RetrogeneDB ID:

retro_hsap_2095

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:38708992..38709943(+)
Located in intron of:ENSG00000231367
Retrocopy
information
Ensembl ID:ENSG00000213553
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPLP0
Ensembl ID:ENSG00000089157
Aliases:RPLP0, L10E, LP0, P0, PRLP0, RPP0
Description:ribosomal protein, large, P0 [Source:HGNC Symbol;Acc:10371]


Retrocopy-Parental alignment summary:






>retro_hsap_2095
ATGCCCAGGGAAGACAGGGCGACCTGGAAGTCCAACTACTTCCTTAAGATCATCCAACTATTGGATGATTATCCAAAATG
TTTCATCGTGGGAGCAGACAATGTGGGCTCCAAGCAGATGCAGCAGATCCGCATGTCCCTTCGCGGGAAGGTCGTGGTGC
TGATGGGCAAGAACACCATGATGCGCAAGGCCATCCGAGGGCACCTGGAAAACAACCCAGCTCTGGAGAAACTGCTGCCT
CATATCTGGGGGAATGTGGGCTTTGTGTTCACCAAGGAGGACCTCACTGAGATCAGGGACATGTTGCTGGCCAATAAGGT
GCCAGCTGCTGCCCGTGCTGGTGCCATTGCCCCATGTGAAGTCACTGTGCCAGCCCAGAACACTGGTCTCGGGCCCGAGA
AGACCTCCTTTTTCCAGGCTTTAGGTATCACCACTAAAATCTCCAGGGGCACCATTGAAATCCTGAGTGATGTGCAGCTG
ATCAAGACTGGAGACAAAGTGGGAGCCAGCGAAGCCACGCTGCTGAACATGCTCAACATCTCCCCCTTCTCCTTTGGGCT
GGTCATCCAGCAGGTATTCGACAATGGCAGCATCTACAACCCTGAAGTGCTTGATAAAACAGAGGAAACTCTGCATTCTC
GCTTCCTGGAGGGTGTCCGCAATGTTGCCAGTGTCTGTCTGCAGACTGGCTACCCAACTGTTGCATCAGTACCCCATTCT
ATCATCAACGGGTACAAACGAGTCCTGGCCTTGTCTGTGGAGACGGATTACACCTTCCCACTTGCTGAAAATGTCAAGGC
CTTCTTGGCTGATCCATCTGCCTTTGTGGCTGCTGCCCCTGTGGCTGCTGACACCACAGCTGCTCCTGCTGCTGCTGCAG
CCCCAGCTAAGGTTGAAGCCAAGGAAGAGTCGGAGGAGTCGGACGAGGATATGGGATTTGGTCTCTTTGAC

ORF - retro_hsap_2095 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.11 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPREDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRGKAVVLMGKNTMMRKAIRGHLE
MPREDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRGK.VVLMGKNTMMRKAIRGHLE
RetrocopyMPREDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRGKVVVLMGKNTMMRKAIRGHLE
ParentalNNPALEKLLPHIRGNVGFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCEVTVPAQNTGLGPEKTSFFQA
NNPALEKLLPHI.GNVGFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCEVTVPAQNTGLGPEKTSFFQA
RetrocopyNNPALEKLLPHIWGNVGFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCEVTVPAQNTGLGPEKTSFFQA
ParentalLGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFSFGLVIQQVFDNGSIYNPEVLDITEET
LGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFSFGLVIQQVFDNGSIYNPEVLD.TEET
RetrocopyLGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFSFGLVIQQVFDNGSIYNPEVLDKTEET
ParentalLHSRFLEGVRNVASVCLQIGYPTVASVPHSIINGYKRVLALSVETDYTFPLAEKVKAFLADPSAFVAAAP
LHSRFLEGVRNVASVCLQ.GYPTVASVPHSIINGYKRVLALSVETDYTFPLAE.VKAFLADPSAFVAAAP
RetrocopyLHSRFLEGVRNVASVCLQTGYPTVASVPHSIINGYKRVLALSVETDYTFPLAENVKAFLADPSAFVAAAP
ParentalVAAATTAAPAAAAAPAKVEAKEESEESDEDMGFGLFD
VAA.TTAAPAAAAAPAKVEAKEESEESDEDMGFGLFD
RetrocopyVAADTTAAPAAAAAPAKVEAKEESEESDEDMGFGLFD

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 2 .48 RPM 635 .70 RPM
bodymap2_adrenal 3 .07 RPM 730 .78 RPM
bodymap2_brain 0 .23 RPM 82 .65 RPM
bodymap2_breast 1 .87 RPM 427 .83 RPM
bodymap2_colon 2 .17 RPM 773 .41 RPM
bodymap2_heart 0 .22 RPM 202 .81 RPM
bodymap2_kidney 1 .68 RPM 471 .29 RPM
bodymap2_liver 0 .55 RPM 442 .56 RPM
bodymap2_lung 1 .41 RPM 667 .16 RPM
bodymap2_lymph_node 1 .90 RPM 1096 .55 RPM
bodymap2_ovary 3 .10 RPM 707 .90 RPM
bodymap2_prostate 2 .91 RPM 1087 .79 RPM
bodymap2_skeletal_muscle 2 .47 RPM 558 .44 RPM
bodymap2_testis 1 .04 RPM 383 .53 RPM
bodymap2_thyroid 2 .05 RPM 482 .21 RPM
bodymap2_white_blood_cells 1 .22 RPM 841 .10 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2095 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2095 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_1226192 libraries0 libraries0 libraries1 library1826 libraries
TSS #2 TSS_1226201420 libraries363 libraries45 libraries1 library0 libraries

The graphical summary, for retro_hsap_2095 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_2095 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2095 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 20 parental genes, and 73 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000051444 retrocopies
retro_amel_1179, retro_amel_1194, retro_amel_1377, retro_amel_847,
Canis familiaris ENSCAFG000000102275 retrocopies
retro_cfam_1580, retro_cfam_224, retro_cfam_487, retro_cfam_534, retro_cfam_693,
Choloepus hoffmanni ENSCHOG000000027452 retrocopies
retro_chof_1115, retro_chof_2341,
Callithrix jacchus ENSCJAG000000086773 retrocopies
retro_cjac_1693, retro_cjac_2840, retro_cjac_786,
Cavia porcellus ENSCPOG000000218125 retrocopies
retro_cpor_298, retro_cpor_449, retro_cpor_475, retro_cpor_498, retro_cpor_601,
Equus caballus ENSECAG000000158162 retrocopies
retro_ecab_1090, retro_ecab_585,
Felis catus ENSFCAG000000133541 retrocopy
retro_fcat_441,
Homo sapiens ENSG00000089157 7 retrocopies
retro_hsap_1403, retro_hsap_1553, retro_hsap_1889, retro_hsap_2095 , retro_hsap_2334, retro_hsap_512, retro_hsap_784,
Gorilla gorilla ENSGGOG000000265825 retrocopies
retro_ggor_1088, retro_ggor_1771, retro_ggor_472, retro_ggor_649, retro_ggor_650,
Myotis lucifugus ENSMLUG0000000197011 retrocopies
retro_mluc_1016, retro_mluc_1460, retro_mluc_1503, retro_mluc_1806, retro_mluc_1966, retro_mluc_2293, retro_mluc_268, retro_mluc_497, retro_mluc_564, retro_mluc_565, retro_mluc_882,
Macaca mulatta ENSMMUG000000091572 retrocopies
retro_mmul_2245, retro_mmul_939,
Mus musculus ENSMUSG000000672742 retrocopies
retro_mmus_143, retro_mmus_2249,
Oryctolagus cuniculus ENSOCUG000000057492 retrocopies
retro_ocun_293, retro_ocun_376,
Otolemur garnettii ENSOGAG000000038434 retrocopies
retro_ogar_2184, retro_ogar_2294, retro_ogar_556, retro_ogar_713,
Procavia capensis ENSPCAG000000164296 retrocopies
retro_pcap_232, retro_pcap_314, retro_pcap_339, retro_pcap_353, retro_pcap_408, retro_pcap_67,
Petromyzon marinus ENSPMAG000000013391 retrocopy
retro_pmar_6,
Pongo abelii ENSPPYG000000050225 retrocopies
retro_pabe_2113, retro_pabe_3035, retro_pabe_568, retro_pabe_66, retro_pabe_749,
Rattus norvegicus ENSRNOG000000011483 retrocopies
retro_rnor_1350, retro_rnor_2092, retro_rnor_2970,
Sarcophilus harrisii ENSSHAG000000016232 retrocopies
retro_shar_286, retro_shar_413,
Tursiops truncatus ENSTTRG000000056581 retrocopy
retro_ttru_965,

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 = 19.46 RPM Legend:


Library Retrogene expression
CEU_NA11831 8 .77 RPM
CEU_NA11843 12 .57 RPM
CEU_NA11930 13 .59 RPM
CEU_NA12004 5 .62 RPM
CEU_NA12400 9 .93 RPM
CEU_NA12751 7 .48 RPM
CEU_NA12760 18 .73 RPM
CEU_NA12827 9 .86 RPM
CEU_NA12872 8 .44 RPM
CEU_NA12873 7 .31 RPM
FIN_HG00183 11 .97 RPM
FIN_HG00277 9 .95 RPM
FIN_HG00315 8 .06 RPM
FIN_HG00321 7 .62 RPM
FIN_HG00328 5 .21 RPM
FIN_HG00338 7 .77 RPM
FIN_HG00349 15 .51 RPM
FIN_HG00375 9 .34 RPM
FIN_HG00377 8 .50 RPM
FIN_HG00378 7 .42 RPM
GBR_HG00099 9 .01 RPM
GBR_HG00111 5 .76 RPM
GBR_HG00114 6 .15 RPM
GBR_HG00119 6 .68 RPM
GBR_HG00131 5 .61 RPM
GBR_HG00133 6 .56 RPM
GBR_HG00134 6 .12 RPM
GBR_HG00137 10 .20 RPM
GBR_HG00142 7 .39 RPM
GBR_HG00143 4 .47 RPM
TSI_NA20512 6 .73 RPM
TSI_NA20513 5 .17 RPM
TSI_NA20518 19 .46 RPM
TSI_NA20532 7 .28 RPM
TSI_NA20538 8 .34 RPM
TSI_NA20756 13 .33 RPM
TSI_NA20765 5 .37 RPM
TSI_NA20771 13 .62 RPM
TSI_NA20786 6 .72 RPM
TSI_NA20798 6 .24 RPM
YRI_NA18870 17 .60 RPM
YRI_NA18907 7 .83 RPM
YRI_NA18916 6 .48 RPM
YRI_NA19093 5 .54 RPM
YRI_NA19099 10 .57 RPM
YRI_NA19114 10 .41 RPM
YRI_NA19118 6 .69 RPM
YRI_NA19213 5 .17 RPM
YRI_NA19214 4 .72 RPM
YRI_NA19223 4 .08 RPM

Indel association:

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



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