RetrogeneDB ID:

retro_hsap_71

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:18:580408..580927(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000177143
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:CETN2
Ensembl ID:ENSG00000147400
Aliases:None
Description:centrin, EF-hand protein, 2 [Source:HGNC Symbol;Acc:1867]


Retrocopy-Parental alignment summary:






>retro_hsap_71
ATGGCTTCCGGCTTCAAGAAGCCCAGCGCTGCCTCCACCGGCCAAAAGAGAAAGGTGGCACCTAAGCCCGAGCTCACTGA
GGATCAGAAGCAAGAAGTTCGGGAAGCATTTGACCTCTTCGACGTGGACGGAAGTGGGACCATCGACGCGAAGGAGCTGA
AGGTGGCCATGAGAGCGCTGGGCTTCGAACCCAGGAAGGAAGAGATGAAGAAAATGATCTCCGAGGTGGACAGGGAAGGC
ACGGGGAAGATCAGCTTCAATGACTTCCTGGCCGTGATGACGCAGAAGATGTCCGAGAAGGACACCAAAGAAGAAATCCT
GAAGGCCTTCAGGCTCTTTGATGACGATGAGACCGGGAAGATCTCGTTCAAAAACCTGAAGCGTGTGGCCAACGAGCTGG
GGGAGAACCTCACGGATGAGGAGCTGCAGGAGATGATCGACGAAGCTGATCGGGATGGGGACGGCGAAGTGAACGAGGAG
GAGTTCCTTCGGATCATGAAGAAGACCAGCCTTTACTGA

ORF - retro_hsap_71 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.72 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMASNFKKANMASSSQRKRMSPKPELTEEQKQEIREAFDLFDADGTGTIDVKELKVAMRALGFEPKKEEIK
MAS.FKK...AS..Q.....PKPELTE.QKQE.REAFDLFD.DG.GTID.KELKVAMRALGFEP.KEE.K
RetrocopyMASGFKKPSAASTGQKRKVAPKPELTEDQKQEVREAFDLFDVDGSGTIDAKELKVAMRALGFEPRKEEMK
ParentalKMISEIDKEGTGKMNFGDFLTVMTQKMSEKDTKEEILKAFKLFDDDETGKISFKNLKRVAKELGENLTDE
KMISE.D.EGTGK..F.DFL.VMTQKMSEKDTKEEILKAF.LFDDDETGKISFKNLKRVA.ELGENLTDE
RetrocopyKMISEVDREGTGKISFNDFLAVMTQKMSEKDTKEEILKAFRLFDDDETGKISFKNLKRVANELGENLTDE
ParentalELQEMIDEADRDGDGEVSEQEFLRIMKKTSLY
ELQEMIDEADRDGDGEV.E.EFLRIMKKTSLY
RetrocopyELQEMIDEADRDGDGEVNEEEFLRIMKKTSLY

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 19 .48 RPM
bodymap2_adrenal 0 .12 RPM 27 .90 RPM
bodymap2_brain 0 .00 RPM 62 .02 RPM
bodymap2_breast 0 .06 RPM 38 .74 RPM
bodymap2_colon 0 .00 RPM 65 .61 RPM
bodymap2_heart 0 .00 RPM 17 .74 RPM
bodymap2_kidney 0 .00 RPM 62 .89 RPM
bodymap2_liver 0 .00 RPM 14 .79 RPM
bodymap2_lung 0 .00 RPM 83 .12 RPM
bodymap2_lymph_node 0 .00 RPM 16 .41 RPM
bodymap2_ovary 0 .00 RPM 95 .69 RPM
bodymap2_prostate 0 .00 RPM 59 .81 RPM
bodymap2_skeletal_muscle 0 .00 RPM 8 .98 RPM
bodymap2_testis 62 .40 RPM 71 .64 RPM
bodymap2_thyroid 0 .00 RPM 78 .60 RPM
bodymap2_white_blood_cells 0 .00 RPM 19 .33 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_71 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_71 retrocopy
EST ID Start End Identity Match Mis-match Score
DB459544 580369 580652 99 283 0 282

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_681801824 libraries2 libraries0 libraries1 library2 libraries
TSS #2 TSS_681811813 libraries11 libraries1 library1 library3 libraries

The graphical summary, for retro_hsap_71 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_71 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_71 has 9 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_108
Gorilla gorilla retro_ggor_74
Pongo abelii retro_pabe_58
Macaca mulatta retro_mmul_176
Callithrix jacchus retro_cjac_316
Oryctolagus cuniculus retro_ocun_180
Bos taurus retro_btau_170
Canis familiaris retro_cfam_199
Equus caballus retro_ecab_49
Parental genes homology:
Parental genes homology involve 28 parental genes, and 44 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000003641 retrocopy
retro_amel_56,
Bos taurus ENSBTAG000000078441 retrocopy
retro_btau_170,
Canis familiaris ENSCAFG000000191701 retrocopy
retro_cfam_199,
Choloepus hoffmanni ENSCHOG000000102441 retrocopy
retro_chof_39,
Callithrix jacchus ENSCJAG000000163383 retrocopies
retro_cjac_106, retro_cjac_185, retro_cjac_316,
Cavia porcellus ENSCPOG000000120812 retrocopies
retro_cpor_1250, retro_cpor_21,
Equus caballus ENSECAG000000007961 retrocopy
retro_ecab_49,
Felis catus ENSFCAG000000049011 retrocopy
retro_fcat_47,
Homo sapiens ENSG00000147400 1 retrocopy
retro_hsap_71 ,
Gorilla gorilla ENSGGOG000000113781 retrocopy
retro_ggor_74,
Loxodonta africana ENSLAFG000000144241 retrocopy
retro_lafr_121,
Microcebus murinus ENSMICG000000058622 retrocopies
retro_mmur_122, retro_mmur_21,
Myotis lucifugus ENSMLUG000000145202 retrocopies
retro_mluc_320, retro_mluc_370,
Macaca mulatta ENSMMUG000000207432 retrocopies
retro_mmul_1127, retro_mmul_176,
Mustela putorius furoENSMPUG000000118581 retrocopy
retro_mputfur_386,
Mus musculus ENSMUSG000000313472 retrocopies
retro_mmus_107, retro_mmus_838,
Nomascus leucogenys ENSNLEG000000138601 retrocopy
retro_nleu_1221,
Oryctolagus cuniculus ENSOCUG000000078971 retrocopy
retro_ocun_180,
Otolemur garnettii ENSOGAG000000053011 retrocopy
retro_ogar_236,
Procavia capensis ENSPCAG000000032031 retrocopy
retro_pcap_149,
Procavia capensis ENSPCAG000000077781 retrocopy
retro_pcap_364,
Pongo abelii ENSPPYG000000208331 retrocopy
retro_pabe_58,
Pan troglodytes ENSPTRG000000223891 retrocopy
retro_ptro_108,
Rattus norvegicus ENSRNOG000000170595 retrocopies
retro_rnor_2376, retro_rnor_2394, retro_rnor_2920, retro_rnor_304, retro_rnor_775,
Sus scrofa ENSSSCG000000127573 retrocopies
retro_sscr_1175, retro_sscr_57, retro_sscr_822,
Ictidomys tridecemlineatus ENSSTOG000000238532 retrocopies
retro_itri_636, retro_itri_91,
Tarsius syrichta ENSTSYG000000038312 retrocopies
retro_tsyr_1142, retro_tsyr_36,
Tursiops truncatus ENSTTRG000000012362 retrocopies
retro_ttru_32, retro_ttru_335,

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 ) Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 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 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 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 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 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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