RetrogeneDB ID: retro_mmul_1211

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 16:5444470..5444798(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPSNAP1
• Ensembl ID: ENSMMUG00000031041
• Aliases: None
• Description: nipsnap homolog 1 (C. elegans) [Source:HGNC Symbol;Acc:7827]

Sequence

>retro_mmul_1211
CATGACAAGGAGTACCTGGAGGTCCGGGAGTGCAGCCGGATGCTGTTGTCCAGGAGACACCAATTGCTCCTTGAGTTCAA
CTTCTGGAATGAGCCACAGCCCAGAGCGGGCTCCAACATCTTATGAGCTGAGGACCTGCAAACTCAAGCCAGGAACCATG
ATGGAGTAGGGGAACAACTGGGCTCCTGCCAGCAGGTACCAGCAACAAGTCCCAGCAGGAGAACCAGGAGGTGATGGTGG
CTTCTCCCATATAGGAGAGCTCCACCTTGTGCATCATCTCTGGGCCGATAAAGACCCACAGTCTTGGCAGGAGACCCACA
GTGCTGCC

Alignment

ORF - retro_mmul_1211 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.77 %
• Parental protein coverage: 83.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NNKEYLEFRRERSQMLLSRRNQLLLEFSFWNEPQPRLGPNI-YELRTYKLKPGTMIEWGNNWARAIKYRQ
          ..KEYLE.R.E.S.MLLSRR.QLLLEF.FWNEPQPR.G.NI.YELRT.KLKPGTM.E.GNNWA.A..Y.Q
Retrocopy HDKEYLEVR-ECSRMLLSRRHQLLLEFNFWNEPQPRAGSNI>YELRTCKLKPGTMME*GNNWAPASRYQQ

Parental  E---NQEAVGGFFSQIGELYVVHHLWAYKDLQSREETRNAA
          ..........G.FS.IGEL..VHHLWA.KD.QS..ET..AA
Retrocopy QVPAGEPGGDGGFSHIGELHLVHHLWADKDPQSWQETHSAA

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	7.28 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	9.28 RPM
SRP007412_cerebellum	0.00 RPM	8.33 RPM
SRP007412_heart	0.00 RPM	1.59 RPM
SRP007412_kidney	0.00 RPM	20.07 RPM
SRP007412_liver	0.00 RPM	33.09 RPM
SRP007412_testis	0.15 RPM	1.62 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1211 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1211 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1211 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1429

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000031041	1 retrocopy	retro_mmul_1211 ,
Pongo abelii	ENSPPYG00000011693	1 retrocopy	retro_pabe_1429,
Tupaia belangeri	ENSTBEG00000004614	3 retrocopies	retro_tbel_247, retro_tbel_4673, retro_tbel_968,