RetrogeneDB ID: retro_mmul_887

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:88961269..88961575(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPD1
• Ensembl ID: ENSMMUG00000003992
• Aliases: None
• Description: small nuclear ribonucleoprotein Sm D1 [Source:RefSeq peptide;Acc:NP_001247758]

Sequence

>retro_mmul_887
CGTTCAGGGAGATTAATCACTGGAACCCACTGATCCAGTGGTCTGGATGTCAGCATGAATACAAATCGTAAAGCTGTGAA
AATGACCCTGAAGAACAAAGAAACTGTACAGCTGGAAACACTGAGTATTAGAAGAAATAACATTTGATATTTTATTCTAC
CATACGGTTTACCTCTGGATACACGACTTGTGGATGGTGAACCTAAGGTGAAATCTAAGAAAAGGGAAGCTGTTGCAGGA
AGAGGCTGAGGCAGAAGAAGAGGAAGAAGACGTGGCCATGGCAGAAGAAGAGGGGGTCCTAGGCGA

Alignment

ORF - retro_mmul_887 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.51 %
• Parental protein coverage: 84.03 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KNGTQVHGT--ITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLLVDVEPKV
          ..G....GT....G.DVSMNT..KAVKMTLKN.E.VQLETLSIR.NNI.YFILP..LPLDT.LVD.EPKV
Retrocopy RSGRLITGTH*SSGLDVSMNTNRKAVKMTLKNKETVQLETLSIRRNNI*YFILPYGLPLDTRLVDGEPKV

Parental  KSKKREAVAGRGRGRGRGRGRGRGRGRGGPRR
          KSKKREAVAGRG.GR.RGR.RG.GR.RGGPRR
Retrocopy KSKKREAVAGRG*GRRRGRRRGHGRRRGGPRR

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	0.45 RPM	14.12 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	11.82 RPM
SRP007412_cerebellum	0.26 RPM	14.40 RPM
SRP007412_heart	0.00 RPM	9.01 RPM
SRP007412_kidney	0.00 RPM	11.15 RPM
SRP007412_liver	0.04 RPM	4.51 RPM
SRP007412_testis	0.26 RPM	15.42 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_887 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_887 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_887 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_948

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006364	1 retrocopy	retro_acar_129,
Bos taurus	ENSBTAG00000008292	3 retrocopies	retro_btau_144, retro_btau_706, retro_btau_84,
Canis familiaris	ENSCAFG00000018247	1 retrocopy	retro_cfam_373,
Dasypus novemcinctus	ENSDNOG00000018773	4 retrocopies	retro_dnov_1254, retro_dnov_1716, retro_dnov_1832, retro_dnov_2403,
Felis catus	ENSFCAG00000012352	1 retrocopy	retro_fcat_1885,
Macaca mulatta	ENSMMUG00000003992	2 retrocopies	retro_mmul_887 , retro_mmul_891,
Mustela putorius furo	ENSMPUG00000005567	1 retrocopy	retro_mputfur_185,
Oryctolagus cuniculus	ENSOCUG00000023761	1 retrocopy	retro_ocun_224,
Pongo abelii	ENSPPYG00000025874	3 retrocopies	retro_pabe_254, retro_pabe_948, retro_pabe_952,
Pan troglodytes	ENSPTRG00000009909	2 retrocopies	retro_ptro_291, retro_ptro_781,
Pteropus vampyrus	ENSPVAG00000005511	1 retrocopy	retro_pvam_450,
Rattus norvegicus	ENSRNOG00000013714	2 retrocopies	retro_rnor_2671, retro_rnor_2729,
Tursiops truncatus	ENSTTRG00000002654	2 retrocopies	retro_ttru_1566, retro_ttru_1890,