RetrogeneDB ID: retro_mmul_1695

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:83358808..83359273(-)
• Located in intron of: ENSMMUG00000022451

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_1695
AAAGTGTGGGATGCTATCCCAGGAGATGAACTGATGACCCTGGCTCATAAAAACATTGTCAAGACTATGGATTTCATGCA
GGATAGTAATTATTTGTTAACCAGGGAACAGGATAAACTGTTACGCATATATGACTTGAACAAACCCGAAGCAGAACCTG
AGGAAGTTAGTGATCACAGCTCTGATATAAAAAAGGCCCTATGGTGCAGTGTGGATAAACAGATTCTTTCTTCTGATGAC
AAAACTGTTAGACTCTGGGATCATGCTACTATGACAGAAATGAAATCTCTAAATTTTAATATGTCAGCTAGTAGTATGGA
ATATATTCCTGAGGGAGATATTTTGGTAATAACTTATGGCTGATCCAGTGCTTTTGATAGTACAGTAAGTTTGGAACCAA
TTAAATCCTTTCAAGCTCCTGTAACCATTAACTCTGAATCTCTTCACCTTAAGAATTTCTTTTTG

Alignment

ORF - retro_mmul_1695 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.29 %
• Parental protein coverage: 58.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KVWDAVSGDELMTLAHKHIVKTVDFTQDSNYLLTGGQDKLLRIYDLNKPEAEPKEISGHTSGIKKALWCS
          KVWDA..GDELMTLAHK.IVKT.DF.QDSNYLLT..QDKLLRIYDLNKPEAEP.E.S.H.S.IKKALWCS
Retrocopy KVWDAIPGDELMTLAHKNIVKTMDFMQDSNYLLTREQDKLLRIYDLNKPEAEPEEVSDHSSDIKKALWCS

Parental  EDKQILSADDKTVRLWDHATMTEVKSLNFNMSVSSMEYIPEGEILVITYGRSIAFHSAVSLDPIKSFEAP
          .DKQILS.DDKTVRLWDHATMTE.KSLNFNMS.SSMEYIPEG.ILVITYG.S.AF.S.VSL.PIKSF.AP
Retrocopy VDKQILSSDDKTVRLWDHATMTEMKSLNFNMSASSMEYIPEGDILVITYG*SSAFDSTVSLEPIKSFQAP

Parental  ATINSASLHPEKEFL
          .TINS.SLH....FL
Retrocopy VTINSESLHLKNFFL

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	0.34 RPM	24.76 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	27.84 RPM
SRP007412_cerebellum	0.77 RPM	20.15 RPM
SRP007412_heart	0.12 RPM	17.49 RPM
SRP007412_kidney	0.23 RPM	17.61 RPM
SRP007412_liver	0.24 RPM	12.79 RPM
SRP007412_testis	0.15 RPM	18.47 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1695 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1695 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1695 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3723
Pan troglodytes	retro_ptro_2616
Pongo abelii	retro_pabe_3134

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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,