RetrogeneDB ID:

retro_hsap_4696

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:70077013..70077594(+)
Located in intron of:ENSG00000120498
Retrocopy
information
Ensembl ID:ENSG00000213747
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CCDC53
Ensembl ID:ENSG00000120860
Aliases:CCDC53, CGI-116
Description:coiled-coil domain containing 53 [Source:HGNC Symbol;Acc:24256]


Retrocopy-Parental alignment summary:






>retro_hsap_4696
ATGGATAAAGATGGGCTTCCTCTCATGGGAGTCAGGCGTAGACTTGATCAAGGTGCCAGCTATTCAGCAGAAAAGAATGG
TGGCTTTTCTAAACCAAAATGTGGTACACACTGTATAGTGCCTCAATCGCTCTTCTACATTTAGTGAGGAGAAACTGGCA
AACCTTTATCTTGGTATCCAGCAAATTGAAACAATTCTCAATACTGTAGATGCAAAGTTGTCATCTATACCAGGCCTAGA
TGATGTCACATTTGAAGTATCTCCTTCAAGTGCCACTAGTGTCACAAATGGATCACATTCTGAAGTCACCTCAGAGTAAT
CACAGCAGGACAGTACATTAAGACTCTGGACCACAGGAAAGTTAAGTATCAGCAGGAAATATCTTAACTGTAGCTAAAGA
TTCAAGATATGTCATATATCTCAAAATGGTTCAAGTGAGTGTACCAGTGATGGCAATAAGAAAAATGATATCAGAAGGAC
TAGACCCAGATCTTCTTGAGAGGTCAGGTGCTCCAGTGCCTGATGGCAAAAGTGAAAATCCTGCAGAACAAAGTTCAGAT
AGCGAATCTTCTTTTAGTGAC

ORF - retro_hsap_4696 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.55 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMDEDGLPLMG-SGIDLTKVPAIQQKRTVAFLNQFVVHTVQFLNRFSTVCEEKLADLSLRIQQIETTLNIL
MD.DGLPLMG.SG.DL.KVPAIQQKR.VAFLNQ.VVHTV..LNR.ST..EEKLA.L.L.IQQIET.LN..
RetrocopyMDKDGLPLMG>SGVDLIKVPAIQQKRMVAFLNQNVVHTV*CLNRSSTFSEEKLANLYLGIQQIETILNTV
ParentalDAKLSSIPGLDDVTVEVSPLNVTSVTNGAHPEATSEQPQQNSTQ-DSGLQESEVSAENILTVAKDPRYAR
DAKLSSIPGLDDVT.EVSP...TSVTNG.H.E.TSE..QQ.ST..DSG.QES.VSA.NILTVAKD.RY..
RetrocopyDAKLSSIPGLDDVTFEVSPSSATSVTNGSHSEVTSE*SQQDSTL>DSGPQES*VSAGNILTVAKDSRYVI
ParentalYLKMVQVGVPVMAIRNKMISEGLDPDLLERPDAPVPDGESEKTVEESSDSESSFSD
YLKMVQV.VPVMAIR.KMISEGLDPDLLER..APVPDG.SE...E.SSDSESSFSD
RetrocopyYLKMVQVSVPVMAIR-KMISEGLDPDLLERSGAPVPDGKSENPAEQSSDSESSFSD

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 12 .32 RPM
bodymap2_adrenal 0 .00 RPM 14 .70 RPM
bodymap2_brain 0 .00 RPM 21 .38 RPM
bodymap2_breast 0 .00 RPM 18 .07 RPM
bodymap2_colon 0 .00 RPM 21 .66 RPM
bodymap2_heart 0 .00 RPM 13 .96 RPM
bodymap2_kidney 0 .00 RPM 24 .16 RPM
bodymap2_liver 0 .00 RPM 10 .18 RPM
bodymap2_lung 0 .00 RPM 10 .11 RPM
bodymap2_lymph_node 0 .00 RPM 19 .72 RPM
bodymap2_ovary 0 .00 RPM 19 .86 RPM
bodymap2_prostate 0 .00 RPM 27 .76 RPM
bodymap2_skeletal_muscle 0 .00 RPM 8 .91 RPM
bodymap2_testis 0 .00 RPM 79 .56 RPM
bodymap2_thyroid 0 .00 RPM 17 .25 RPM
bodymap2_white_blood_cells 0 .00 RPM 15 .69 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4696 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4696 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4696 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4696 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4696 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3121
Gorilla gorilla retro_ggor_2922
Pongo abelii retro_pabe_3649
Callithrix jacchus retro_cjac_4073
Parental genes homology:
Parental genes homology involve 21 parental genes, and 36 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000063291 retrocopy
retro_amel_791,
Canis familiaris ENSCAFG000000072702 retrocopies
retro_cfam_53, retro_cfam_550,
Callithrix jacchus ENSCJAG000000142251 retrocopy
retro_cjac_4073,
Echinops telfairi ENSETEG000000022541 retrocopy
retro_etel_1917,
Felis catus ENSFCAG000000193581 retrocopy
retro_fcat_498,
Homo sapiens ENSG00000120860 1 retrocopy
retro_hsap_4696 ,
Gorilla gorilla ENSGGOG000000149751 retrocopy
retro_ggor_2922,
Loxodonta africana ENSLAFG000000078501 retrocopy
retro_lafr_761,
Macropus eugenii ENSMEUG000000048883 retrocopies
retro_meug_1441, retro_meug_576, retro_meug_629,
Myotis lucifugus ENSMLUG000000004014 retrocopies
retro_mluc_2014, retro_mluc_2015, retro_mluc_2633, retro_mluc_502,
Monodelphis domestica ENSMODG000000025791 retrocopy
retro_mdom_959,
Mus musculus ENSMUSG000000200561 retrocopy
retro_mmus_1773,
Nomascus leucogenys ENSNLEG000000063651 retrocopy
retro_nleu_2366,
Otolemur garnettii ENSOGAG000000033222 retrocopies
retro_ogar_3267, retro_ogar_738,
Pongo abelii ENSPPYG000000048781 retrocopy
retro_pabe_3649,
Pan troglodytes ENSPTRG000000053581 retrocopy
retro_ptro_3121,
Ictidomys tridecemlineatus ENSSTOG000000018701 retrocopy
retro_itri_970,
Tupaia belangeri ENSTBEG000000084983 retrocopies
retro_tbel_1036, retro_tbel_1165, retro_tbel_2967,
Tarsius syrichta ENSTSYG000000005874 retrocopies
retro_tsyr_1100, retro_tsyr_265, retro_tsyr_443, retro_tsyr_955,
Tursiops truncatus ENSTTRG000000172214 retrocopies
retro_ttru_1569, retro_ttru_1865, retro_ttru_1919, retro_ttru_935,
Vicugna pacos ENSVPAG000000020101 retrocopy
retro_vpac_446,

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 = 0.02 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 .02 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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