RetrogeneDB ID: retro_mmul_985

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:37799758..37800224(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STRAP
• Ensembl ID: ENSMMUG00000013307
• Aliases: None
• Description: None

Sequence

>retro_mmul_985
GTGTATTTCATGCAGGATAGTAATTATTTGTTAACTGAGGGACAGGATAAACTGTTACGCATCTATGACTTGAACAAACC
CGAAGCAAGACCTAAGGAAATTAGTGGTCACACTTCTGGTATAAAAAAGGCTCCTATGGTGCAGTGAGGATAAACAGATT
CTTTCTGCTGATGATAAAACTGCTTGACTTTGGGATCATGCTACTCTGACAGAAGTGAAATCTCTAAATTTTAATATGTC
TGTTAATGATATAAAAATATATTCCTGAAATTTTGGTTATAACTTATGGACAATCGATTGCTTTTCATAGTGCAGTAAGT
TTGAACCCAATTAAATCCTTTGAAGCTCCTGCAACCATCAATTCTGCATCTCTTCATCCTGAGAAAGAATTTCTTGTTGC
AGGTGGTGAAATTTTTAACTTTGTAAGTATGATTATAACCATGGAGAAGAATTCGAATCCTACAAG

Alignment

ORF - retro_mmul_985 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.75 %
• Parental protein coverage: 59.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VDFTQDSNYLLTGGQDKLLRIYDLNKPEAEPKEISGHTSGIKKA-LWCSEDKQILSADDKTVRLWDHATM
          V.F.QDSNYLLT.GQDKLLRIYDLNKPEA.PKEISGHTSGIKKA.LWCSEDKQILSADDKT..LWDHAT.
Retrocopy VYFMQDSNYLLTEGQDKLLRIYDLNKPEARPKEISGHTSGIKKA>LWCSEDKQILSADDKTA*LWDHATL

Parental  TEVKSLNFNMSVSSME-YIPEGEILVITYGRSIAFHSAVSLDPIKSFEAPATINSASLHPEKEFLVAGGE
          TEVKSLNFNMSV.....YIPE..ILVITYG.SIAFHSAVSL.PIKSFEAPATINSASLHPEKEFLVAGGE
Retrocopy TEVKSLNFNMSVNDIK>YIPE--ILVITYGQSIAFHSAVSLNPIKSFEAPATINSASLHPEKEFLVAGGE

Parental  -DFKLYKYDYNSGEELVSFR
          ..F.L.KYDYN.GEE..S..
Retrocopy <NF*LCKYDYNHGEEFESYK

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	24.76 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	27.84 RPM
SRP007412_cerebellum	0.00 RPM	20.15 RPM
SRP007412_heart	0.00 RPM	17.49 RPM
SRP007412_kidney	0.00 RPM	17.61 RPM
SRP007412_liver	0.00 RPM	12.79 RPM
SRP007412_testis	0.04 RPM	18.47 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_985 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_985 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_985 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007422	2 retrocopies	retro_chof_1098, retro_chof_1620,
Callithrix jacchus	ENSCJAG00000021593	1 retrocopy	retro_cjac_2503,
Homo sapiens	ENSG00000023734	2 retrocopies	retro_hsap_2092, retro_hsap_3723,
Gorilla gorilla	ENSGGOG00000009939	1 retrocopy	retro_ggor_1633,
Macaca mulatta	ENSMMUG00000006119	2 retrocopies	retro_mmul_1730, retro_mmul_1733,
Macaca mulatta	ENSMMUG00000013307	2 retrocopies	retro_mmul_1695, retro_mmul_985 ,
Mus musculus	ENSMUSG00000030224	1 retrocopy	retro_mmus_794,
Nomascus leucogenys	ENSNLEG00000004160	2 retrocopies	retro_nleu_1301, retro_nleu_1970,
Ochotona princeps	ENSOPRG00000015211	3 retrocopies	retro_opri_1029, retro_opri_217, retro_opri_541,
Pongo abelii	ENSPPYG00000004334	3 retrocopies	retro_pabe_2005, retro_pabe_3134, retro_pabe_3212,
Pan troglodytes	ENSPTRG00000004734	2 retrocopies	retro_ptro_1538, retro_ptro_2616,
Tursiops truncatus	ENSTTRG00000003466	2 retrocopies	retro_ttru_581, retro_ttru_974,