RetrogeneDB ID:

retro_mmus_163

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:4:133601022..133601769(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000047281
Aliases:Sfn, Er, Mme1, Ywhas
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Ywhaz
Ensembl ID:ENSMUSG00000022285
Aliases:Ywhaz, 1110013I11Rik, 14-3-3zeta, AI596267, AL022924, AU020854
Description:tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide [Source:MGI Symbol;Acc:MGI:109484]


Retrocopy-Parental alignment summary:






>retro_mmus_163
ATGGAGAGAGCCAGTCTGATCCAGAAGGCCAAGTTGGCTGAACAGGCCGAACGGTATGAAGACATGGCAGCTTTCATGAA
GAGCGCCGTGGAAAAGGGCGAGGAGCTCTCCTGCGAGGAGCGAAACCTGCTTTCCGTAGCTTACAAGAACGTGGTGGGCG
GCCAGAGAGCGGCCTGGAGGGTCCTGTCCAGCATCGAGCAGAAGAGCAACGAGGAGGGGTCAGAAGAGAAGGGCCCCGAG
GTGAAAGAGTACCGGGAGAAGGTAGAGACCGAGCTCAGAGGTGTGTGCGACACCGTACTCGGCCTGCTGGACTCGCACCT
CATCAAAGGGGCTGGAGATGCAGAGAGCCGCGTCTTCTACCTGAAGATGAAGGGTGACTACTACCGCTACCTAGCCGAGG
TGGCCACTGGCGATGACAAGAAGCGCATCATCGATTCTGCCCGGTCAGCCTACCAGGAGGCCATGGACATCAGCAAGAAG
GAGATGCCGCCTACCAACCCCATCCGCCTGGGCCTGGCCCTGAACTTTTCAGTCTTCCACTACGAGATAGCCAACAGCCC
CGAGGAGGCCATCTCGCTGGCCAAGACCACCTTCGACGAGGCCATGGCCGACCTGCACACCCTCAGTGAGGACTCCTACA
AGGACAGCACCCTCATCATGCAGCTCCTGAGAGACAACCTGACGCTGTGGACAGCCGACAGTGCTGGGGAAGAGGGTGGT
GAGGCTCCGGAGGAGCCCCAGAGCTGA

ORF - retro_mmus_163 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.27 %
Parental protein coverage: 96.33 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKT-
M....L.QKAKLAEQAERY.DMAA.MKS..E.G.ELS.EERNLLSVAYKNVVG..R..WRV.SSIEQK..
RetrocopyMERASLIQKAKLAEQAERYEDMAAFMKSAVEKGEELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSN
Parental-EGAEKKQQMAREYREKIETELRDICNDVLSLLEKFLIPNASQPESKVFYLKMKGDYYRYLAEVAAGDDK
.EG.E.K.....EYREK.ETELR..C..VL.LL...LI..A...ES.VFYLKMKGDYYRYLAEVA.GDDK
RetrocopyEEGSEEKGPEVKEYREKVETELRGVCDTVLGLLDSHLIKGAGDAESRVFYLKMKGDYYRYLAEVATGDDK
ParentalKGIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLSE
K.I.D....AYQEA..ISKKEM.PT.PIRLGLALNFSVF.YEI.NSPE.A.SLAKT.FDEA.A.L.TLSE
RetrocopyKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSE
ParentalESYKDSTLIMQLLRDNLTLWTSDTQGDE
.SYKDSTLIMQLLRDNLTLWT.D..G.E
RetrocopyDSYKDSTLIMQLLRDNLTLWTADSAGEE

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 .65 RPM 458 .26 RPM
SRP007412_cerebellum 0 .56 RPM 217 .63 RPM
SRP007412_heart 0 .93 RPM 51 .05 RPM
SRP007412_kidney 1 .39 RPM 179 .21 RPM
SRP007412_liver 0 .22 RPM 47 .57 RPM
SRP007412_testis 0 .05 RPM 65 .77 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_163 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_163 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_101345662 libraries68 libraries130 libraries53 libraries159 libraries
TSS #2 TSS_101346640 libraries77 libraries132 libraries62 libraries161 libraries
TSS #3 TSS_101347694 libraries131 libraries181 libraries52 libraries14 libraries
TSS #4 TSS_101348747 libraries169 libraries117 libraries34 libraries5 libraries

The graphical summary, for retro_mmus_163 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_163 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_163 has 10 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_8
Pan troglodytes retro_ptro_3
Gorilla gorilla retro_ggor_211
Pongo abelii retro_pabe_103
Callithrix jacchus retro_cjac_31
Oryctolagus cuniculus retro_ocun_248
Bos taurus retro_btau_86
Sus scrofa retro_sscr_35
Canis familiaris retro_cfam_233
Equus caballus retro_ecab_31
Parental genes homology:
Parental genes homology involve 35 parental genes, and 143 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000086942 retrocopies
retro_acar_25, retro_acar_44,
Ailuropoda melanoleuca ENSAMEG000000003281 retrocopy
retro_amel_562,
Bos taurus ENSBTAG000000002364 retrocopies
retro_btau_1482, retro_btau_635, retro_btau_68, retro_btau_910,
Canis familiaris ENSCAFG000000005806 retrocopies
retro_cfam_1302, retro_cfam_1521, retro_cfam_158, retro_cfam_1840, retro_cfam_233, retro_cfam_465,
Choloepus hoffmanni ENSCHOG000000027989 retrocopies
retro_chof_1572, retro_chof_1703, retro_chof_1890, retro_chof_2321, retro_chof_2346, retro_chof_2669, retro_chof_292, retro_chof_315, retro_chof_933,
Callithrix jacchus ENSCJAG000000158445 retrocopies
retro_cjac_1769, retro_cjac_2164, retro_cjac_3000, retro_cjac_31, retro_cjac_881,
Cavia porcellus ENSCPOG000000202855 retrocopies
retro_cpor_220, retro_cpor_323, retro_cpor_434, retro_cpor_592, retro_cpor_644,
Dasypus novemcinctus ENSDNOG0000000167210 retrocopies
retro_dnov_1007, retro_dnov_117, retro_dnov_1354, retro_dnov_1579, retro_dnov_1769, retro_dnov_1907, retro_dnov_1993, retro_dnov_2588, retro_dnov_892, retro_dnov_99,
Equus caballus ENSECAG000000218823 retrocopies
retro_ecab_202, retro_ecab_31, retro_ecab_624,
Ficedula albicollis ENSFALG000000058601 retrocopy
retro_falb_13,
Felis catus ENSFCAG000000320174 retrocopies
retro_fcat_1563, retro_fcat_1631, retro_fcat_1697, retro_fcat_60,
Homo sapiens ENSG000001649241 retrocopy
retro_hsap_549,
Gallus gallus ENSGALG000000107251 retrocopy
retro_ggal_3,
Gorilla gorilla ENSGGOG000000221339 retrocopies
retro_ggor_1092, retro_ggor_1754, retro_ggor_211, retro_ggor_2379, retro_ggor_2997, retro_ggor_2998, retro_ggor_3020, retro_ggor_499, retro_ggor_544,
Loxodonta africana ENSLAFG000000049442 retrocopies
retro_lafr_1089, retro_lafr_112,
Myotis lucifugus ENSMLUG000000173233 retrocopies
retro_mluc_1617, retro_mluc_1686, retro_mluc_296,
Macaca mulatta ENSMMUG000000064897 retrocopies
retro_mmul_1859, retro_mmul_1883, retro_mmul_2136, retro_mmul_2247, retro_mmul_2422, retro_mmul_2503, retro_mmul_451,
Monodelphis domestica ENSMODG000000061588 retrocopies
retro_mdom_1589, retro_mdom_1664, retro_mdom_1763, retro_mdom_1815, retro_mdom_1875, retro_mdom_1958, retro_mdom_255, retro_mdom_446,
Mustela putorius furoENSMPUG000000151584 retrocopies
retro_mputfur_1000, retro_mputfur_239, retro_mputfur_7, retro_mputfur_864,
Mus musculus ENSMUSG00000022285 3 retrocopies
retro_mmus_163 , retro_mmus_2187, retro_mmus_744,
Mus musculus ENSMUSG0000007643210 retrocopies
retro_mmus_1076, retro_mmus_1378, retro_mmus_1926, retro_mmus_2250, retro_mmus_2299, retro_mmus_2471, retro_mmus_2689, retro_mmus_3250, retro_mmus_3308, retro_mmus_406,
Nomascus leucogenys ENSNLEG000000032207 retrocopies
retro_nleu_1368, retro_nleu_1426, retro_nleu_2186, retro_nleu_23, retro_nleu_449, retro_nleu_487, retro_nleu_722,
Oryctolagus cuniculus ENSOCUG000000007342 retrocopies
retro_ocun_1091, retro_ocun_248,
Ochotona princeps ENSOPRG000000002763 retrocopies
retro_opri_1218, retro_opri_218, retro_opri_967,
Procavia capensis ENSPCAG000000107441 retrocopy
retro_pcap_170,
Pongo abelii ENSPPYG000000187917 retrocopies
retro_pabe_103, retro_pabe_1242, retro_pabe_2047, retro_pabe_3417, retro_pabe_3740, retro_pabe_556, retro_pabe_89,
Pelodiscus sinensis ENSPSIG000000037031 retrocopy
retro_psin_13,
Pteropus vampyrus ENSPVAG000000166411 retrocopy
retro_pvam_1101,
Sarcophilus harrisii ENSSHAG000000126712 retrocopies
retro_shar_126, retro_shar_409,
Sus scrofa ENSSSCG000000060622 retrocopies
retro_sscr_222, retro_sscr_35,
Ictidomys tridecemlineatus ENSSTOG000000238643 retrocopies
retro_itri_162, retro_itri_483, retro_itri_887,
Taeniopygia guttata ENSTGUG000000120781 retrocopy
retro_tgut_4,
Tarsius syrichta ENSTSYG0000000615010 retrocopies
retro_tsyr_1047, retro_tsyr_1075, retro_tsyr_1419, retro_tsyr_1941, retro_tsyr_2022, retro_tsyr_2066, retro_tsyr_2085, retro_tsyr_720, retro_tsyr_900, retro_tsyr_985,
Tursiops truncatus ENSTTRG000000159064 retrocopies
retro_ttru_15, retro_ttru_1540, retro_ttru_207, retro_ttru_455,
Vicugna pacos ENSVPAG000000058651 retrocopy
retro_vpac_350,


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