RetrogeneDB ID:

retro_mmul_2495

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:X:54866255..54866940(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.18258
Ensembl ID:ENSMMUG00000021233
Aliases:None
Description:selenide, water dikinase 1 [Source:RefSeq peptide;Acc:NP_001177347]


Retrocopy-Parental alignment summary:






>retro_mmul_2495
CTGATGGGTTTTAAAGATGCAGCTGAGGAAGCAGGAACGTCTATAAGGGCTGGCCAAACAGTATTAAACCCCTGGATTGT
TGTGGGAGGAGTTGCTGCCAATGTCTGCCAGCCCAGTGAATTTATCATGCCAGACAATGCAGTGCCAGGGGATGTGCCAG
TGTTGACAAAACCCCTGGGGACACATGTGGCAGTGGTTGTACACCAGTGGCTGGATATTACTGGAAAACAGAATAAAATT
AAATTAGTGGTCACCCAAGAACATGTAGAATTGGTCTACCAGGAGGTGATGATGAACATAAGGAGGCTCAACAAGACAAC
TGCAGGACTCATGCACACGTTCAATTCCCACGCGGCCACCAACATCATGGGCTTTGGGATTTGGGGTCTGGAGCAGAGCC
TGGCCAAGTAGCAGAGGAACAAGGTGTCGTTTGTGATTCACAATGTCCCAGTGCTGGTCAAGATGCCTGCGGTGAGCAAA
GCCTGCAGAAACATGTTCTGCCTCATGTACAGGACCTGCCAGGAGACATCAGGAGGCCTTCTGATCTGTTTACCACATGC
GCAAGCAGGTCGATTCCATGCAGAGATGAAGTCCCCCAACTGTGGTGAAGGCCACCAAGCATGAAATTATTGGGATTGAA
GAGAAGGGCAACCACACAGCCAGAATCATAGACAAACCCTGGATC

ORF - retro_mmul_2495 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.73 %
Parental protein coverage: 58.16 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalIQGFKDAAEEAGTSVTGGQTVLNPWIVLGGVATTVCQPNEFIMPDNAVPGDVLVLTKPLGTQVAVAVHQW
..GFKDAAEEAGTS...GQTVLNPWIV.GGVA..VCQP.EFIMPDNAVPGDV.VLTKPLGT.VAV.VHQW
RetrocopyLMGFKDAAEEAGTSIRAGQTVLNPWIVVGGVAANVCQPSEFIMPDNAVPGDVPVLTKPLGTHVAVVVHQW
ParentalLDIPEKWNKIKLVVTQEDVELAYQEAMMNMARLNRTAAGLMHTFNAHAATDITGFGILGHAQNLAKQQRN
LDI..K.NKIKLVVTQE.VEL.YQE.MMN..RLN.T.AGLMHTFN.HAAT.I.GFGI.G..Q.LAK.QRN
RetrocopyLDITGKQNKIKLVVTQEHVELVYQEVMMNIRRLNKTTAGLMHTFNSHAATNIMGFGIWGLEQSLAK*QRN
ParentalEVSFVIHNLPVLAKMAAVSKACGNMFGLMHGTCPETSGGLLICLPREQAARFCAEIKSPKYGEGHQA-WI
.VSFVIHN.PVL.KM.AVSKAC.NMF.LM..TC.ETSGGLLICLP..QA.RF.AE.KSP..GEGHQA..I
RetrocopyKVSFVIHNVPVLVKMPAVSKACRNMFCLMYRTCQETSGGLLICLPHAQAGRFHAEMKSPNCGEGHQA>EI
ParentalIGIVEKGNRTARIIDKPRI
IGI.EKGN.TARIIDKP.I
RetrocopyIGIEEKGNHTARIIDKPWI

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






RNA-Seq - click to see more details

(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 10 .76 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 19 .12 RPM
SRP007412_cerebellum 0 .00 RPM 17 .18 RPM
SRP007412_heart 0 .00 RPM 8 .72 RPM
SRP007412_kidney 0 .00 RPM 20 .30 RPM
SRP007412_liver 0 .00 RPM 30 .40 RPM
SRP007412_testis 0 .00 RPM 8 .33 RPM

ChIP-Seq - click to see more details

Macaca mulatta was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mmul_2495 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_2495 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_2495 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 23 parental genes, and 46 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000135551 retrocopy
retro_amel_21,
Canis familiaris ENSCAFG000000047432 retrocopies
retro_cfam_1787, retro_cfam_250,
Callithrix jacchus ENSCJAG000000094942 retrocopies
retro_cjac_166, retro_cjac_2219,
Dipodomys ordii ENSDORG000000141191 retrocopy
retro_dord_792,
Equus caballus ENSECAG000000142811 retrocopy
retro_ecab_77,
Felis catus ENSFCAG000000039211 retrocopy
retro_fcat_96,
Homo sapiens ENSG000000864753 retrocopies
retro_hsap_2196, retro_hsap_3860, retro_hsap_4705,
Gorilla gorilla ENSGGOG000000038062 retrocopies
retro_ggor_147, retro_ggor_2924,
Loxodonta africana ENSLAFG000000046701 retrocopy
retro_lafr_125,
Macropus eugenii ENSMEUG000000121881 retrocopy
retro_meug_245,
Myotis lucifugus ENSMLUG000000019712 retrocopies
retro_mluc_2350, retro_mluc_728,
Macaca mulatta ENSMMUG00000021233 4 retrocopies
retro_mmul_1607, retro_mmul_2495 , retro_mmul_2647, retro_mmul_922,
Monodelphis domestica ENSMODG000000168641 retrocopy
retro_mdom_86,
Mustela putorius furoENSMPUG000000009481 retrocopy
retro_mputfur_20,
Mus musculus ENSMUSG000000266621 retrocopy
retro_mmus_248,
Nomascus leucogenys ENSNLEG000000122057 retrocopies
retro_nleu_1868, retro_nleu_2211, retro_nleu_234, retro_nleu_2668, retro_nleu_2873, retro_nleu_3004, retro_nleu_327,
Otolemur garnettii ENSOGAG000000078071 retrocopy
retro_ogar_3026,
Procavia capensis ENSPCAG000000156171 retrocopy
retro_pcap_341,
Pongo abelii ENSPPYG000000020996 retrocopies
retro_pabe_1324, retro_pabe_1378, retro_pabe_2074, retro_pabe_2620, retro_pabe_3047, retro_pabe_3652,
Pan troglodytes ENSPTRG000000023033 retrocopies
retro_ptro_1135, retro_ptro_1669, retro_ptro_3126,
Pteropus vampyrus ENSPVAG000000029452 retrocopies
retro_pvam_115, retro_pvam_566,
Rattus norvegicus ENSRNOG000000181251 retrocopy
retro_rnor_59,
Tursiops truncatus ENSTTRG000000111141 retrocopy
retro_ttru_649,


Copyright © RetrogeneDB 2014-2017