RetrogeneDB ID: retro_mmul_1768

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:61266505..61267357(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.386
• Ensembl ID: ENSMMUG00000017583
• Aliases: None
• Description: single-stranded DNA-binding protein 2 [Source:RefSeq peptide;Acc:NP_001247611]

Sequence

>retro_mmul_1768
ATGTACGGCAAAGGCAAGAGTAACAGCAGCGCCGTCCCGTCCGACAGCCAGGCCCGGGAGAAGTTAGCACTCTACGTATA
TGAATATCTGCTCCATGTAGGAGCTCAGAAATCAGCTCAAACATTTTTATCAGAGATAAGATGGGAAAAAAACATCACAT
TGGGGGAACCACTAGGATTCTTACATTCTTGGTGGTGTGTATTTTGGGATCTCTACTGTGCAGCTCCAGAGAGACGTGAA
ACATGTGAACACTCAAGTGAAGCAAAAGCCTTCCATGATTATAGTGCTGCAGCAGCTCCCAGTCCAGTGCTAGGAAACAT
TCCCCCAGGAGATGGCATGCCAGTAGGTCCTGTACCACCAGGGTTCTTTCAGCCTTTTATGCCACCTCGGTACCCTGGAG
GTCCAAGGCCCCCATTGAGGATACCTAATCAGGCGCTTGGAGGTGTCCCAGGAAGTCAGCCATTACTCCCCAGTGGAATG
GATCCAACTCGACAACAAGGACATCCAAATATGGGTGGGCCAATGCAGAGAATGACTCCTCCAAGAGGAATGGTGCCCTT
AGGACCACAGAACTATAGAGGTGCAATGAGACCCCCACTGAATGCTTTAGGTGGCCCTGGAATTCCTGGAATGAACATGG
GTCCAGGTGGTGGTAGACCTTGGCCAAACCCAACAAATGCCAATTCAATACCATACTCCTCAGCATCTCCTGGGAATTAT
GTAGGTCCTCCAGGAGGTGGAAGGCAACCAGGAACACCCATCATGCCTAGTCCAGCAGATTCAACCAACTCTGGCGATAA
CATGTATACTTTAATGAATGCAGTACCTCCTGGACCTAACAGACCTAATTTT

Alignment

ORF - retro_mmul_1768 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.89 %
• Parental protein coverage: 78.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MYGKGKSNSSAVPSDSQAREKLALYVYEYLLHVGAQKSAQTFLSEIRWEKNITLGEPPGFLHSWWCVFWD
          MYGKGKSNSSAVPSDSQAREKLALYVYEYLLHVGAQKSAQTFLSEIRWEKNITLGEP.GFLHSWWCVFWD
Retrocopy MYGKGKSNSSAVPSDSQAREKLALYVYEYLLHVGAQKSAQTFLSEIRWEKNITLGEPLGFLHSWWCVFWD

Parental  LYCAAPERRETCEHSSEAKAFHDYSAAAAPSPVLGNIPPGDGMPVGPVPPGFFQPFMSPRYPGGPRPPLR
          LYCAAPERRETCEHSSEAKAFHDYSAAAAPSPVLGNIPPGDGMPVGPVPPGFFQPFM.PRYPGGPRPPLR
Retrocopy LYCAAPERRETCEHSSEAKAFHDYSAAAAPSPVLGNIPPGDGMPVGPVPPGFFQPFMPPRYPGGPRPPLR

Parental  IPNQALGGVPGSQPLLPSGMDPTRQQGHPNMGGPMQRMTPPRGMVPLGPQNYGGAMRPPLNALGGPGMPG
          IPNQALGGVPGSQPLLPSGMDPTRQQGHPNMGGPMQRMTPPRGMVPLGPQNY.GAMRPPLNALGGPG.PG
Retrocopy IPNQALGGVPGSQPLLPSGMDPTRQQGHPNMGGPMQRMTPPRGMVPLGPQNYRGAMRPPLNALGGPGIPG

Parental  MNMGPGGGRPWPNPTNANSIPYSSASPGNYVGPPGGGGPPGTPIMPSPADSTNSGDNMYTLMNAVPPGPN
          MNMGPGGGRPWPNPTNANSIPYSSASPGNYVGPPGGG..PGTPIMPSPADSTNSGDNMYTLMNAVPPGPN
Retrocopy MNMGPGGGRPWPNPTNANSIPYSSASPGNYVGPPGGGRQPGTPIMPSPADSTNSGDNMYTLMNAVPPGPN

Parental  RPNF
          RPNF
Retrocopy RPNF

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	0.11 RPM	26.44 RPM
SRP007412_brain_prefrontal_cortex	0.40 RPM	34.35 RPM
SRP007412_cerebellum	0.06 RPM	25.70 RPM
SRP007412_heart	0.00 RPM	9.36 RPM
SRP007412_kidney	0.00 RPM	4.81 RPM
SRP007412_liver	0.00 RPM	0.91 RPM
SRP007412_testis	0.00 RPM	2.00 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1768 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1768 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1768 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000145687	1 retrocopy	retro_hsap_3622,
Myotis lucifugus	ENSMLUG00000001897	1 retrocopy	retro_mluc_1814,
Macaca mulatta	ENSMMUG00000017583	1 retrocopy	retro_mmul_1768 ,
Mus musculus	ENSMUSG00000003992	1 retrocopy	retro_mmus_2353,