RetrogeneDB ID:

retro_mmul_1834

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:4:59907631..59908249(-)
Located in intron of:ENSMMUG00000029597
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.1876
Ensembl ID:ENSMMUG00000008069
Aliases:None
Description:ubiquitin-conjugating enzyme E2 E3 [Source:RefSeq peptide;Acc:NP_001244500]


Retrocopy-Parental alignment summary:






>retro_mmul_1834
ATGTCCAGTGATAGGCAAAGGTCCGATGATGAGAGCCCCAGCACCAGCAGTGGCAGTTCAGATGCGGACCAGCGAGACCC
AGCCTCTCTAGAGCCTGAAGAACAAGAGGAAAGAAAACCTTCTGCCTCCCAGCAGAAGAAAAACACCAAACTCTCCAGCA
AAACCACTGCTAAGTTATCCACTAGTGCTAAAAGAATTCAGAAGAGCTAGCTGAAATAACCCTTGATCCTCCTCCTAACT
GCAGTGCTGGGCCTAAAGGAGCTAACATTTATGAATGGAGATGAACTATACTTGGTCCGCTGGGTTCTGTCTATGAAGGT
GGTGTGTTTTTTCTGGATATCACATTTTCAACAGATTATCCATTTAAGCTACCAAAGGTTACTTCTGCACCGGAATCTAT
CACTGCAACATCAACAGTTAAGGAGTCATCTGTCTGGACATCCTTAAAGACAACTGGAGTCCCGCTTTGACTATTTCAAA
GGTTTTGCTGTCTGTTTGTTCCCTTTTGACAGACTGCAACCCTGCGGATCCTCTGGTTGGAAGCATAGCCACTCAGTATT
TAACCACCGAGCAGAACACGACAGGCTAGCCAGACAGTGGACCAAGAGACACGCAACA

ORF - retro_mmul_1834 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.43 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMSSDRQRSDDESPSTSSGSSDADQRDPAAPEPEEQEERKPSAAQQKKNTKLSSKTTAKLSTSAKRIQK-E
MSSDRQRSDDESPSTSSGSSDADQRDPA..EPEEQEERKPSA.QQKKNTKLSSKTTAKLSTSAKRIQK.E
RetrocopyMSSDRQRSDDESPSTSSGSSDADQRDPASLEPEEQEERKPSASQQKKNTKLSSKTTAKLSTSAKRIQK<E
ParentalLAEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFSSDYPFKPPKVT-FRTRIYHCNI
LAEITLDPPPNCSAGPKG.NIYEWR.TILGP.GSVYEGGVFFLDITFS.DYPFK.PKVT.F.T.IYHCNI
RetrocopyLAEITLDPPPNCSAGPKGANIYEWR*TILGPLGSVYEGGVFFLDITFSTDYPFKLPKVT<FCTGIYHCNI
ParentalNSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYLT-NRAEHDRIARQWTKRYAT
NS.GVICLDILKDNWSPALTISKVLLS.CSLLTDCNPADPLVGSIATQYLT..RAEHDR.ARQWTKR.AT
RetrocopyNS*GVICLDILKDNWSPALTISKVLLSVCSLLTDCNPADPLVGSIATQYLT<HRAEHDRLARQWTKRHAT

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 .45 RPM 41 .01 RPM
SRP007412_brain_prefrontal_cortex 1 .03 RPM 40 .22 RPM
SRP007412_cerebellum 0 .06 RPM 54 .31 RPM
SRP007412_heart 0 .00 RPM 16 .13 RPM
SRP007412_kidney 0 .00 RPM 26 .29 RPM
SRP007412_liver 0 .20 RPM 9 .26 RPM
SRP007412_testis 0 .45 RPM 15 .23 RPM
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_1834 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_1834 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_1834 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 18 parental genes, and 44 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000141633 retrocopies
Choloepus hoffmanni ENSCHOG000000073253 retrocopies
Ciona intestinalis ENSCING000000068601 retrocopy
Callithrix jacchus ENSCJAG000000115593 retrocopies
Equus caballus ENSECAG000000072331 retrocopy
Echinops telfairi ENSETEG000000193242 retrocopies
Homo sapiens ENSG000001700351 retrocopy
Macaca mulatta ENSMMUG000000024105 retrocopies
Macaca mulatta ENSMMUG00000008069 2 retrocopies
retro_mmul_1382, retro_mmul_1834 ,
Macaca mulatta ENSMMUG000000206663 retrocopies
Monodelphis domestica ENSMODG000000103012 retrocopies
Mus musculus ENSMUSG000000270114 retrocopies
Nomascus leucogenys ENSNLEG000000062901 retrocopy
Otolemur garnettii ENSOGAG000000149564 retrocopies
Rattus norvegicus ENSRNOG000000045441 retrocopy
Tupaia belangeri ENSTBEG000000099322 retrocopies
Tarsius syrichta ENSTSYG000000022815 retrocopies
Tursiops truncatus ENSTTRG000000013611 retrocopy



Copyright © RetrogeneDB 2014-2017