RetrogeneDB ID:

retro_hsap_3476

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:56894385..56894671(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:C2orf15
Ensembl ID:ENSG00000241962
Aliases:MRPL30, L28MT, L30MT, MRP-L28, MRP-L30, MRPL28, MRPL28M, RPML28
Description:chromosome 2 open reading frame 15 [Source:HGNC Symbol;Acc:28436]


Retrocopy-Parental alignment summary:






>retro_hsap_3476
AGTCTCATTTGTACAGATTGGATTCGTCACAAATTCACCAGATCAAAAATTCCAGATAAAGTGTTTCACGCCTCACCTGA
AGATCATGAAAAATATGGTGGGGATCCACAGAACCCTCATAAACTGCATATTGTTACCAGAATAAAAAGTACAAAATACG
TCCATATTGGGAAAAAGATATAATAAAGAAGCTTGGATTGGAAAAATCACATATCCCTCAAGTTCACCAGAATTCCCTTC
AGTGAATGCAAAATTGAAAGTGGTTAAGCATTTGATAAGAATTGAA

ORF - retro_hsap_3476 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.73 %
Parental protein coverage: 59.63 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalSLICTDWIRHKFTRSRIPEKVFQASPEDHEKYGGDPQNPHKLHIVTRIKSTRR-RPYWEKDIIKMLGLEK
SLICTDWIRHKFTRS.IP.KVF.ASPEDHEKYGGDPQNPHKLHIVTRIKST...RPYWEKDIIK.LGLEK
RetrocopySLICTDWIRHKFTRSKIPDKVFHASPEDHEKYGGDPQNPHKLHIVTRIKSTKY<RPYWEKDIIKKLGLEK
ParentalAHTPQVHKN-IPSVNAKLKVVKHLIRIK
.H.PQVH.N..PSVNAKLKVVKHLIRI.
RetrocopySHIPQVHQN<FPSVNAKLKVVKHLIRIE

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
bodymap2_adipose 0 .00 RPM 0 .54 RPM
bodymap2_adrenal 0 .00 RPM 2 .23 RPM
bodymap2_brain 0 .00 RPM 2 .77 RPM
bodymap2_breast 0 .00 RPM 2 .10 RPM
bodymap2_colon 0 .00 RPM 0 .37 RPM
bodymap2_heart 0 .00 RPM 0 .31 RPM
bodymap2_kidney 0 .00 RPM 6 .25 RPM
bodymap2_liver 0 .00 RPM 0 .27 RPM
bodymap2_lung 0 .00 RPM 0 .65 RPM
bodymap2_lymph_node 0 .09 RPM 2 .19 RPM
bodymap2_ovary 0 .00 RPM 1 .91 RPM
bodymap2_prostate 0 .16 RPM 1 .92 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .18 RPM
bodymap2_testis 0 .00 RPM 3 .09 RPM
bodymap2_thyroid 0 .00 RPM 3 .37 RPM
bodymap2_white_blood_cells 0 .16 RPM 1 .10 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3476 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3476 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_1670171247 libraries559 libraries23 libraries0 libraries0 libraries

The graphical summary, for retro_hsap_3476 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 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_hsap_3476 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3476 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2356
Gorilla gorilla retro_ggor_2343
Parental genes homology:
Parental genes homology involve 26 parental genes, and 77 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000133441 retrocopy
retro_amel_1121,
Bos taurus ENSBTAG000000389491 retrocopy
retro_btau_1542,
Canis familiaris ENSCAFG000000316281 retrocopy
retro_cfam_1703,
Choloepus hoffmanni ENSCHOG000000058042 retrocopies
retro_chof_2339, retro_chof_715,
Callithrix jacchus ENSCJAG000000070851 retrocopy
retro_cjac_758,
Dasypus novemcinctus ENSDNOG000000186485 retrocopies
retro_dnov_1430, retro_dnov_1469, retro_dnov_2019, retro_dnov_2348, retro_dnov_571,
Equus caballus ENSECAG000000159931 retrocopy
retro_ecab_309,
Echinops telfairi ENSETEG000000050064 retrocopies
retro_etel_168, retro_etel_2176, retro_etel_232, retro_etel_605,
Felis catus ENSFCAG000000242334 retrocopies
retro_fcat_1430, retro_fcat_196, retro_fcat_528, retro_fcat_669,
Homo sapiens ENSG00000241962 2 retrocopies
retro_hsap_3476 , retro_hsap_981,
Gorilla gorilla ENSGGOG000000116772 retrocopies
retro_ggor_2343, retro_ggor_783,
Microcebus murinus ENSMICG000000116274 retrocopies
retro_mmur_109, retro_mmur_1281, retro_mmur_61, retro_mmur_897,
Myotis lucifugus ENSMLUG000000298512 retrocopies
retro_mluc_1543, retro_mluc_1786,
Mustela putorius furoENSMPUG000000110851 retrocopy
retro_mputfur_214,
Mus musculus ENSMUSG000000260877 retrocopies
retro_mmus_1171, retro_mmus_1367, retro_mmus_1758, retro_mmus_331, retro_mmus_3680, retro_mmus_3724, retro_mmus_755,
Nomascus leucogenys ENSNLEG000000269742 retrocopies
retro_nleu_2761, retro_nleu_337,
Oryctolagus cuniculus ENSOCUG000000041111 retrocopy
retro_ocun_1946,
Otolemur garnettii ENSOGAG0000000224111 retrocopies
retro_ogar_1328, retro_ogar_1429, retro_ogar_2160, retro_ogar_2277, retro_ogar_2389, retro_ogar_3516, retro_ogar_401, retro_ogar_466, retro_ogar_549, retro_ogar_879, retro_ogar_908,
Ochotona princeps ENSOPRG000000073312 retrocopies
retro_opri_826, retro_opri_989,
Pan troglodytes ENSPTRG000000122752 retrocopies
retro_ptro_2356, retro_ptro_765,
Pteropus vampyrus ENSPVAG000000065875 retrocopies
retro_pvam_1469, retro_pvam_1484, retro_pvam_321, retro_pvam_432, retro_pvam_764,
Rattus norvegicus ENSRNOG000000185116 retrocopies
retro_rnor_2018, retro_rnor_2683, retro_rnor_2684, retro_rnor_2873, retro_rnor_570, retro_rnor_916,
Rattus norvegicus ENSRNOG000000493301 retrocopy
retro_rnor_2976,
Sus scrofa ENSSSCG000000081832 retrocopies
retro_sscr_529, retro_sscr_555,
Tarsius syrichta ENSTSYG000000053454 retrocopies
retro_tsyr_1736, retro_tsyr_2153, retro_tsyr_368, retro_tsyr_866,
Tursiops truncatus ENSTTRG000000049373 retrocopies
retro_ttru_1126, retro_ttru_1379, retro_ttru_78,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.03 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).





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