RetrogeneDB ID: retro_mmul_30

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214779962:443..1727(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000019197
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000004810
• Aliases: None
• Description: None

Sequence

>retro_mmul_30
ATGTCGGACTTCGACGAGTTCGAGCGGCAGCTCAACGAGAATAAACAAGAGAGGGACAAGGAGAACCGGCATAGGAAGCG
CAGCCACAGCCGCTCTCGAAGCCGGGACCGCAAACGCCGGAGCCGGAGCCGTGACCGGCGCAACCGGGACCAGCGGAGCG
CCTCCCGGGACAGGCGGCGACGAAGCAAACCTTTGACCAGAGGCGCTAAAGAGGAGCACGGTGGACTGATTCGTTCCCCC
CGCCATGAGAAGAAGAAGAAGGTCCGTAAATACTGGGACGTGCCACCTCCGGGCTTTGAGCACATCACCCCAATGCAGTA
CAAGGCCATGCAAGCTGCGGGTCAGATTCCAGCCACTGCTCTTCTCCCCACCATGACCCCTGACGGTCTGGCTGTGACCC
CAACGCCGGTGCCCGTGGTTGGGAGCCAGATGACTAGACAAGCCCGGCGCCTCTACGTGGGCAACATCCCCTTTGGCATC
ACTGAGGAGGCCATGATGGATTTCTTCAATGCCCAGATGCGCCTGGGGGGGCTGACCCAGGCCCCTGGCAACCCGGTGTT
GGCTGTGCAGATTAACCAGGACAAGAATTTTGCCTTTTTGGAGTTCCGCTCAGTGGACGAGACTACCCAGGCCATGGCCT
TTGACGGCATCATCTTCCAGGGCCAGTCACTAAAGATCCGCAGGCCTCATGACTACCAGCCGCTTCCTGGCATGTCAGAG
AACCCCTCCGTCTATGTGCCTGGGGTTGTGTCCACTGTGGTCCCTGACTCTGCCCACAAGCTGTTCATCGGGGGCTTACC
CAACTACCTGAACGATGACCAGGTCAAAGAGCTGCTGACATCCTTTGGGCCCCTCAAGGCCTTCAACCTGGTCAAGGACA
GTGCCACGGGGCTCTCCAAGGGCTACGCCTTCTGTGAGTACGTGGACATCAACGTCACGGATCAGGCCATTGCGGGGCTG
AACGGTATGCAGCTGGGGGATAAGAAGCTGCTGGTGCAGAGGGCGAGTGTGGGAGCCAAGAATGCCACGCTGAGCACCAT
CAATCAGACGCCAGTGACCCTGCAAGTGCCGGGCCTGATGAGCTCCCAGGTGCAGATGGGCGGCCACCCGACTGAGGTCC
TGTGCCTCATGAACATGGTGCTGCCGGAGGAGCTGCTGGACGACGAGGAGTACGAGGAGATCGTGGAGGACGTGCGGGAC
GAGTGCAGCAAGTATGGGCTTGTCAAGTCCATCGAGATCCCCCGGCTTGTGGACGGTGTCGAGGTGCCCGGCTGCGGAAA
GGTC

Alignment

ORF - retro_mmul_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.32 %
• Parental protein coverage: 90.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDFDEFERQLNENKQASAFFECRHAHILHMRNFWRSRESRYGVFETNLKSFRSAPRSVFPKQYKPLTRG
          MSDFDEFERQLNENKQ.....E.RH....H.R...R.R..R...........RSA.R.......KPLTRG
Retrocopy MSDFDEFERQLNENKQERDK-ENRHRKRSHSRSRSRDRKRRSRSRDRRNRDQRSASRDR-RRRSKPLTRG

Parental  AKEEHGGLIRSPRHEKKKKVRKYWDVPPPGFEHITPMQYKAMQAAGQIPATALLPTMTPDGLAVTPTPVP
          AKEEHGGLIRSPRHEKKKKVRKYWDVPPPGFEHITPMQYKAMQAAGQIPATALLPTMTPDGLAVTPTPVP
Retrocopy AKEEHGGLIRSPRHEKKKKVRKYWDVPPPGFEHITPMQYKAMQAAGQIPATALLPTMTPDGLAVTPTPVP

Parental  VVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET
          VVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET
Retrocopy VVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET

Parental  TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKEL
          TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKEL
Retrocopy TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKEL

Parental  LTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNATLVSPP
          LTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNATL....
Retrocopy LTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNATL----

Parental  STINQTPVTLQVPGLMSSQVQMGGHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIP
          STINQTPVTLQVPGLMSSQVQMGGHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIP
Retrocopy STINQTPVTLQVPGLMSSQVQMGGHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIP

Parental  RPVDGVEVPGCGKI
          R.VDGVEVPGCGK.
Retrocopy RLVDGVEVPGCGKV

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	2.35 RPM	5.49 RPM
SRP007412_brain_prefrontal_cortex	9.52 RPM	41.81 RPM
SRP007412_cerebellum	2.97 RPM	7.88 RPM
SRP007412_heart	4.18 RPM	10.72 RPM
SRP007412_kidney	3.99 RPM	8.57 RPM
SRP007412_liver	4.83 RPM	19.32 RPM
SRP007412_testis	7.46 RPM	17.08 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_30 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_30 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_30 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000018056	1 retrocopy	retro_lafr_94,
Myotis lucifugus	ENSMLUG00000011051	2 retrocopies	retro_mluc_406, retro_mluc_797,
Macaca mulatta	ENSMMUG00000004810	1 retrocopy	retro_mmul_30 ,
Mus musculus	ENSMUSG00000030435	3 retrocopies	retro_mmus_2251, retro_mmus_3663, retro_mmus_991,
Otolemur garnettii	ENSOGAG00000007206	1 retrocopy	retro_ogar_3304,