RetrogeneDB ID: retro_mmul_1461

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:131481256..131481806(+)
• Located in intron of: ENSMMUG00000016968

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.10145
• Ensembl ID: ENSMMUG00000019406
• Aliases: SNRNP40, WDR57
• Description: None

Sequence

>retro_mmul_1461
CAGCTTGTTTGCACTAGCAGTGACGATGGCAGTTAAGTTTTGGGACGTCTGGAAGAAAGCAGCCATCCAAACATTTCGGA
ACATGTACCAGGTGTTAGCTGTGACCCCCAGTGACCCAAGTGATCAGATTATTTCTTATGGAATAGACAATGATATCAAG
GTCTGGGACCTGCACCAGAACAAACTAATGTACACCATGACAGGCCATGCAGATTCAGTGACTGGCCTGAGCTTAAGTTC
TGAAGGCTCTTGTCTCTTGTCCAATGCAATGGACAATACAGTTCTTGTCTGGGATGTCTGGCCATTTGCCCCCAAAGAGA
GGTGTGTAAAGATATTTCAAGGAAATGTGCACAACTTTGAAAAGAACCTTCTAAGATGTTCTTGGTCACCTGATGGAAGC
AAAATAGCAGCTAGCTCAGCCGACAGGTTTGTGTATGTGTGGGATACCACAAGCAGAAGAATATTGTATAAGCTGCCCGG
CCATGCTGGCTCCATCAGTGAAGTTGCTTTCCACCCTGACTAGCCCATCATTATCTCAGCATCGAGTGAC

Alignment

ORF - retro_mmul_1461 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.57 %
• Parental protein coverage: 51.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QLVCTGSDDG-TVKLWDIRKKAAIQTFQNTYQVLAVTFNDTSDQIISGGIDNDIKVWDLRQNKLTYTMRG
          QLVCT.S.D...VK.WD..KKAAIQTF.N.YQVLAVT..D.SDQIIS.GIDNDIKVWDL.QNKL.YTM.G
Retrocopy QLVCT-SSDD>AVKFWDVWKKAAIQTFRNMYQVLAVTPSDPSDQIISYGIDNDIKVWDLHQNKLMYTMTG

Parental  HADSVTGLSLSSEGSYLLSNAMDNTVRVWDVRPFAPKERCVKIFQGNVHNFEKNLLRCSWSPDGSKIAAG
          HADSVTGLSLSSEGS.LLSNAMDNTV.VWDV.PFAPKERCVKIFQGNVHNFEKNLLRCSWSPDGSKIAA.
Retrocopy HADSVTGLSLSSEGSCLLSNAMDNTVLVWDVWPFAPKERCVKIFQGNVHNFEKNLLRCSWSPDGSKIAAS

Parental  SADRFVYVWDTTSRRILYKLPGHAGSINEVAFHPDEPIIISASSD
          SADRFVYVWDTTSRRILYKLPGHAGSI.EVAFHPD.PIIISASSD
Retrocopy SADRFVYVWDTTSRRILYKLPGHAGSISEVAFHPD*PIIISASSD

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	15.46 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	13.88 RPM
SRP007412_cerebellum	0.06 RPM	26.73 RPM
SRP007412_heart	0.00 RPM	11.54 RPM
SRP007412_kidney	0.00 RPM	21.13 RPM
SRP007412_liver	0.00 RPM	11.40 RPM
SRP007412_testis	0.00 RPM	26.69 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1461 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1461 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1461 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000000586	3 retrocopies	retro_mluc_2200, retro_mluc_2609, retro_mluc_318,
Macaca mulatta	ENSMMUG00000014159	1 retrocopy	retro_mmul_190,
Macaca mulatta	ENSMMUG00000019406	1 retrocopy	retro_mmul_1461 ,
Rattus norvegicus	ENSRNOG00000012219	1 retrocopy	retro_rnor_2604,