RetrogeneDB ID: retro_mmul_39

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:64740849..64741668(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000001881
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: C18H18ORF19
• Ensembl ID: ENSMMUG00000011961
• Aliases: None
• Description: None

Sequence

>retro_mmul_39
ATGCAGTGGAATGTACCACGGACTGTATCTCGACTGGCACGCAGGACATGCTTGGAACCACATAATGCTGGTCTTTTTGG
ACGCTGTCAAAATGTAAAGGGACCTTTACTTTTGTACAATGCTGATTCCAAAGTGGTTTTGGTACAAGGCCTTCAAAAAC
AATGGTTGAATTTATCTGCTGCCCAGTGCGTTGCAAAGGAAAGGAGGCCGTTGGATGCTCATTCACCCCAACCAGGAGTC
CTTCGCTATAAGCAAGGGAAGCAACATGTTTCATTCAAGAGGGTTTTTTCATCCAGTGCCACAGCTCAGGGAACTCCAGA
AAAAAAGGAAGAGCCTGATCCTTTGCAAGACAAATCTATTAGTCTTTATCAACGATTCAAGAAGATATTTAGACAGTATG
GAAAAGTTCTGATTCCAGTGCATCTAATAACTTCTGGTGTTTGGTTTGGAACATTTTATTATGCGGCCTTGAAAGGAGTG
AATGTCGTTCCTTTTCTAGAACTCATTGGGTTACCTGACAGTGTGGTAAGCATCCTGAAAAACTCCCAGAGTGGAAATGC
ACTCACAGCATATGCCTTGTTTAAGATTGCAACACCTGCTCGGTACACCGTGACTTTGGAAGGAACATCCTTCACTGTGA
AGTATCTGCGCAGTCATGGCTACATGTCCACGCCACCACCCATCAAGGAATATCTACAGGACAGGATGGAGGAGACAAAG
GAGCTTATCACAGAGAAGATGGAAGAAACAAAAGACAGACTCACTGAAAAGTTACAAGAAACCAAAGAAAAGGTTTCCTT
TAAGAAAAAAGTGGAATAA

Alignment

ORF - retro_mmul_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.32 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQWSVPRTVSRLARRTCLEPHNAGLFGRCQNVKGPLLLYNAESKVVLVQGPQKQWLNLSAAQYVAKERRP
          MQW.VPRTVSRLARRTCLEPHNAGLFGRCQNVKGPLLLYNA.SKVVLVQG.QKQWLNLSAAQ.VAKERRP
Retrocopy MQWNVPRTVSRLARRTCLEPHNAGLFGRCQNVKGPLLLYNADSKVVLVQGLQKQWLNLSAAQCVAKERRP

Parental  LDAHSPQPGVLRHKQGKQHVSFKRVFSSSATAQGTPEKKEEPDPLQDKSISLYQRFKKTFRQYGKVLIPV
          LDAHSPQPGVLR.KQGKQHVSFKRVFSSSATAQGTPEKKEEPDPLQDKSISLYQRFKK.FRQYGKVLIPV
Retrocopy LDAHSPQPGVLRYKQGKQHVSFKRVFSSSATAQGTPEKKEEPDPLQDKSISLYQRFKKIFRQYGKVLIPV

Parental  HLITSGVWFGTFYYAALKGVNVVPFLELIGLPDGVVSILKNSQSGNALTAYALFKIATPARYTVTLGGTS
          HLITSGVWFGTFYYAALKGVNVVPFLELIGLPD.VVSILKNSQSGNALTAYALFKIATPARYTVTL.GTS
Retrocopy HLITSGVWFGTFYYAALKGVNVVPFLELIGLPDSVVSILKNSQSGNALTAYALFKIATPARYTVTLEGTS

Parental  FTVKYLRSHGYMSTPPPVKEYLQDRMEETKGLITEKMEETKDRLTEKLQETKEKVSFKKKVE
          FTVKYLRSHGYMSTPPP.KEYLQDRMEETK.LITEKMEETKDRLTEKLQETKEKVSFKKKVE
Retrocopy FTVKYLRSHGYMSTPPPIKEYLQDRMEETKELITEKMEETKDRLTEKLQETKEKVSFKKKVE

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	4.71 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	6.90 RPM
SRP007412_cerebellum	0.00 RPM	5.68 RPM
SRP007412_heart	0.00 RPM	9.30 RPM
SRP007412_kidney	0.00 RPM	7.39 RPM
SRP007412_liver	0.00 RPM	5.46 RPM
SRP007412_testis	0.00 RPM	5.09 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_39 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_39 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_39 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
Echinops telfairi	ENSETEG00000007826	1 retrocopy	retro_etel_244,
Macaca mulatta	ENSMMUG00000011961	1 retrocopy	retro_mmul_39 ,
Ictidomys tridecemlineatus	ENSSTOG00000019999	1 retrocopy	retro_itri_915,
Tursiops truncatus	ENSTTRG00000007425	1 retrocopy	retro_ttru_245,