RetrogeneDB ID:

retro_mmus_2113

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:2:156347204..156347840(-)
Located in intron of:ENSMUSG00000038085
Retrocopy
information
Ensembl ID:ENSMUSG00000082321
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Pdcd10
Ensembl ID:ENSMUSG00000027835
Aliases:Pdcd10, 2410003B13Rik, Ccm3, Tfa15, Tfar15
Description:programmed cell death 10 [Source:MGI Symbol;Acc:MGI:1928396]


Retrocopy-Parental alignment summary:






>retro_mmus_2113
ATGAGGATGACAATGGAAGAGATGAAGAATGAAGCTGAGATCACTTCCATGGTTTCTATGCCTCTCTATGCAGTCATGTA
TCCTGTGTTTAATGAGCTAGAACGAGTAAATTTGTCTGCAGCTCAGACTCTGAGAGCCGCTTTCATTAAGGCTGAAAAGG
AAAATCCAGGCCTCACACAAGACATCATTATGAAAATATTAGAGAAAAAAAGTGTAGAAGTTAACTTCACTGAGTCCCTC
CTTCGTATGGCAGCTGATGACGTAGAAGAGTACATGATTGAGCGGCCAGAGCCAGAATTCCAGGACCTAAATGAAAAGGC
ACGGGCACTTAAACAGATTCTCAGTAAGATTCCCGATGAGATCAATGACAGAGTGAGGTTTCTGCAGACAATCAAGGATA
TAGCTAGTGCAATAAAAGAACTACTTGATACAGTGAATAATGTCTTCAAAAAATATCAGTACCAGAACCGCAGGGCACTT
GAACACCAAAAGAAAGAATTTGTAAAATACTCCAAAAGTTTCAGTGACACTCTAAAGACTTATTTTAAAGATGGCAAGGC
AATAAATGTGTTCATAAGTGCCAACCGGCTAATTCATCAAACCAACTTGATACTTCAGACCTTCAAAACTGTGGCC

ORF - retro_mmus_2113 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.53 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMRMTMEEMKNEAETTSMVSMPLYAVMYPVFNELERVNLSAAQTLRAAFIKAEKENPGLTQDIIMKILEKK
MRMTMEEMKNEAE.TSMVSMPLYAVMYPVFNELERVNLSAAQTLRAAFIKAEKENPGLTQDIIMKILEKK
RetrocopyMRMTMEEMKNEAEITSMVSMPLYAVMYPVFNELERVNLSAAQTLRAAFIKAEKENPGLTQDIIMKILEKK
ParentalSVEVNFTESLLRMAADDVEEYMIERPEPEFQDLNEKARALKQILSKIPDEINDRVRFLQTIKDIASAIKE
SVEVNFTESLLRMAADDVEEYMIERPEPEFQDLNEKARALKQILSKIPDEINDRVRFLQTIKDIASAIKE
RetrocopySVEVNFTESLLRMAADDVEEYMIERPEPEFQDLNEKARALKQILSKIPDEINDRVRFLQTIKDIASAIKE
ParentalLLDTVNNVFKKYQYQNRRALEHQKKEFVKYSKSFSDTLKTYFKDGKAINVFISANRLIHQTNLILQTFKT
LLDTVNNVFKKYQYQNRRALEHQKKEFVKYSKSFSDTLKTYFKDGKAINVFISANRLIHQTNLILQTFKT
RetrocopyLLDTVNNVFKKYQYQNRRALEHQKKEFVKYSKSFSDTLKTYFKDGKAINVFISANRLIHQTNLILQTFKT
ParentalVA
VA
RetrocopyVA

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 .23 RPM 13 .11 RPM
SRP007412_cerebellum 0 .04 RPM 8 .73 RPM
SRP007412_heart 0 .06 RPM 4 .42 RPM
SRP007412_kidney 0 .15 RPM 9 .97 RPM
SRP007412_liver 0 .03 RPM 7 .24 RPM
SRP007412_testis 0 .00 RPM 10 .79 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_2113 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_2113 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_82192433 libraries511 libraries123 libraries4 libraries1 library
TSS #2 TSS_82193524 libraries499 libraries47 libraries1 library1 library

The graphical summary, for retro_mmus_2113 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_2113 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2113 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 24 parental genes, and 38 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000021811 retrocopy
retro_amel_420,
Bos taurus ENSBTAG000000317092 retrocopies
retro_btau_1623, retro_btau_713,
Canis familiaris ENSCAFG000000145692 retrocopies
retro_cfam_1988, retro_cfam_687,
Callithrix jacchus ENSCJAG000000027632 retrocopies
retro_cjac_1442, retro_cjac_4178,
Dasypus novemcinctus ENSDNOG000000158541 retrocopy
retro_dnov_351,
Homo sapiens ENSG000001142091 retrocopy
retro_hsap_3953,
Gorilla gorilla ENSGGOG000000086211 retrocopy
retro_ggor_2656,
Loxodonta africana ENSLAFG000000068231 retrocopy
retro_lafr_409,
Microcebus murinus ENSMICG000000070041 retrocopy
retro_mmur_1008,
Myotis lucifugus ENSMLUG000000169781 retrocopy
retro_mluc_1331,
Macaca mulatta ENSMMUG000000059382 retrocopies
retro_mmul_1090, retro_mmul_2288,
Mustela putorius furoENSMPUG000000170751 retrocopy
retro_mputfur_298,
Mus musculus ENSMUSG00000027835 1 retrocopy
retro_mmus_2113 ,
Nomascus leucogenys ENSNLEG000000048741 retrocopy
retro_nleu_532,
Otolemur garnettii ENSOGAG000000138871 retrocopy
retro_ogar_540,
Oreochromis niloticus ENSONIG000000055531 retrocopy
retro_onil_40,
Procavia capensis ENSPCAG000000103851 retrocopy
retro_pcap_283,
Pongo abelii ENSPPYG000000297501 retrocopy
retro_pabe_3257,
Pan troglodytes ENSPTRG000000155981 retrocopy
retro_ptro_2683,
Sarcophilus harrisii ENSSHAG000000054431 retrocopy
retro_shar_414,
Ictidomys tridecemlineatus ENSSTOG000000284423 retrocopies
retro_itri_1208, retro_itri_1377, retro_itri_322,
Tupaia belangeri ENSTBEG000000002409 retrocopies
retro_tbel_1498, retro_tbel_1690, retro_tbel_2223, retro_tbel_2903, retro_tbel_3430, retro_tbel_3898, retro_tbel_3900, retro_tbel_4532, retro_tbel_95,
Tarsius syrichta ENSTSYG000000007081 retrocopy
retro_tsyr_1786,
Tursiops truncatus ENSTTRG000000163151 retrocopy
retro_ttru_635,


Copyright © RetrogeneDB 2014-2017