RetrogeneDB ID:

retro_mmul_2420

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:9:99851488..99852284(+)
Located in intron of:ENSMMUG00000018472
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.2808
Ensembl ID:ENSMMUG00000000156
Aliases:PHB, ZNF607
Description:prohibitin [Source:RefSeq peptide;Acc:NP_001253252]


Retrocopy-Parental alignment summary:






>retro_mmul_2420
AAGTGTTATGAGTCCGTCAGCAAGTTTGGCCTGGACTTAGCTGTTGCAGGAGACGTGGTGAACTCTGCCCTGTATGACAT
GGATGCTGGGCAAAGAGCTGTCATCTTTGACCAATTCTGTGGAATAGAGAATATTGTGGTAGGGGAAGGGATTCACTTTC
TCATTCCATGGGTACAGAAACCAATTATCTTTGACTGCCGTTCTTGACCATGTAATGTGCCAGGCATCACTGATAGCAAA
GATATGCAGAATGACATCACGGTGCACATGGGGGCCTGTCACTAGCCAGCTTCCTCGCATCTTGACCAGCATTGAAGAGG
ATTATGATGAGCGTGTGCTGCTGTCCATCACTACCGAGATCCTCAAGTCAGTGGTGGCTCACTTTGATGCTGGAGAACTA
ATCACCTAAAGAGAGCTGGTCTCCAGGCAGATGAGCAATGACCTTATGGAGTGAGCAGCCACCTTTGGGCTCATCCTGGA
TGACAAGTCCTTGACACATCTGACCTTTGGGAAGGAGTTCACAGAAGCAGTGGAAGCCAAACAGGTGGCTCAGCAGGAAG
CAGAGAGCGCCAGATTTGTGGTAGAAAAGGCTGAGCAGCAGAAAAAGGCAGCCATCATCTCTGCTGAGGGCGATTCCAAG
GCAGCCAAGCTGATCGCCAACTTACTGGCCACCACAGGGAACAGCCTGATCGAGCTGCGCAAGCTGGAAGCTGCAGAGGA
CATCACATACCAGCTCTCACACTCTGGGAACATCACCTCCCCTCCAGCGGGGCAGTCCATGCTCCTCCAGCTGCCC

ORF - retro_mmul_2420 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.07 %
Parental protein coverage: 98.53 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalKVFESIGKFGLALAVAGGVVNSALYNVDAGHRAVIFDRFRGVQDIVVGEGTHFLIPWVQKPIIFDCRSRP
K..ES..KFGL.LAVAG.VVNSALY..DAG.RAVIFD.F.G...IVVGEG.HFLIPWVQKPIIFDCRS.P
RetrocopyKCYESVSKFGLDLAVAGDVVNSALYDMDAGQRAVIFDQFCGIENIVVGEGIHFLIPWVQKPIIFDCRS*P
ParentalRNVPVITGSKDLQNVN-ITLRILFRPVASQLPRIFTSIGEDYDERVLPSITTEILKSVVARFDAGELITQ
.N.....G..D.......T.R....PV.SQLPRI.TSI.EDYDERVL.SITTEILKSVVA.FDAGELIT.
RetrocopyCN---VPGITDSKDMQ>MTSRCTWGPVTSQLPRILTSIEEDYDERVLLSITTEILKSVVAHFDAGELIT*
ParentalRELVSRQVSDDLTERAATFGLILDDVSLTHLTFGKEFTEAVEAKQVAQQEAERARFVVEKAEQQKKAAII
RELVSRQ.S.DL.E.AATFGLILDD.SLTHLTFGKEFTEAVEAKQVAQQEAE.ARFVVEKAEQQKKAAII
RetrocopyRELVSRQMSNDLME*AATFGLILDDKSLTHLTFGKEFTEAVEAKQVAQQEAESARFVVEKAEQQKKAAII
ParentalSAEGDSKAAELIANSLATAGDGLIELRKLEAAEDIAYQLSRSRNITYLPAGQSVLLQLP
SAEGDSKAA.LIAN.LAT.G..LIELRKLEAAEDI.YQLS.S.NIT..PAGQS.LLQLP
RetrocopySAEGDSKAAKLIANLLATTGNSLIELRKLEAAEDITYQLSHSGNITSPPAGQSMLLQLP

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 2 .02 RPM 18 .15 RPM
SRP007412_brain_prefrontal_cortex 1 .27 RPM 59 .58 RPM
SRP007412_cerebellum 2 .26 RPM 18 .15 RPM
SRP007412_heart 0 .82 RPM 57 .83 RPM
SRP007412_kidney 1 .53 RPM 79 .93 RPM
SRP007412_liver 0 .79 RPM 155 .21 RPM
SRP007412_testis 2 .45 RPM 10 .48 RPM
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_2420 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_2420 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_2420 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_617
Pan troglodytes retro_ptro_451
Pongo abelii retro_pabe_552

Parental genes homology:
Parental genes homology involve 26 parental genes, and 165 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000047971 retrocopy
Ailuropoda melanoleuca ENSAMEG000000123641 retrocopy
Bos taurus ENSBTAG000000171201 retrocopy
Canis familiaris ENSCAFG000000169261 retrocopy
Choloepus hoffmanni ENSCHOG000000075882 retrocopies
Callithrix jacchus ENSCJAG0000000717422 retrocopies
Erinaceus europaeus ENSEEUG000000064813 retrocopies
Homo sapiens ENSG0000016708515 retrocopies
Gorilla gorilla ENSGGOG0000002800212 retrocopies
Macropus eugenii ENSMEUG000000051221 retrocopy
Microcebus murinus ENSMICG000000069669 retrocopies
Myotis lucifugus ENSMLUG000000082032 retrocopies
Macaca mulatta ENSMMUG00000000156 13 retrocopies
Monodelphis domestica ENSMODG000000122101 retrocopy
Mus musculus ENSMUSG000000388458 retrocopies
Nomascus leucogenys ENSNLEG0000000297813 retrocopies
Oryctolagus cuniculus ENSOCUG000000072091 retrocopy
Otolemur garnettii ENSOGAG000000270151 retrocopy
Ochotona princeps ENSOPRG000000008682 retrocopies
Procavia capensis ENSPCAG000000088511 retrocopy
Pongo abelii ENSPPYG0000000892016 retrocopies
Pan troglodytes ENSPTRG0000000937614 retrocopies
Rattus norvegicus ENSRNOG0000004679918 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000199292 retrocopies
Tupaia belangeri ENSTBEG000000105374 retrocopies
Tursiops truncatus ENSTTRG000000108361 retrocopy



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