RetrogeneDB ID:

retro_mmus_138

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:6:135309783..135310347(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000047104
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Pebp1
Ensembl ID:ENSMUSG00000032959
Aliases:Pebp1, HCNP, Pbp, Pbp1, Pbpr, Rkip
Description:phosphatidylethanolamine binding protein 1 [Source:MGI Symbol;Acc:MGI:1344408]


Retrocopy-Parental alignment summary:






>retro_mmus_138
ATGCCTACAGACATGAGCATGTGGACCGGGCCGCTGAGCCTCCACGAAGTGGATGAGCAGCCCCAGCACCTACTGCGGGT
CACCTACACCGAGGCGGAGGTGGAAGAGCTGGGCCAAGTGCTGACGCCCACCCAGGTTAAGCACAGACCCGGAAGCATTT
CATGGGATGGCCTTGACACAGGGAAACTCTACACCTTGATCCTCACAGACCCGGATGCTCCCAGTAGGAAGAAACCCGTG
TACAGGGAATGGCACCATTTTCTGGTGGTCAACATGAAAGGCAATGACATCAGCAGTGGGAACGTCCTCTCGGATTACGT
GGGTTCCGGACCTCCCAAGGGCACTGGCCTCCATCGCTATGTCTGGCTGGTGTACCAGCAGGACAAGCCACTGAGATGTG
ACGAACCCATCCTCACCAACCGGTCTGGAGACCATCGTGGGAAGTTCAAAACTGCAGCCTTCCGCAAGAAGTATCACCTG
GGAGCCCCGGTGGCCGGCACGTGTTACCAGGCAGAATGGGACAGCTATGTACCAAAGCTGTACAAACAGCTGTCTGGGAA
ATAG

ORF - retro_mmus_138 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.14 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAADISQWAGPLCLQEVDEPPQHALRVDYAGVTVDELGKVLTPTQVMNRPSSISWDGLDPGKLYTLVLTD
M..D.S.W.GPL.L.EVDE.PQH.LRV.Y....V.ELG.VLTPTQV..RP.SISWDGLD.GKLYTL.LTD
RetrocopyMPTDMSMWTGPLSLHEVDEQPQHLLRVTYTEAEVEELGQVLTPTQVKHRPGSISWDGLDTGKLYTLILTD
ParentalPDAPSRKDPKFREWHHFLVVNMKGNDISSGTVLSDYVGSGPPSGTGLHRYVWLVYEQEQPLSCDEPILSN
PDAPSRK.P..REWHHFLVVNMKGNDISSG.VLSDYVGSGPP.GTGLHRYVWLVY.Q..PL.CDEPIL.N
RetrocopyPDAPSRKKPVYREWHHFLVVNMKGNDISSGNVLSDYVGSGPPKGTGLHRYVWLVYQQDKPLRCDEPILTN
ParentalKSGDNRGKFKVETFRKKYNLGAPVAGTCYQAEWDDYVPKLYEQLSGK
.SGD.RGKFK...FRKKY.LGAPVAGTCYQAEWD.YVPKLY.QLSGK
RetrocopyRSGDHRGKFKTAAFRKKYHLGAPVAGTCYQAEWDSYVPKLYKQLSGK

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 .07 RPM 66 .21 RPM
SRP007412_cerebellum 0 .00 RPM 54 .32 RPM
SRP007412_heart 0 .00 RPM 46 .63 RPM
SRP007412_kidney 0 .02 RPM 53 .36 RPM
SRP007412_liver 0 .00 RPM 45 .36 RPM
SRP007412_testis 47 .29 RPM 301 .74 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_138 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_138 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_1196181063 libraries2 libraries1 library2 libraries4 libraries
TSS #2 TSS_1196191065 libraries2 libraries2 libraries0 libraries3 libraries

The graphical summary, for retro_mmus_138 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_138 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_138 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Rattus norvegicus retro_rnor_46
Parental genes homology:
Parental genes homology involve 21 parental genes, and 52 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000161432 retrocopies
retro_amel_1355, retro_amel_754,
Bos taurus ENSBTAG000000181152 retrocopies
retro_btau_1183, retro_btau_705,
Canis familiaris ENSCAFG000000099101 retrocopy
retro_cfam_526,
Callithrix jacchus ENSCJAG000000093142 retrocopies
retro_cjac_1410, retro_cjac_818,
Erinaceus europaeus ENSEEUG000000036891 retrocopy
retro_eeur_292,
Felis catus ENSFCAG000000022773 retrocopies
retro_fcat_1317, retro_fcat_1360, retro_fcat_299,
Homo sapiens ENSG000000892203 retrocopies
retro_hsap_1456, retro_hsap_2288, retro_hsap_492,
Gorilla gorilla ENSGGOG000000132813 retrocopies
retro_ggor_1121, retro_ggor_1701, retro_ggor_461,
Myotis lucifugus ENSMLUG000000022597 retrocopies
retro_mluc_103, retro_mluc_1612, retro_mluc_1742, retro_mluc_2357, retro_mluc_2373, retro_mluc_984, retro_mluc_998,
Macaca mulatta ENSMMUG000000050984 retrocopies
retro_mmul_1621, retro_mmul_2272, retro_mmul_328, retro_mmul_442,
Mustela putorius furoENSMPUG000000028613 retrocopies
retro_mputfur_1228, retro_mputfur_1361, retro_mputfur_223,
Mus musculus ENSMUSG00000032959 4 retrocopies
retro_mmus_138 , retro_mmus_1857, retro_mmus_2314, retro_mmus_542,
Nomascus leucogenys ENSNLEG000000003221 retrocopy
retro_nleu_1966,
Oryctolagus cuniculus ENSOCUG000000083952 retrocopies
retro_ocun_1329, retro_ocun_1900,
Otolemur garnettii ENSOGAG000000017401 retrocopy
retro_ogar_2750,
Pongo abelii ENSPPYG000000050112 retrocopies
retro_pabe_1202, retro_pabe_241,
Pan troglodytes ENSPTRG000000055123 retrocopies
retro_ptro_1621, retro_ptro_371, retro_ptro_992,
Rattus norvegicus ENSRNOG000000011363 retrocopies
retro_rnor_1223, retro_rnor_46, retro_rnor_541,
Ictidomys tridecemlineatus ENSSTOG000000040852 retrocopies
retro_itri_1603, retro_itri_961,
Tupaia belangeri ENSTBEG000000001772 retrocopies
retro_tbel_272, retro_tbel_2728,
Tursiops truncatus ENSTTRG000000006581 retrocopy
retro_ttru_1164,


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