RetrogeneDB ID:

retro_mmus_274

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:6:86524844..86525915(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000051695
Aliases:Pcbp1, WBP17, [a]CP-1, alphaCP-1
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Pcbp2
Ensembl ID:ENSMUSG00000056851
Aliases:Pcbp2, AW412548, Hnrpx, alphaCP-2
Description:poly(rC) binding protein 2 [Source:MGI Symbol;Acc:MGI:108202]


Retrocopy-Parental alignment summary:






>retro_mmus_274
ATGGACGCCGGTGTGACTGAAAGCGGACTCAACGTGACTCTCACCATTCGGCTGCTGATGCACGGAAAGGAAGTAGGCAG
CATCATCGGGAAGAAAGGGGAGTCGGTGAAGAGGATCCGCGAGGAGAGCGGCGCGCGGATCAACATCTCGGAGGGGAACT
GCCCGGAGAGGATCATCACGCTGACTGGGCCTACCAATGCCATCTTTAAGGCCTTCGCCATGATCATCGACAAGCTGGAG
GAAGATATCAACAGCTCCATGACCAACAGTACGGCGGCCAGCAGGCCCCCGGTCACACTTCGGCTGGTCGTGCCCGCCAC
CCAGTGTGGCTCCCTGATCGGCAAGGGCGGCTGCAAGATCAAGGAGATCCGCGAGAGCACCGGGGCCCAGGTCCAGGTGG
CGGGGGATATGCTGCCCAACTCGACCGAGCGGGCTATCACTATCGCCGGCGTGCCGCAGTCCGTCACCGAGTGTGTGAAG
CAGATCTGCCTGGTCATGCTGGAGACGCTCTCCCAGTCTCCACAGGGGAGAGTCATGACCATCCCGTACCAGCCCATGCC
GGCCAGCTCGCCAGTCATCTGCGCGGGCGGCCAAGATCGCTGCAGCGACGCGGCGGGCTACCCCCACGCCACCCACGACC
TGGAGGGACCACCTCTAGACGCCTACTCGATTCAAGGACAACACACCATTTCTCCGCTGGATCTGGCCAAGCTGAACCAG
GTGGCAAGACAACAGTCTCACTTTGCCATGATGCACGGCGGGACGGGATTCGCCGGAATTGACTCCAGCTCTCCAGAGGT
GAAAGGCTATTGGGCAAGTTTGGATGCATCTACTCAAACCACCCATGAACTCACCATTCCAAATAACTTAATCGGCTGCA
TAATCGGGCGCCAAGGCGCCAACATCAATGAGATCCGCCAGATGTCCGGGGCCCAGATCAAAATTGCCAACCCGGTGGAA
GGCTCTTCTGGAAGGCAGGTCACTATTACTGGCTCGGCTGCCAGTATTAGCCTGGCCCAGTATCTAATCAATGCCAGGCT
TTCCTCTGAGAAGGGGATGGGGTGCAGCTAG

ORF - retro_mmus_274 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.58 %
Parental protein coverage: 57.73 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMDTGVIEGGLNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFK
MD.GV.E.GLNVTLTIRLLMHGKEVGSIIGKKGESVK..REESGARINISEGNCPERIITL.GPTNAIFK
RetrocopyMDAGVTESGLNVTLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFK
ParentalAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
AFAMIIDKLEEDI.SSMTNSTAASRPPVTLRLVVPA.QCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
RetrocopyAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
ParentalSTERAITIAGIPQSIIECVKQICVVMLES---PPKG--VTIPYRPKPSSSPVIFAGGQDRYSTGSDSASF
STERAITIAG.PQS..ECVKQIC.VMLE.....P.G...TIPY.P.P.SSPVI.AGGQDR.S...D.A..
RetrocopySTERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPYQPMPASSPVICAGGQDRCS---DAAGY
ParentalPHTT
PH.T
RetrocopyPHAT

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 72 .17 RPM 134 .13 RPM
SRP007412_cerebellum 95 .92 RPM 161 .53 RPM
SRP007412_heart 94 .45 RPM 131 .68 RPM
SRP007412_kidney 131 .42 RPM 169 .69 RPM
SRP007412_liver 107 .90 RPM 129 .58 RPM
SRP007412_testis 73 .73 RPM 272 .51 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_mmus_274 in 4 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001XVA POLR2A 6:86525115..86526248
ENCFF001YIJ POLR2A 6:86524779..86528619
ENCFF001YJZ POLR2A 6:86525208..86528215
ENCFF001YKA POLR2A 6:86522183..86528161

EST - click to see more details

No EST(s) were mapped for retro_mmus_274 retrocopy.

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_12529915 libraries0 libraries16 libraries146 libraries895 libraries
TSS #2 TSS_12530097 libraries182 libraries692 libraries77 libraries24 libraries
TSS #3 TSS_1253011 library0 libraries0 libraries0 libraries1071 libraries
TSS #4 TSS_12530218 libraries0 libraries24 libraries360 libraries670 libraries

The graphical summary, for retro_mmus_274 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_274 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_274 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 24 parental genes, and 53 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000207571 retrocopy
retro_btau_175,
Canis familiaris ENSCAFG000000068211 retrocopy
retro_cfam_54,
Callithrix jacchus ENSCJAG000000185902 retrocopies
retro_cjac_3253, retro_cjac_754,
Cavia porcellus ENSCPOG000000009672 retrocopies
retro_cpor_193, retro_cpor_97,
Dasypus novemcinctus ENSDNOG000000086886 retrocopies
retro_dnov_1146, retro_dnov_1399, retro_dnov_1672, retro_dnov_1823, retro_dnov_2434, retro_dnov_452,
Equus caballus ENSECAG000000223891 retrocopy
retro_ecab_67,
Echinops telfairi ENSETEG000000147413 retrocopies
retro_etel_1170, retro_etel_2108, retro_etel_840,
Homo sapiens ENSG000001971112 retrocopies
retro_hsap_4077, retro_hsap_83,
Gorilla gorilla ENSGGOG000000126132 retrocopies
retro_ggor_212, retro_ggor_2734,
Macropus eugenii ENSMEUG000000018877 retrocopies
retro_meug_1143, retro_meug_1988, retro_meug_432, retro_meug_526, retro_meug_618, retro_meug_828, retro_meug_964,
Microcebus murinus ENSMICG000000116512 retrocopies
retro_mmur_1226, retro_mmur_1228,
Myotis lucifugus ENSMLUG000000099713 retrocopies
retro_mluc_2199, retro_mluc_314, retro_mluc_571,
Macaca mulatta ENSMMUG000000066082 retrocopies
retro_mmul_1263, retro_mmul_1994,
Mus musculus ENSMUSG000000215462 retrocopies
retro_mmus_1131, retro_mmus_2137,
Mus musculus ENSMUSG00000056851 1 retrocopy
retro_mmus_274 ,
Nomascus leucogenys ENSNLEG000000176931 retrocopy
retro_nleu_10,
Oryctolagus cuniculus ENSOCUG000000224903 retrocopies
retro_ocun_10, retro_ocun_1622, retro_ocun_898,
Pongo abelii ENSPPYG000000045812 retrocopies
retro_pabe_3346, retro_pabe_92,
Pan troglodytes ENSPTRG000000050181 retrocopy
retro_ptro_113,
Pteropus vampyrus ENSPVAG000000122843 retrocopies
retro_pvam_1168, retro_pvam_1369, retro_pvam_868,
Rattus norvegicus ENSRNOG000000368522 retrocopies
retro_rnor_1238, retro_rnor_2088,
Sus scrofa ENSSSCG000000002741 retrocopy
retro_sscr_61,
Ictidomys tridecemlineatus ENSSTOG000000036352 retrocopies
retro_itri_1522, retro_itri_557,
Vicugna pacos ENSVPAG000000004061 retrocopy
retro_vpac_471,


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