNGIMDTVQFGKDAYVYLKNPPRDFLLKMGVITVSGLAGLVSARKGSKFKKITYPLGLAT
          GWCKGVYVF.KNGI.DTV.FGKDA.VYLKNPP.DFL.KMGVITVSGL.GLVSARKGSK.KKITYPLGL.T
Retrocopy GWCKGVYVFGKNGIIDTVEFGKDAHVYLKNPPQDFLPKMGVITVSGLVGLVSARKGSKCKKITYPLGLTT

Parental  LGATVCYPVQSIIIAKV-NGKRYMLQASKFLEQLNHCGK-KAAKKSHSLNIK-KKLRLGSSVEIEVPAKT
          L.ATVCYPV.S.IIAKV..GKRYMLQ.S.FLEQLNHCG..KAA..SHSLN.K.KK..LGSS.EIEVPAKT
Retrocopy L*ATVCYPVWSVIIAKV>QGKRYMLQTSTFLEQLNHCGQ<KAAETSHSLNLK>KKAKLGSSAEIEVPAKT

Parental  TDVLKHSVPLPTELSSEAKTKSESTSGATQFMPDPKLMDHGQSHPEDIDMYSTRS
          T.VLKH.VPLPTELS.EAKTKSES.SGATQFMPDPK.MD.G.SHPEDID.YST.S
Retrocopy THVLKHAVPLPTELSLEAKTKSESNSGATQFMPDPKFMDCGWSHPEDIDKYSTGS

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	0.11 RPM	7.28 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	6.82 RPM
SRP007412_cerebellum	0.00 RPM	6.13 RPM
SRP007412_heart	0.00 RPM	8.89 RPM
SRP007412_kidney	0.00 RPM	11.15 RPM
SRP007412_liver	0.00 RPM	5.23 RPM
SRP007412_testis	0.04 RPM	1.13 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2045 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2045 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2045 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3253
Pan troglodytes	retro_ptro_2200
Gorilla gorilla	retro_ggor_2213
Pongo abelii	retro_pabe_2697

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000829	1 retrocopy	retro_amel_1035,
Canis familiaris	ENSCAFG00000017383	1 retrocopy	retro_cfam_1490,
Callithrix jacchus	ENSCJAG00000008249	2 retrocopies	retro_cjac_1783, retro_cjac_2464,
Dipodomys ordii	ENSDORG00000011045	1 retrocopy	retro_dord_373,
Equus caballus	ENSECAG00000009229	1 retrocopy	retro_ecab_577,
Homo sapiens	ENSG00000155008	1 retrocopy	retro_hsap_3253,
Gorilla gorilla	ENSGGOG00000016329	1 retrocopy	retro_ggor_2213,
Loxodonta africana	ENSLAFG00000008844	1 retrocopy	retro_lafr_1035,
Microcebus murinus	ENSMICG00000015844	1 retrocopy	retro_mmur_1511,
Myotis lucifugus	ENSMLUG00000011384	1 retrocopy	retro_mluc_1364,
Macaca mulatta	ENSMMUG00000004335	1 retrocopy	retro_mmul_2045 ,
Macaca mulatta	ENSMMUG00000016361	4 retrocopies	retro_mmul_1584, retro_mmul_1886, retro_mmul_2051, retro_mmul_814,
Mustela putorius furo	ENSMPUG00000001899	3 retrocopies	retro_mputfur_606, retro_mputfur_734, retro_mputfur_874,
Nomascus leucogenys	ENSNLEG00000002634	1 retrocopy	retro_nleu_1702,
Pongo abelii	ENSPPYG00000020516	1 retrocopy	retro_pabe_2697,
Pan troglodytes	ENSPTRG00000022067	1 retrocopy	retro_ptro_2200,
Sus scrofa	ENSSSCG00000012459	1 retrocopy	retro_sscr_610,
Tursiops truncatus	ENSTTRG00000000429	1 retrocopy	retro_ttru_1337,