RetrogeneDB ID:

retro_mmus_1453

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:16:23050281..23050851(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Rps3
Ensembl ID:ENSMUSG00000030744
Aliases:Rps3, D7Ertd795e, Rs_3
Description:ribosomal protein S3 [Source:MGI Symbol;Acc:MGI:1350917]


Retrocopy-Parental alignment summary:






>retro_mmus_1453
AGGACACAGAATGTTCTTGGGGAGAAGGGTCGTTGGATCAGAGAGTTGACCACAGTTGGCCAGAAGCTCTTTGGCTTCCC
TGAAGGCAGTGTAGAGCTTTATACAGAGAAAGTGGCCACAAGAGGTCTGTGTGCCATTGCCCAGGCAGAGTCTCTACGCT
ACAAACTCCTAGGGGGGCTTGGGGTTCGAAGGGCCTGCTATGGTGTGCTTCGGTTCACTATGGAGAGTGGGGCCAAGGAC
TGAGAGGTTGTGGTGTCTGGGAAGCTCCAAGGACAGAGGGCCAAGTCCATGAAGTTTGTGGATGGTCTGATGATTCACAG
TGGAGACCCTGTTAACTACTAGGTCGGCACAGCCGTGCGCCATGTGCTCCTCAGACAGGGTGTGCTAGGCATCAAAGTGA
AGATCATGCTGCCCTGGGACCCAAGTGGTAAGATTGGTCCCAAGAAGCCTTTGCCTGATCATGTGAGCATCGCAGAACCT
AAAGATGAAATCCTGCCCACAACCCCCATCTCCGAACAGAAGGATGGGAAGCCAGAGCCACCGGCCATGCCCCAGCCAGT
GCCAACAGCA

ORF - retro_mmus_1453 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.63 %
Parental protein coverage: 78.19 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRTQNVLGEKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVL
RTQNVLGEKGR.IRELT.V.QK.FGFPEGSVELY.EKVATRGLCAIAQAESLRYKLLGGL.VRRACYGVL
RetrocopyRTQNVLGEKGRWIRELTTVGQKLFGFPEGSVELYTEKVATRGLCAIAQAESLRYKLLGGLGVRRACYGVL
ParentalRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWD
RF.MESGAK..EVVVSGKL.GQRAKSMKFVDGLMIHSGDPVNY.V.TAVRHVLLRQGVLGIKVKIMLPWD
RetrocopyRFTMESGAKD*EVVVSGKLQGQRAKSMKFVDGLMIHSGDPVNY*VGTAVRHVLLRQGVLGIKVKIMLPWD
ParentalPSGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPVPTA
PSGKIGPKKPLPDHVSI.EPKDEILPTTPISEQK.GKPEPPAMPQPVPTA
RetrocopyPSGKIGPKKPLPDHVSIAEPKDEILPTTPISEQKDGKPEPPAMPQPVPTA

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 163 .56 RPM
SRP007412_cerebellum 0 .22 RPM 152 .50 RPM
SRP007412_heart 0 .06 RPM 212 .46 RPM
SRP007412_kidney 0 .27 RPM 257 .79 RPM
SRP007412_liver 0 .25 RPM 188 .29 RPM
SRP007412_testis 0 .09 RPM 73 .50 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_1453 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_1453 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_45904217 libraries280 libraries354 libraries178 libraries43 libraries

The graphical summary, for retro_mmus_1453 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_1453 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1453 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 30 parental genes, and 97 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000170512 retrocopies
retro_amel_1483, retro_amel_465,
Bos taurus ENSBTAG000000056204 retrocopies
retro_btau_1626, retro_btau_425, retro_btau_909, retro_btau_924,
Canis familiaris ENSCAFG000000054022 retrocopies
retro_cfam_1411, retro_cfam_1569,
Choloepus hoffmanni ENSCHOG000000053288 retrocopies
retro_chof_1301, retro_chof_1369, retro_chof_1492, retro_chof_199, retro_chof_2477, retro_chof_2506, retro_chof_452, retro_chof_571,
Callithrix jacchus ENSCJAG000000154244 retrocopies
retro_cjac_2355, retro_cjac_2593, retro_cjac_388, retro_cjac_3963,
Cavia porcellus ENSCPOG000000046651 retrocopy
retro_cpor_995,
Dipodomys ordii ENSDORG000000029742 retrocopies
retro_dord_608, retro_dord_758,
Equus caballus ENSECAG000000139152 retrocopies
retro_ecab_588, retro_ecab_96,
Echinops telfairi ENSETEG000000155003 retrocopies
retro_etel_1225, retro_etel_1757, retro_etel_857,
Felis catus ENSFCAG000000119423 retrocopies
retro_fcat_1462, retro_fcat_1490, retro_fcat_981,
Homo sapiens ENSG000001492734 retrocopies
retro_hsap_1124, retro_hsap_1655, retro_hsap_2736, retro_hsap_3552,
Gorilla gorilla ENSGGOG000000065194 retrocopies
retro_ggor_1248, retro_ggor_1509, retro_ggor_216, retro_ggor_878,
Loxodonta africana ENSLAFG000000042973 retrocopies
retro_lafr_278, retro_lafr_600, retro_lafr_861,
Macropus eugenii ENSMEUG000000115814 retrocopies
retro_meug_1724, retro_meug_399, retro_meug_431, retro_meug_774,
Myotis lucifugus ENSMLUG000000040793 retrocopies
retro_mluc_1092, retro_mluc_680, retro_mluc_934,
Macaca mulatta ENSMMUG000000090196 retrocopies
retro_mmul_1166, retro_mmul_1634, retro_mmul_1779, retro_mmul_1816, retro_mmul_665, retro_mmul_871,
Monodelphis domestica ENSMODG000000069451 retrocopy
retro_mdom_304,
Mustela putorius furoENSMPUG000000091973 retrocopies
retro_mputfur_412, retro_mputfur_443, retro_mputfur_936,
Mus musculus ENSMUSG00000030744 2 retrocopies
retro_mmus_1453 , retro_mmus_1776,
Nomascus leucogenys ENSNLEG000000269152 retrocopies
retro_nleu_103, retro_nleu_236,
Oryctolagus cuniculus ENSOCUG000000224123 retrocopies
retro_ocun_11, retro_ocun_1934, retro_ocun_787,
Otolemur garnettii ENSOGAG000000053187 retrocopies
retro_ogar_1180, retro_ogar_1354, retro_ogar_1559, retro_ogar_1574, retro_ogar_2577, retro_ogar_2786, retro_ogar_999,
Pongo abelii ENSPPYG000000036884 retrocopies
retro_pabe_1367, retro_pabe_2274, retro_pabe_2933, retro_pabe_929,
Pteropus vampyrus ENSPVAG000000112711 retrocopy
retro_pvam_1388,
Rattus norvegicus ENSRNOG000000174183 retrocopies
retro_rnor_2328, retro_rnor_283, retro_rnor_930,
Sarcophilus harrisii ENSSHAG000000111981 retrocopy
retro_shar_705,
Sus scrofa ENSSSCG000000148554 retrocopies
retro_sscr_283, retro_sscr_556, retro_sscr_568, retro_sscr_900,
Tupaia belangeri ENSTBEG000000070534 retrocopies
retro_tbel_1194, retro_tbel_2090, retro_tbel_265, retro_tbel_4262,
Tursiops truncatus ENSTTRG000000058585 retrocopies
retro_ttru_1108, retro_ttru_1413, retro_ttru_1927, retro_ttru_50, retro_ttru_544,
Vicugna pacos ENSVPAG000000116152 retrocopies
retro_vpac_131, retro_vpac_145,


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