RetrogeneDB ID:

retro_mmus_159

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:4:86575918..86576860(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000070934
Aliases:Rraga, 1300010C19Rik, AI255374, FIP-1, RAGA
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Rragb
Ensembl ID:ENSMUSG00000041658
Aliases:None
Description:Ras-related GTP binding B [Source:MGI Symbol;Acc:MGI:3038613]


Retrocopy-Parental alignment summary:






>retro_mmus_159
ATGCCCAATACAGCCATGAAGAAAAAGGTGCTGTTGATGGGAAAGAGCGGGTCGGGGAAGACCAGCATGAGGTCGATCAT
CTTTGCAAATTATATTGCGCGCGACACTAGGCGCCTGGGTGCCACCATCGACGTGGAGCACTCCCACGTCCGATTCTTGG
GGAACCTGGTGCTGAACCTGTGGGACTGTGGCGGCCAGGACACCTTTATGGAAAATTACTTCACCAGCCAGCGGGACAAC
ATCTTCCGTAATGTGGAGGTTCTGATATACGTGTTTGACGTAGAGAGCCGCGAACTGGAAAAAGATATGCATTATTACCA
ATCGTGTCTGGAAGCCATCCTCCAGAATTCACCTGACGCCAAAATCTTCTGCCTGGTGCACAAAATGGATCTGGTTCAGG
AAGATCAACGTGACCTGATTTTTAAAGAGCGAGAGGAAGACCTGAGGCGTTTGTCTCGCCCGCTGGAGTGCGCTTGTTTT
CGAACGTCCATCTGGGATGAGACGCTCTACAAAGCCTGGTCCAGCATCGTCTATCAGCTGATCCCCAACGTTCAGCAGCT
GGAGATGAACCTAAGGAATTTTGCCCAGATTATTGAGGCTGATGAAGTTCTGCTGTTCGAGAGAGCTACGTTCTTGGTGA
TTTCCCACTACCAGTGCAAAGAGCAGCGAGATGTGCACCGCTTTGAGAAGATCAGCAACATCATCAAGCAGTTTAAGCTG
AGCTGCAGTAAATTGGCCGCTTCTTTCCAGAGCATGGAAGTGAGGAATTCTAACTTCGCTGCCTTCATCGACATCTTTAC
ATCAAACACGTACGTGATGGTGGTCATGTCAGATCCATCCATCCCTTCTGCAGCTACTCTGATCAACATTCGTAATGCCA
GGAAACACTTTGAGAAGCTAGAAAGAGTAGATGGGCCCAAGCACAGCCTCCTCATGCGTTGA

ORF - retro_mmus_159 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.43 %
Parental protein coverage: 72.73 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalTFDVEHSHVRFLGNLVLNLWDCGGQDTFMENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLE
T.DVEHSHVRFLGNLVLNLWDCGGQDTFMENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLE
RetrocopyTIDVEHSHVRFLGNLVLNLWDCGGQDTFMENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLE
ParentalAILQNSPEAKIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLECSCFRTSIWDETLYKAWSSIVYQLI
AILQNSP.AKIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLEC.CFRTSIWDETLYKAWSSIVYQLI
RetrocopyAILQNSPDAKIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLECACFRTSIWDETLYKAWSSIVYQLI
ParentalPNVQQLEMNLRNFAEIIEADEVLLFERATFLVISHYQCKEQRDAHRFEKISNIIKQFKLSCSKLAASFQS
PNVQQLEMNLRNFA.IIEADEVLLFERATFLVISHYQCKEQRD.HRFEKISNIIKQFKLSCSKLAASFQS
RetrocopyPNVQQLEMNLRNFAQIIEADEVLLFERATFLVISHYQCKEQRDVHRFEKISNIIKQFKLSCSKLAASFQS
ParentalMEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKLERVDGPKQCLLMR
MEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKLERVDGPK..LLMR
RetrocopyMEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKLERVDGPKHSLLMR

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 66 .63 RPM 55 .04 RPM
SRP007412_cerebellum 65 .83 RPM 55 .71 RPM
SRP007412_heart 28 .36 RPM 2 .77 RPM
SRP007412_kidney 30 .66 RPM 2 .62 RPM
SRP007412_liver 19 .91 RPM 0 .14 RPM
SRP007412_testis 13 .13 RPM 7 .50 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity may be related with retro_mmus_159 in 3 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001XVA POLR2A 4:86575320..86576152
ENCFF001YIJ POLR2A 4:86574905..86578992
ENCFF001YKA POLR2A 4:86574943..86579071

EST - click to see more details

6 EST(s) were mapped to retro_mmus_159 retrocopy
EST ID Start End Identity Match Mis-match Score
AA673540 86576223 86576550 99.1 324 3 321
AA690642 86576035 86576235 99.5 199 0 197
AW259959 86575920 86576167 96 237 10 227
BF123878 86576063 86576391 97.3 326 2 321
CV676679 86576136 86576394 100 257 0 256
CX212840 86576036 86576356 98.5 320 0 318

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_10668819 libraries 1 library 87 libraries 282 libraries 683 libraries
TSS #2 TSS_1066894 libraries 0 libraries 0 libraries 3 libraries 1065 libraries
TSS #3 TSS_10669040 libraries 10 libraries 629 libraries 366 libraries 27 libraries
TSS #4 TSS_10669171 libraries 137 libraries 740 libraries 117 libraries 7 libraries
TSS #5 TSS_106692298 libraries 529 libraries 232 libraries 12 libraries 1 library
TSS #6 TSS_106693492 libraries 447 libraries 109 libraries 15 libraries 9 libraries

The graphical summary, for retro_mmus_159 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_159 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_159 has 8 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4
Pan troglodytes retro_ptro_48
Pongo abelii retro_pabe_191
Macaca mulatta retro_mmul_249
Callithrix jacchus retro_cjac_117
Sus scrofa retro_sscr_15
Canis familiaris retro_cfam_421
Equus caballus retro_ecab_608
Parental genes homology:
Parental genes homology involve 21 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000129201 retrocopy
retro_amel_1842,
Canis familiaris ENSCAFG000000165031 retrocopy
retro_cfam_421,
Callithrix jacchus ENSCJAG000000073171 retrocopy
retro_cjac_117,
Cavia porcellus ENSCPOG000000112661 retrocopy
retro_cpor_86,
Equus caballus ENSECAG000000060201 retrocopy
retro_ecab_608,
Felis catus ENSFCAG000000139321 retrocopy
retro_fcat_21,
Homo sapiens ENSG000000837501 retrocopy
retro_hsap_4,
Gorilla gorilla ENSGGOG000000115011 retrocopy
retro_ggor_65,
Loxodonta africana ENSLAFG000000161441 retrocopy
retro_lafr_102,
Myotis lucifugus ENSMLUG000000157201 retrocopy
retro_mluc_40,
Macaca mulatta ENSMMUG000000176351 retrocopy
retro_mmul_249,
Mustela putorius furoENSMPUG000000037301 retrocopy
retro_mputfur_87,
Mus musculus ENSMUSG00000041658 1 retrocopy
retro_mmus_159 ,
Nomascus leucogenys ENSNLEG000000163501 retrocopy
retro_nleu_13,
Oryctolagus cuniculus ENSOCUG000000086661 retrocopy
retro_ocun_166,
Otolemur garnettii ENSOGAG000000003451 retrocopy
retro_ogar_675,
Procavia capensis ENSPCAG000000034171 retrocopy
retro_pcap_6,
Pongo abelii ENSPPYG000000203981 retrocopy
retro_pabe_191,
Pan troglodytes ENSPTRG000000219551 retrocopy
retro_ptro_48,
Rattus norvegicus ENSRNOG000000031601 retrocopy
retro_rnor_2,
Sus scrofa ENSSSCG000000298001 retrocopy
retro_sscr_15,


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