RetrogeneDB ID:

retro_mmus_19

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:12:34984887..34985844(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000092305
Aliases:Prps1l1, 1700011K15Rik
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Prps1
Ensembl ID:ENSMUSG00000031432
Aliases:Prps1, 2310010D17Rik, C76571, C76678, PRS-I, Prps-1
Description:phosphoribosyl pyrophosphate synthetase 1 [Source:MGI Symbol;Acc:MGI:97775]


Retrocopy-Parental alignment summary:






>retro_mmus_19
ATGCCAAACATCAAACTCTTCAGCGGAAGCTCCCACCAGGACTTATCCCAGAAGATTACTGAGCGCCTGGGCCTCGAGCT
CAGCAAGGTGGTCACTAAGAAGTTCAGCAACCAGGAGACCTGCGTGGAAATTGGTGAGAGTGTGCGTGGAGAAGATGTCT
ACATCGTTCAGAGCGGTTGTGGTGAGATCAACGACAGTCTAATGGAACTTTTGATCATGATCAATGCCTGCAAGATCGCT
TCAGCCAGCAGGGTGACTGCAGTCATCCCGTGCTTCCCTTATGCCCGGCAGGATAAAAAGGATAAGAGCCGGGCTCCCAT
CTCTGCGAAGCTCGTAGCAAATATGCTGTCTATAGCAGGTGCAGATCACATTATCACCATGGACCTACATGCTTCTCAGA
TCCAGGGGTTTTTTGACATCCCGGTAGACAATTTGTATGCAGAGCCAGCTGTGCTGAAGTGGATAAAGGAGAATATTTCT
GACTGGAGGAACTGCACGATTGTCTCTCCTGATGCTGGCGGAGCCAAGAGGGTCACTTCCATCGCGGACCATTTGAATGT
GGATTTTGCCTTGATTCACAAAGAACGGAAGAAAGCCAATGAAGTGGACCGCATGGTGCTTGTGGGTGATGTGAAGGATC
GGGTGGCTATTCTTGTAGATGACATGGCTGATACTTGTGGTACAATCTGTTACGCGGCGGACAAACTTCTCTCAGAGGGA
GCTACCAGAGTTTATGCCATCTTGACTCATGGCATCTTTTCTGGCCCAGCTATTGCTCGCATCAATGGCGCATGCTTTGA
AGCAGTAGTAGTCACAAACACCATACCTCAAGAAGACAAGATGAAACAGTGTAGCAAAATCCAGGTGATTGACATCGCCA
TGATCCTTGCTGAAGCCATCCGGAGAACCCATAACGGAGAATCTGTTTCCTACCTGTTCAGTCACGTACCCTTGTAA

ORF - retro_mmus_19 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.28 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPNIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGEDVYIVQSGCGEINDNLMEL
MPNIK.FSGSSHQDLSQKI..RLGLEL.KVVTKKFSNQETCVEIGESVRGEDVYIVQSGCGEIND.LMEL
RetrocopyMPNIKLFSGSSHQDLSQKITERLGLELSKVVTKKFSNQETCVEIGESVRGEDVYIVQSGCGEINDSLMEL
ParentalLIMINACKIASASRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDI
LIMINACKIASASRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLS.AGADHIITMDLHASQIQGFFDI
RetrocopyLIMINACKIASASRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSIAGADHIITMDLHASQIQGFFDI
ParentalPVDNLYAEPAVLKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHKERKKANEVDRMVLVGD
PVDNLYAEPAVLKWI.ENIS.WRNCTIVSPDAGGAKRVTSIAD.LNVDFALIHKERKKANEVDRMVLVGD
RetrocopyPVDNLYAEPAVLKWIKENISDWRNCTIVSPDAGGAKRVTSIADHLNVDFALIHKERKKANEVDRMVLVGD
ParentalVKDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQEDK
VKDRVAILVDDMADTCGTIC.AADKLLS.GATRVYAILTHGIFSGPAI.RIN.ACFEAVVVTNTIPQEDK
RetrocopyVKDRVAILVDDMADTCGTICYAADKLLSEGATRVYAILTHGIFSGPAIARINGACFEAVVVTNTIPQEDK
ParentalMKHCSKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL
MK.CSKIQVIDI.MILAEAIRRTHNGESVSYLFSHVPL
RetrocopyMKQCSKIQVIDIAMILAEAIRRTHNGESVSYLFSHVPL

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 .09 RPM 56 .84 RPM
SRP007412_cerebellum 0 .00 RPM 49 .59 RPM
SRP007412_heart 0 .03 RPM 22 .07 RPM
SRP007412_kidney 0 .02 RPM 25 .56 RPM
SRP007412_liver 0 .03 RPM 27 .17 RPM
SRP007412_testis 125 .64 RPM 11 .11 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_19 was not detected

EST - click to see more details

2 EST(s) were mapped to retro_mmus_19 retrocopy
EST ID Start End Identity Match Mis-match Score
CF104386 34984893 34985414 99.5 518 3 515
Z31209 34985194 34985469 97.5 268 7 261

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_229991064 libraries4 libraries1 library1 library2 libraries
TSS #2 TSS_230001056 libraries9 libraries3 libraries0 libraries4 libraries
TSS #3 TSS_230011061 libraries6 libraries1 library1 library3 libraries
TSS #4 TSS_230021054 libraries8 libraries5 libraries2 libraries3 libraries

The graphical summary, for retro_mmus_19 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_mmus_19 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_19 has 6 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_10
Pan troglodytes retro_ptro_2600
Pongo abelii retro_pabe_46
Macaca mulatta retro_mmul_305
Oryctolagus cuniculus retro_ocun_430
Equus caballus retro_ecab_73
Parental genes homology:
Parental genes homology involve 25 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000027841 retrocopy
retro_amel_22,
Bos taurus ENSBTAG000000197033 retrocopies
retro_btau_157, retro_btau_1686, retro_btau_914,
Canis familiaris ENSCAFG000000179761 retrocopy
retro_cfam_1443,
Equus caballus ENSECAG000000247112 retrocopies
retro_ecab_433, retro_ecab_73,
Felis catus ENSFCAG000000122861 retrocopy
retro_fcat_394,
Homo sapiens ENSG000001472241 retrocopy
retro_hsap_10,
Gorilla gorilla ENSGGOG000000124181 retrocopy
retro_ggor_2583,
Macropus eugenii ENSMEUG000000100712 retrocopies
retro_meug_1612, retro_meug_443,
Microcebus murinus ENSMICG000000019295 retrocopies
retro_mmur_1223, retro_mmur_1422, retro_mmur_514, retro_mmur_810, retro_mmur_90,
Myotis lucifugus ENSMLUG000000154982 retrocopies
retro_mluc_107, retro_mluc_356,
Macaca mulatta ENSMMUG000000046743 retrocopies
retro_mmul_1204, retro_mmul_1619, retro_mmul_305,
Mustela putorius furoENSMPUG000000037932 retrocopies
retro_mputfur_183, retro_mputfur_430,
Mus musculus ENSMUSG000000205282 retrocopies
retro_mmus_1937, retro_mmus_3515,
Mus musculus ENSMUSG00000031432 2 retrocopies
retro_mmus_19 , retro_mmus_33,
Nomascus leucogenys ENSNLEG000000139112 retrocopies
retro_nleu_1456, retro_nleu_217,
Oryctolagus cuniculus ENSOCUG000000123913 retrocopies
retro_ocun_430, retro_ocun_867, retro_ocun_912,
Ochotona princeps ENSOPRG000000131401 retrocopy
retro_opri_704,
Pongo abelii ENSPPYG000000206122 retrocopies
retro_pabe_3061, retro_pabe_46,
Pan troglodytes ENSPTRG000000221632 retrocopies
retro_ptro_2600, retro_ptro_2612,
Rattus norvegicus ENSRNOG000000251662 retrocopies
retro_rnor_249, retro_rnor_341,
Sus scrofa ENSSSCG000000125601 retrocopy
retro_sscr_1068,
Ictidomys tridecemlineatus ENSSTOG000000076382 retrocopies
retro_itri_11, retro_itri_173,
Tarsius syrichta ENSTSYG000000135562 retrocopies
retro_tsyr_1063, retro_tsyr_1567,
Tursiops truncatus ENSTTRG000000038352 retrocopies
retro_ttru_307, retro_ttru_485,
Vicugna pacos ENSVPAG000000002551 retrocopy
retro_vpac_274,


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