RetrogeneDB ID: retro_mmul_277

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:59961493..59962702(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000030261
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000012843
• Aliases: None
• Description: None

Sequence

>retro_mmul_277
GCGTTCATGGGCAGGATGAATGCAGGCTCAGATCCTGTGGTCATCGTCTCGGCGGCGCGGACCATCATAGGTTCCTTCAA
TGGTGCCTTAGCTACTGTTCCTGTCCAAGACTTGGGCTCCACTGTCATCAAAGAAGACTTGAAGAGGGCCACTGTGGTTC
CTGAAGATGTGTGGGAGGTCATCTTTGGACATGTTTTGGCAGCAGGCTGTGGGCAGAATCCTGTTAGACAAGCCAGTGTG
GGTGCAGGAATTCCCTACTGTATTCCAGCATGGAGCTGCCAGATGATCTGTGGGTCAGGTCTAAAAGCTGTGTGCCTTGC
AGCCCAGTCAATAGGGATAGGAGACTCCAGCACTGTGGTTGCAGGAGGCATGGAAAATATGAGCAAGGCTCCTCACTTGG
CTCACTTGAGAACAGGACTAAAGATAGGTGAGATGCCGCTGACTGACAGTATACTCTGTGATGTTCTTACAGATGCATTT
CACAACTGTCATATGGGTATTACAGCTGAAAACGTAGCCAAAAAATGGCAAGTGGTTAGAGAAGATCAGGATGAGATTGC
AGTTCTGTCTCAGAATAGGACAGAGAATACACAGAAAGCTAGCCATTTTGACAAAGAGGTTGTAGCAGTTTTGGTGTCAT
CTAGAAAAGGTCTTATTGAAGTTAAAACAGATGAGTTTCCTCGCCATGGGAGCAACATAGAAGCCATGTCCACGCTAAAG
CCTTACTTTCTTACCGATGGAATGGGAACCGTCACCCCAGCCAACGCTTCAGGAATAAATGATGGTGCTGCAGCTGTGGT
TCATATGAAGAAGTCAGAAGCTGATAAACGTGGGCTTACACCTTTAGCACGGATAGTTTCCTGGTCCCAAGTGGGTGTGG
AGCCTTCTATTATGGGAATAGGACCAATTCTAGCCACAAAACAAGCAGTTACAAAAGCAGATTGGTCACTGGAGGATGTT
GATATATTTGGAATCAATGAAGCCTTTGCAGCCCTCTCTGTTGTCACAGTTAAAGAACTTGGATTAAACCCAGAGAAGGT
CAACATTGAAGGAGGGGCTATAGCCGTGGGCCACCCTCTTGGAGCATATGGCTGTCGAATTCTTGTGACCCTGTTACACA
CACTGGAGAGAATGGGAGGAAGCTGTGGTATTGTGGCCCTGTGCATTGGGGGTGGGATGGGAATAGCAATGTGTGTTCAG
AGAGGATGA

Alignment

ORF - retro_mmul_277 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNAGSDPVVIVSAARTIIGERPAGLAQRPDLALGWGPAVTQWLEVATSSPSSLCSSVF---LFLGCGQNP
          MNAGSDPVVIVSAARTIIG.....LA..P...LG........L..AT..P.......F...L..GCGQNP
Retrocopy MNAGSDPVVIVSAARTIIGSFNGALATVPVQDLG-STVIKEDLKRATVVPEDVWEVIFGHVLAAGCGQNP

Parental  VRQASVGAGIPYSVPAWSCQMICGSGLKAVCLAAQSIGIGDSSIVVAGGMENMSKAPHLAHLRTGVKIGE
          VRQASVGAGIPY..PAWSCQMICGSGLKAVCLAAQSIGIGDSS.VVAGGMENMSKAPHLAHLRTG.KIGE
Retrocopy VRQASVGAGIPYCIPAWSCQMICGSGLKAVCLAAQSIGIGDSSTVVAGGMENMSKAPHLAHLRTGLKIGE

Parental  MPLTDSILCDGLTDAFHNYHMGITAENVAKKWQVSREDQDKVAVLSQNRTENAQKAGHFDKEIVPVLVSS
          MPLTDSILCD.LTDAFHN.HMGITAENVAKKWQV.REDQD..AVLSQNRTEN.QKA.HFDKE.V.VLVSS
Retrocopy MPLTDSILCDVLTDAFHNCHMGITAENVAKKWQVVREDQDEIAVLSQNRTENTQKASHFDKEVVAVLVSS

Parental  RKGLIEVKTDEFPRHGSNIEDMSKLKPYFLTDGTGTVTPANASGINDGAAAVVLMKKSEADKRGLTPLAQ
          RKGLIEVKTDEFPRHGSNIE.MS.LKPYFLTDG.GTVTPANASGINDGAAAVV.MKKSEADKRGLTPLA.
Retrocopy RKGLIEVKTDEFPRHGSNIEAMSTLKPYFLTDGMGTVTPANASGINDGAAAVVHMKKSEADKRGLTPLAR

Parental  IVSWSQVGVEPSIMGIGPIPAIKQAVTKAGWSLEDVDVFEINEAFAALSVAIVKELGLNPQKVNIEGGAI
          IVSWSQVGVEPSIMGIGPI.A.KQAVTKA.WSLEDVD.F.INEAFAALSV..VKELGLNP.KVNIEGGAI
Retrocopy IVSWSQVGVEPSIMGIGPILATKQAVTKADWSLEDVDIFGINEAFAALSVVTVKELGLNPEKVNIEGGAI

Parental  ALGHPLGASGCRILVTLLHTLERTGGIRGVAALCIGGGMGIAMCVQRG
          A.GHPLGA.GCRILVTLLHTLER.GG..G..ALCIGGGMGIAMCVQRG
Retrocopy AVGHPLGAYGCRILVTLLHTLERMGGSCGIVALCIGGGMGIAMCVQRG

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	0.90 RPM	28.80 RPM
SRP007412_brain_prefrontal_cortex	3.01 RPM	23.80 RPM
SRP007412_cerebellum	0.90 RPM	22.08 RPM
SRP007412_heart	0.35 RPM	6.12 RPM
SRP007412_kidney	6.10 RPM	98.12 RPM
SRP007412_liver	14.01 RPM	146.97 RPM
SRP007412_testis	1.32 RPM	17.04 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_277 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_277 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_277 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002827	1 retrocopy	retro_btau_560,
Callithrix jacchus	ENSCJAG00000011777	1 retrocopy	retro_cjac_1372,
Dasypus novemcinctus	ENSDNOG00000002502	1 retrocopy	retro_dnov_331,
Macaca mulatta	ENSMMUG00000012843	1 retrocopy	retro_mmul_277 ,
Monodelphis domestica	ENSMODG00000007156	1 retrocopy	retro_mdom_1493,
Rattus norvegicus	ENSRNOG00000019189	1 retrocopy	retro_rnor_1055,
Xenopus tropicalis	ENSXETG00000021174	1 retrocopy	retro_xtro_45,