RetrogeneDB ID: retro_mmul_153

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:113413469..113415248(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000003305
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.2347
• Ensembl ID: ENSMMUG00000019637
• Aliases: None
• Description: None

Sequence

>retro_mmul_153
ATGTCGGATTCTGGAAGTTACAGTCAGTCTGGGGGTGAGCAGCAAAGTTATTCTTCCTATGGAAATCAAGGCAACCAAGG
CTATGGACAAGCACCACAAAGCTATTCTGGCTATGGGCAAACGACTGATTCCTCTTATGGACAGAACTACAGCGGTTACT
CCAGTTATGGACAAAGTCAGTCAGGTTATTCACAGTCCTATGGTGGTTATGAGAATCAAAAGCAGAGCTCATATGGCCAG
CAACCATATAATAACCAGGGACAGCAGCAAAACATGGAATCATCAGGAAGCCAAGGTGGAAGAGCACCTTCCTATGACCA
GCCAGACTATGGTCAACAAGATTCCTATGACCAGCAGTCAGGCTATGATCAACATCAAGGCTCATATGATGAGCAGTCAA
ATTATGATCAGCAGCATGATTCCTATAATCAAAACCAGCAGTCCTATCATTCACAAAGGGAAAATTACAGCCACCACACA
CAAGATGACCGTCGTGATGTGAGTAGGTATGGAGAAGATAATAGAGGATATGGCGGGTCACAGGGAGGAGGTAGAGGGCG
TGGGGGATATGACAAGGATGGAAGAGGTCCTATGACAGGATCAAGTGGTGGTGACCGCGGTGGCTTCAAAAATTTTGGTG
GTCACAGGGATTATGGACCCAGACCAGATGCTGATTCAGAATCTGATAATTCAGATAACAACACAATCTTTGTGCAAGGC
CTTGGGGAGGGTGTGTCTACAGATCAAGTTGGGGAGTTCTTTAAACAAATAGGAATTATCAAGACAAATAAGAAGACTGG
AAAACCAATGATAAATCTTTATACAGACAAGGACACAGGAAAGCCAAAGGGGGAGGCAACAGTGTCATTTGATGACCCTC
CTTCAGCTAAGGCAGCCATTGACTGGTTTGATGGAAAAGAATTCCATGGCAACATCATTAAAGTGTCCTTTGCCACTAGA
AGACCTGAATTCATGAGAGGAGGTGGAAGTGGAGGTGGGCGGCGAGGCCGTGGAGGATATAGAGGTCGTGGAGGCTTTCA
AGGGAGAGGTGGAGACCCCAAAAGTGGGGATTGGGTTTGCCCTAATCCGTCATGCGGAAATATGAACTTTGCTCGAAGGA
ATTCCTGCAATCAGTGCAATGAGCCTAGACCAGAGGACTCTCGTCCCTCAGGAGGAGATTTCCGGGGGAGAGGCTACGGT
GGAGAGAGGGGCTACAGAGGTCGTGGGGGCAGAGGTGGAGACCGAGGCGGCTATGGTGGAGACAGAAGTGGGGGTGGCTA
TGGTGGAGACAGAAGCAGCGGTGGTGGCTACAGCGGAGATAGAAGTGGGGGCGGCTATGGTGGAGACAGAAGTGGGGGTG
GCTATGGTGGGGACAGAGGCGGCGGCTATGGTGGGGACAGAGGAGGCGGCTATGGAGGAGACCGAGGAGGTGGCTATGGA
GGAGATCGAGGTGGCTATGGAGGAGACCGAGGAGGCGGCTATGGCGGAGACCGAGGCGGCTATGGAGGAGATCGAGGAGG
TTACGGAGGAGATCGAGGAGGTTATGGAGGAGATCGAGGAGGCTATGGAGGAGACAGAATCCGGGGGGGCTATGGAGGAG
ACCGTGGTGGTGGCAGTGGCTACGGTGGAGACCGAAGTGGAGGCTATGGAGGAGACAGGAGTGGTGGCGGCTATGGAGGA
GACCGAGGTGGGGGCTACGGAGGAGACCGAGGTGGCTATGGAGGCAAAATGGGAGGAAGAAACGACTACAGAAATGATCA
GCGCAACCGACCATACTGA

Alignment

ORF - retro_mmul_153 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.21 %
• Parental protein coverage: 68.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQSTDTSGYGQSSYSSYGQSQSTGYGTQSAPQGYGSTGGYGSSQSSQSSYGQQ-SSYPGYGQQPTPSSTS
          S.S...SG..Q.SYSSYG.....GYG...APQ.Y....GYG..Q...SSYGQ..S.Y..YGQ.....S.S
Retrocopy SGSYSQSGGEQQSYSSYGNQGNQGYG--QAPQSY---SGYG--QTTDSSYGQNYSGYSSYGQSQSGYSQS

Parental  GSYGSSSQTSSYGQPPSGGYGQQPSYGGQQQSYGQQQSYNPPQGYGQQNQYNSSS---SGSGGGGEICSY
          .........SSYGQ.P....GQQ..........G...SY..P..YGQQ..Y...S......G...E...Y
Retrocopy YGGYENQKQSSYGQQPYNNQGQQQNMESSGSQGGRAPSYDQPD-YGQQDSYDQQSGYDQHQGSYDEQSNY

Parental  GQDQSSMSGGGGGGYGNQDQSGGGGSGYGQQDRGGRGRGGSSGGGGGGGGYNRSSGGYEPRGRGGGRGGR
          .Q...S........Y..Q.............D....G......GG..GGG..R..GGY...GRG...G..
Retrocopy DQQHDSYN-QNQQSYHSQRENYSHHTQDDRRDVSRYGEDNRGYGGSQGGG--RGRGGYDKDGRGPMTGSS

Parental  GGMGGSDRGGFNKFGGPRDQGSR--HDSEQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQ
          GG....DRGGF..FGG.RD.G.R...DSE.DNSDNNTIFVQGLGE.V....V...FKQIGIIKTNKKTG.
Retrocopy GG----DRGGFKNFGGHRDYGPRPDADSESDNSDNNTIFVQGLGEGVSTDQVGEFFKQIGIIKTNKKTGK

Parental  PMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGGRGRG
          PMINLYTD..TGK.KGEATVSFDDPPSAKAAIDWFDGKEF.GN.IKVSFATRR..F.RGGG.G.G.RGRG
Retrocopy PMINLYTDKDTGKPKGEATVSFDDPPSAKAAIDWFDGKEFHGNIIKVSFATRRPEFMRGGGSGGGRRGRG

Parental  GPMGRGGYGGGG
          G..GRGG..G.G
Retrocopy GYRGRGGFQGRG

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	42.92 RPM	142.53 RPM
SRP007412_brain_prefrontal_cortex	53.31 RPM	154.77 RPM
SRP007412_cerebellum	47.59 RPM	188.56 RPM
SRP007412_heart	44.40 RPM	185.25 RPM
SRP007412_kidney	39.79 RPM	126.88 RPM
SRP007412_liver	30.68 RPM	107.98 RPM
SRP007412_testis	92.50 RPM	295.37 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_153 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_153 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_153 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000000968	1 retrocopy	retro_meug_1986,
Myotis lucifugus	ENSMLUG00000004806	3 retrocopies	retro_mluc_1934, retro_mluc_608, retro_mluc_638,
Macaca mulatta	ENSMMUG00000019637	1 retrocopy	retro_mmul_153 ,
Mus musculus	ENSMUSG00000030795	2 retrocopies	retro_mmus_2710, retro_mmus_2952,
Rattus norvegicus	ENSRNOG00000023360	4 retrocopies	retro_rnor_1439, retro_rnor_2727, retro_rnor_2894, retro_rnor_913,