RetrogeneDB ID: retro_mmul_1489

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:186990398..186991337(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.9
• Ensembl ID: ENSMMUG00000013680
• Aliases: None
• Description: None

Sequence

>retro_mmul_1489
ATGGCCTGCAGGGAGCAGTTGTCGAAGAATCGGGTCAGGTGGGGGTTGGCTGGCATTACCTGTGTTTCTGTGGTGGTCAT
GGCTGCGGTAGTCCTTGCCATCACCCTGCGGCGGCCAGGCTGTGAGCTGGAGGCCTGCAGCCCCGAGGCCGACATGCTGG
ATTACCTGCTGGGCCTGGGTCAGACCAGCCGCCGAGGTGCCCCGGAGGTCACCTGGTACCACGCAGCCAACAGCAAGGAA
GCCACGACAGCTGCCCCAAACGGCAACATCACCGTCCTGGAGGCTGACGTCAATGTCAAAGGGCTCGGCACAGCCGATGA
GACAGGAGTTCCCATCATGGCACACCCCCTGGCTATCCGTAGCTTCAACACACTGGAGCAGTGGCTGGACGGTATGCCAG
GCTCTTCCCAGAAGGGCATCAAACTGGACTTCAAGAACATCAAGGCGGTGGGCCCCTCCCTGGACCTCCTGTGGCAGCTG
ACAGAAGGGGGCAAAGTCTGGCGGCCCACGCGGATCAACACTGACATCTTAAAGGGCTCTGACATGCCCATCTCAACTGA
GGTCAGTGCCACAGAGTTCCTAGCCCTCATCCAGGAGAAGTATCCCCAGGCCACCCTGTCTCCAGGCTGGACCACCATCT
ACGTGCCCATGTTCCCAAACAGGATGTACACCCGAGCGATGGTGGAGAAGATGCACGAGCTGGTAGGAGTGGTGCCCCAG
AGAGTCACCTTCCCTGTGCTGTCTTCCACGGTGCGAGCCACCTGGCCCCACTCCAGCTGGCTGCTGAGCCAGTCTGAGAG
GTACAGCCTGATGCTGTGGCAGGTCGCCTCGGACCCCATGTCGGCAGAGGATCTGCTCTACCTCTAGGACAACACTGCCA
TCCATCAAGTCTACTATGACATCTTTGAGCCTTTCCTGTTGCAGTTCAAGCAGCTGGCC

Alignment

ORF - retro_mmul_1489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.11 %
• Parental protein coverage: 53.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAWREQLSKNQVNWVFAGITCVSVVVIATTVLAITLRRPGCELEACSPDADMLDYLLSLGQISRRDALEV
          MA.REQLSKN.V.W..AGITCVSVVV.A..VLAITLRRPGCELEACSP.ADMLDYLL.LGQ.SRR.A.EV
Retrocopy MACREQLSKNRVRWGLAGITCVSVVVMAAVVLAITLRRPGCELEACSPEADMLDYLLGLGQTSRRGAPEV

Parental  TWYHAANSKEAMTAALNSNITVLEADVNVEGLGTANETGVPIMAHPPAIYSDNTLEQWLDAVLGSSQKGI
          TWYHAANSKEA.TAA.N.NITVLEADVNV.GLGTA.ETGVPIMAHP.AI.S.NTLEQWLD...GSSQKGI
Retrocopy TWYHAANSKEATTAAPNGNITVLEADVNVKGLGTADETGVPIMAHPLAIRSFNTLEQWLDGMPGSSQKGI

Parental  KLDFKNIKAVGPSLDLLRRLTEEGKVRRPVWINADILKGPNMLISTEVNATQFLALVQEKYPKATLSPGW
          KLDFKNIKAVGPSLDLL..LTE.GKV.RP..IN.DILKG..M.ISTEV.AT.FLAL.QEKYP.ATLSPGW
Retrocopy KLDFKNIKAVGPSLDLLWQLTEGGKVWRPTRINTDILKGSDMPISTEVSATEFLALIQEKYPQATLSPGW

Parental  TTFYMSTFPNRTYTRAMVEKMHELVGVVPQRVTFPVRSSMVRAAWPHFSWLLSQSERYSLTLWQAASDPL
          TT.Y...FPNR.YTRAMVEKMHELVGVVPQRVTFPV.SS.VRA.WPH.SWLLSQSERYSL.LWQ.ASDP.
Retrocopy TTIYVPMFPNRMYTRAMVEKMHELVGVVPQRVTFPVLSSTVRATWPHSSWLLSQSERYSLMLWQVASDPM

Parental  SVEDLLYVRDNTAVHQVYYDIFEPLLSQFKQLA
          S.EDLLY..DNTA.HQVYYDIFEP.L.QFKQLA
Retrocopy SAEDLLYL*DNTAIHQVYYDIFEPFLLQFKQLA

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	1.68 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	5.00 RPM
SRP007412_cerebellum	0.00 RPM	0.84 RPM
SRP007412_heart	0.06 RPM	9.60 RPM
SRP007412_kidney	0.00 RPM	60.56 RPM
SRP007412_liver	0.00 RPM	0.08 RPM
SRP007412_testis	0.15 RPM	0.64 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1489 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1489 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1489 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2742

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019801	1 retrocopy	retro_btau_325,
Homo sapiens	ENSG00000162391	1 retrocopy	retro_hsap_2742,
Myotis lucifugus	ENSMLUG00000014446	1 retrocopy	retro_mluc_965,
Macaca mulatta	ENSMMUG00000013680	1 retrocopy	retro_mmul_1489 ,
Pongo abelii	ENSPPYG00000001314	1 retrocopy	retro_pabe_2276,