RetrogeneDB ID:

retro_mmul_1704

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:3:102619097..102619571(-)
Located in intron of:ENSMMUG00000030291
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FCF1
Ensembl ID:ENSMMUG00000008887
Aliases:None
Description:rRNA-processing protein FCF1 homolog [Source:RefSeq peptide;Acc:NP_001248471]


Retrocopy-Parental alignment summary:






>retro_mmul_1704
GGGAAGCAAAAGAAAACAAGGAAGTATGCAACCATGAAGTGCATGCTTAGACTCAGAGATCAGAGGCTTAAAGAAAAGGA
TAGATTAAAACCTAAAAAGAAAGAAAAGAAGGATCCCAGCACATTAAAGGAAAGAGAAGTTCCCCAACACCCTTCCTGCT
TATTTTTCCAATGTAATACACAGCTGGGCCCACCTTACTACATCCTCATTGATACCAACTTTATCAACTTTTCCTTAAAA
GCGAAACTGGATTTAGTGCAGTCAGCGATGGACTGTCTGTATGCCAAGTGTATCCCTTGTATAACTGATTGTGTAATGGC
TGAAATTGAGAAATTGGGGCAGAAGTATTGAGTGGCTCTAAGGATTGCCAAGGATCCAAGATTTGAACTGTGTACACACA
AAGGAACCTATGCAAATGACTGCTTAGTACAGAGAGTAGCTCAGCATAAGTGTTACATTGTGGCCACAGTTGAC

ORF - retro_mmul_1704 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.88 %
Parental protein coverage: 81.22 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGKQKKTRKYATMKRMLSLRDQRLKEKDRLKPKKKEKKDPSALKEREVPQHPSCLFFQYNTQLGPPYHILV
GKQKKTRKYATMK.ML.LRDQR...............DPS.LKEREVPQHPSCLFFQ.NTQLGPPY.IL.
RetrocopyGKQKKTRKYATMKCMLRLRDQRXXXXXXXXXXXXXXXDPSTLKEREVPQHPSCLFFQCNTQLGPPYYILI
ParentalDTNFINFSIKAKLDLVQSMMDCLYAKCIPCITDCVMAEIEKLGQKYRVALRIAKDPRFERLPCTHKGTYA
DTNFINFS.KAKLDLVQS.MDCLYAKCIPCITDCVMAEIEKLGQKY.VALRIAKDPRFE...CTHKGTYA
RetrocopyDTNFINFSLKAKLDLVQSAMDCLYAKCIPCITDCVMAEIEKLGQKY*VALRIAKDPRFEL--CTHKGTYA
ParentalDDCLVQRVTQHKCYIVATVD
.DCLVQRV.QHKCYIVATVD
RetrocopyNDCLVQRVAQHKCYIVATVD

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 0 .00 RPM 4 .48 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 3 .89 RPM
SRP007412_cerebellum 0 .00 RPM 3 .42 RPM
SRP007412_heart 0 .12 RPM 3 .12 RPM
SRP007412_kidney 0 .12 RPM 6 .10 RPM
SRP007412_liver 0 .04 RPM 2 .45 RPM
SRP007412_testis 0 .19 RPM 8 .71 RPM
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_1704 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_1704 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_1704 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 29 parental genes, and 164 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000182967 retrocopies
Bos taurus ENSBTAG000000203811 retrocopy
Canis familiaris ENSCAFG000000169713 retrocopies
Callithrix jacchus ENSCJAG000000205189 retrocopies
Cavia porcellus ENSCPOG000000011496 retrocopies
Equus caballus ENSECAG000000082611 retrocopy
Erinaceus europaeus ENSEEUG000000071731 retrocopy
Felis catus ENSFCAG000000227533 retrocopies
Homo sapiens ENSG000001196166 retrocopies
Gorilla gorilla ENSGGOG000000163183 retrocopies
Latimeria chalumnae ENSLACG000000188791 retrocopy
Loxodonta africana ENSLAFG000000007241 retrocopy
Microcebus murinus ENSMICG000000060615 retrocopies
Macaca mulatta ENSMMUG00000008887 8 retrocopies
Monodelphis domestica ENSMODG000000061795 retrocopies
Mustela putorius furoENSMPUG000000093217 retrocopies
Mus musculus ENSMUSG000000212433 retrocopies
Nomascus leucogenys ENSNLEG000000163117 retrocopies
Oryctolagus cuniculus ENSOCUG000000141201 retrocopy
Otolemur garnettii ENSOGAG0000000271119 retrocopies
Pongo abelii ENSPPYG0000000599110 retrocopies
Pan troglodytes ENSPTRG000000065406 retrocopies
Pteropus vampyrus ENSPVAG000000006573 retrocopies
Rattus norvegicus ENSRNOG000000047235 retrocopies
Sorex araneus ENSSARG000000032703 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000080834 retrocopies
Tupaia belangeri ENSTBEG0000001355730 retrocopies
Tarsius syrichta ENSTSYG000000063273 retrocopies
Tursiops truncatus ENSTTRG000000024403 retrocopies



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