RetrogeneDB ID: retro_mmul_532

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:131907558..131908366(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAPTM4B
• Ensembl ID: ENSMMUG00000008926
• Aliases: None
• Description: None

Sequence

>retro_mmul_532
CGGCGGGCGCACAGGCGAGCGGGCCGGGAGTGGCCGAAGAGCCTGCAGCAGCAGCGCAGCGGACCCGGGCAAGGAGGTCA
ACGCTCCTGGAAACTTGGGCGCCCCTCCGCGCCAGGAGCGATGAAGACTGTCGCGCCCCGGTGGCGCCCTGGATGCGGTT
CTACTCCAACAGCTGCTGCCTGTGCCGCCATGTCGGCGCCGGCACCATCCAGCTCGGTGTCTGGTACCTGATCATCAATG
CCGTGGTACTGTTGATTTTGTTGAGTGCCCGGCTGATCCGGATCAGTATCACTTTTCAAGTTCTGAACTGGGAGGCGACT
TTGAGTTCATGGATGATGCCAATATGTGCATTGCTATTGTGATTTATCTTCTTATGATACTGATATGCACTATGGCTAAT
TACGAAGCATACAGGCAAAACGCAACCTGGATCATCCCATTCTTCTATTACCAGATCTTTGATTTTTCTCTGAACACCTT
GGTTGCAATCACTGTGCTTGTTTATCCAAACTCCATGTAGGAATACATACGACAACTGCCTCCTAATTTTCCCTGCAGAG
ATGATGTCATGTCAGTGAATCCTACCTGTTTGGTCCTTATTATTCTTCTGTTTATTAGCATTATCTTAACTATTAAGGGT
TACTTGATTAGCTGTGTTTGGAACTGCTGCCGATACATCAATGGCAGGAGTTCCTCCTATGTCCTGGTTTATGTTACCAG
CAATGACACTACGGTGCTCCCACCCCCCTATGATGATGCCACTGTGAATGGTGCTGCCAAGGAGCCGCCACCACCCTAGG
TGTCTGCC

Alignment

ORF - retro_mmul_532 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.39 %
• Parental protein coverage: 75.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RRAHGREGREPERRRSRQQRRGGP-QARRSTL-KTWARARATAPGAMKM-VAPWTRFYSNSCCLCCHVRT
          RRAH.R.GRE.....S.QQ.R.GP..ARRSTL..TWA..RA.........VAPW.RFYSNSCCLC.HV..
Retrocopy RRAHRRAGREWPK--SLQQQRSGP<RARRSTLLETWAPLRARSDEDCRAPVAPWMRFYSNSCCLCRHVGA

Parental  GTILLGVWYLIINAVVLLILLSAL-ADPDQYHFSSSELGGDFEFMDDANMCIAIAISLLMILICAMATYG
          GTI.LGVWYLIINAVVLLILLSA..ADPDQYHFSSSELGGDFEFMDDANMCIAI.I.LLMILIC.MA.Y.
Retrocopy GTIQLGVWYLIINAVVLLILLSAR<ADPDQYHFSSSELGGDFEFMDDANMCIAIVIYLLMILICTMANYE

Parental  AYKQRAAWIIPFFCYQIFDFALNTLVAITVLVYPNSIQEYIRQLPPNFPYRDDVMSVNPTCLVLIILLFI
          AY.Q.A.WIIPFF.YQIFDF.LNTLVAITVLVYPNS..EYIRQLPPNFP.RDDVMSVNPTCLVLIILLFI
Retrocopy AYRQNATWIIPFFYYQIFDFSLNTLVAITVLVYPNSM*EYIRQLPPNFPCRDDVMSVNPTCLVLIILLFI

Parental  SIILTFKGYLISCVWNCYRYINGRNSSDVLVYVTSNDTTVLLPPYDDATVNGAAKEPPPPYVSA
          SIILT.KGYLISCVWNC.RYINGR.SS.VLVYVTSNDTTVL.PPYDDATVNGAAKEPPPP.VSA
Retrocopy SIILTIKGYLISCVWNCCRYINGRSSSYVLVYVTSNDTTVLPPPYDDATVNGAAKEPPPP*VSA

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	37.87 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	38.55 RPM
SRP007412_cerebellum	0.00 RPM	32.87 RPM
SRP007412_heart	0.00 RPM	273.76 RPM
SRP007412_kidney	0.00 RPM	62.32 RPM
SRP007412_liver	0.00 RPM	33.77 RPM
SRP007412_testis	0.00 RPM	84.36 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_532 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_532 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_532 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016959	3 retrocopies	retro_btau_1493, retro_btau_1759, retro_btau_786,
Callithrix jacchus	ENSCJAG00000031235	3 retrocopies	retro_cjac_1368, retro_cjac_1664, retro_cjac_3027,
Macaca mulatta	ENSMMUG00000008926	1 retrocopy	retro_mmul_532 ,
Nomascus leucogenys	ENSNLEG00000003756	1 retrocopy	retro_nleu_1531,
Otolemur garnettii	ENSOGAG00000000512	3 retrocopies	retro_ogar_1977, retro_ogar_2856, retro_ogar_2902,
Pongo abelii	ENSPPYG00000018771	2 retrocopies	retro_pabe_2311, retro_pabe_279,
Pan troglodytes	ENSPTRG00000020448	1 retrocopy	retro_ptro_546,
Tursiops truncatus	ENSTTRG00000003124	1 retrocopy	retro_ttru_76,