RetrogeneDB ID:

retro_mmus_358

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:1:119526510..119527560(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000037015
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:BC023829
Ensembl ID:ENSMUSG00000073139
Aliases:BC023829, Tmem185a
Description:cDNA sequence BC023829 [Source:MGI Symbol;Acc:MGI:2448555]


Retrocopy-Parental alignment summary:






>retro_mmus_358
ATGAACCCCAGGGGCCTGTTCCAGGACTTCAACCCCAGTAAGTTCCTCATTTATGCCTGCTTGCTACTCTTCTCCGTGCT
GCTGCCCCTGCGCCTGGACGGCATCATCCAGTGGAGCTACTGGGCAGTCTTCGCCCCCATCTGGCTGTGGAAGCTCCTGG
TCATCGTGGGCGCCTCGGTGGGTGCGGGCGTGTGGGCCCGCAACCCACGCTACCGTACAGAGGGGGAAGCCTGCGTGGAA
TTCAAAGCCATGCTTATCGCCGTGGGCATCCACCTGCTACTACTCATGTTTGAGATACTAGTCTGCGACAGGGTGGAGAG
GGGCACCCACTTTTGGCTGCTGGTCTTCATGCCACTCTTCTTCGTTTCCCCTGTGTCCGTGGCCGCCTGTGTCTGGGGCT
TCCGACACGACAGGTCTTTGGAACTGGAGATCCTGTGCTCTGTCAACATCCTGCAGTTCATCTTCATCGCCCTGAGGCTG
GACAGGATTATCCACTGGCCGTGGCTAGTGGTGTTCGTGCCCCTGTGGATCCTCATGTCATTCCTCTGCCTGGTAGTTCT
CTATTACATCGTGTGGTCCCTCCTATTCCTGCGGTCCCTGGATGTGGTTGCAGAGCAGCGAAGAACACATGTGACCATGG
CCATCAGCTGGATCACCATTGTCGTGCCCCTGCTCATTTTTGAGGTCCTGCTAGTTCACAGACTGGATGACCACAATACG
TTCTCTTACATTTCCATTTTCATCCCGCTTTGGCTCTCATTACTGACTTTGATGGCTACAACGTTCAGGCGGAAAGGGGG
CAATCATTGGTGGTTTGGGATTCGCAGGGATTTCTGTCAGTTTCTACTAGAAGTTTTTCCGTTTTTAAGAGAATATGGAA
ATATCTCTTACGATCTCCATCACGAAGACAGTGAAGATGCTGAAGACGCATCGGTGTCAGAAGCTCCGAAAATTGCTCCA
ATGTTTGGAAAGAAGGCGCGGGTAGTTATAACACAGAGCCCTGGGAAATATGTGCCTCCACCTCCCAAGTTAAACATTGA
TATGCCAGAC

ORF - retro_mmus_358 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.29 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMNLRGLFQDFNPSKFLIYACLLLFSVLLALRLDGIIQWSYWAVFAPIWLWKLMVIVGASVGTGVWARNPQ
MN.RGLFQDFNPSKFLIYACLLLFSVLL.LRLDGIIQWSYWAVFAPIWLWKL.VIVGASVG.GVWARNP.
RetrocopyMNPRGLFQDFNPSKFLIYACLLLFSVLLPLRLDGIIQWSYWAVFAPIWLWKLLVIVGASVGAGVWARNPR
ParentalYRAEGETCVEFKAMLIAVGIHLLLLMFEVLVCDRIERGSHFWLLVFMPLFFVSPVSVAACVWGFRHDRSL
YR.EGE.CVEFKAMLIAVGIHLLLLMFE.LVCDR.ERG.HFWLLVFMPLFFVSPVSVAACVWGFRHDRSL
RetrocopyYRTEGEACVEFKAMLIAVGIHLLLLMFEILVCDRVERGTHFWLLVFMPLFFVSPVSVAACVWGFRHDRSL
ParentalELEILCSVNILQFIFIALRLDKIIHWPWLVVCVPLWILMSFLCLVVLYYIVWSVLFLRSMDVIAEQRRTH
ELEILCSVNILQFIFIALRLD.IIHWPWLVV.VPLWILMSFLCLVVLYYIVWS.LFLRS.DV.AEQRRTH
RetrocopyELEILCSVNILQFIFIALRLDRIIHWPWLVVFVPLWILMSFLCLVVLYYIVWSLLFLRSLDVVAEQRRTH
ParentalITMALSWMTIVVPLLTFEILLVHKLDGHNAFSCIPIFVPLWLSLITLMATTFGQKGGNHWWFGIRKDFCQ
.TMA.SW.TIVVPLL.FE.LLVH.LD.HN.FS.I.IF.PLWLSL.TLMATTF..KGGNHWWFGIR.DFCQ
RetrocopyVTMAISWITIVVPLLIFEVLLVHRLDDHNTFSYISIFIPLWLSLLTLMATTFRRKGGNHWWFGIRRDFCQ
ParentalFLLEIFPFLREYGNISYDLHHEDSEETEETPVPEPPKIAPMFRKKARVVITQSPGKYVLPPPKLNIEMPD
FLLE.FPFLREYGNISYDLHHEDSE..E...V.E.PKIAPMF.KKARVVITQSPGKYV.PPPKLNI.MPD
RetrocopyFLLEVFPFLREYGNISYDLHHEDSEDAEDASVSEAPKIAPMFGKKARVVITQSPGKYVPPPPKLNIDMPD

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 6 .45 RPM 34 .48 RPM
SRP007412_cerebellum 6 .64 RPM 31 .31 RPM
SRP007412_heart 6 .97 RPM 16 .72 RPM
SRP007412_kidney 12 .32 RPM 22 .58 RPM
SRP007412_liver 5 .16 RPM 21 .03 RPM
SRP007412_testis 6 .86 RPM 13 .58 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_mmus_358 in 3 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001XVA POLR2A 1:119525846..119526680
ENCFF001YIJ POLR2A 1:119525842..119526794
ENCFF001YKA POLR2A 1:119525160..119530127

EST - click to see more details

2 EST(s) were mapped to retro_mmus_358 retrocopy
EST ID Start End Identity Match Mis-match Score
AW455820 119526517 119526772 98.9 252 3 249
D21770 119526555 119526887 98.2 325 1 316

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_6824410 libraries0 libraries9 libraries74 libraries979 libraries
TSS #2 TSS_68245247 libraries529 libraries281 libraries15 libraries0 libraries

The graphical summary, for retro_mmus_358 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_358 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_358 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_104
Gorilla gorilla retro_ggor_189
Pongo abelii retro_pabe_118
Macaca mulatta retro_mmul_310
Rattus norvegicus retro_rnor_6
Parental genes homology:
Parental genes homology involve 26 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000086371 retrocopy
retro_acar_65,
Ailuropoda melanoleuca ENSAMEG000000093511 retrocopy
retro_amel_8,
Bos taurus ENSBTAG000000068181 retrocopy
retro_btau_1,
Canis familiaris ENSCAFG000000191031 retrocopy
retro_cfam_159,
Cavia porcellus ENSCPOG000000036221 retrocopy
retro_cpor_5,
Dasypus novemcinctus ENSDNOG000000118641 retrocopy
retro_dnov_2451,
Dipodomys ordii ENSDORG000000150271 retrocopy
retro_dord_67,
Equus caballus ENSECAG000000093991 retrocopy
retro_ecab_426,
Felis catus ENSFCAG000000244831 retrocopy
retro_fcat_1116,
Homo sapiens ENSG000001559841 retrocopy
retro_hsap_104,
Gorilla gorilla ENSGGOG000000242681 retrocopy
retro_ggor_189,
Loxodonta africana ENSLAFG000000030441 retrocopy
retro_lafr_898,
Microcebus murinus ENSMICG000000046391 retrocopy
retro_mmur_106,
Myotis lucifugus ENSMLUG000000013191 retrocopy
retro_mluc_2075,
Macaca mulatta ENSMMUG000000028881 retrocopy
retro_mmul_310,
Mustela putorius furoENSMPUG000000118961 retrocopy
retro_mputfur_46,
Mus musculus ENSMUSG00000073139 1 retrocopy
retro_mmus_358 ,
Nomascus leucogenys ENSNLEG000000134871 retrocopy
retro_nleu_2723,
Otolemur garnettii ENSOGAG000000164141 retrocopy
retro_ogar_88,
Procavia capensis ENSPCAG000000091601 retrocopy
retro_pcap_260,
Pongo abelii ENSPPYG000000208091 retrocopy
retro_pabe_118,
Pteropus vampyrus ENSPVAG000000138221 retrocopy
retro_pvam_30,
Rattus norvegicus ENSRNOG000000110471 retrocopy
retro_rnor_6,
Sus scrofa ENSSSCG000000127391 retrocopy
retro_sscr_494,
Ictidomys tridecemlineatus ENSSTOG000000144841 retrocopy
retro_itri_8,
Tursiops truncatus ENSTTRG000000006431 retrocopy
retro_ttru_868,


Copyright © RetrogeneDB 2014-2017