RetrogeneDB ID:

retro_hsap_2960

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:89448749..89449241(+)
Located in intron of:ENSG00000138641
Retrocopy
information
Ensembl ID:ENSG00000249755
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CD53
Ensembl ID:ENSG00000143119
Aliases:CD53, MOX44, TSPAN25
Description:CD53 molecule [Source:HGNC Symbol;Acc:1686]


Retrocopy-Parental alignment summary:






>retro_hsap_2960
GGGATGTACCCGCTGATCCACAACAGTTTGGGAGTGCTCTTCCATAAGCTCCCCTCCCTCATGCCGGGCAATGTGCTTGT
CATCGTGGTCTCCATTATCACGGTGGTTGCCTTCCTGGGCTGCATAGGTTCTGTCAAGAAAAACAGGTGCCTGCTTATGT
CCTTGTTCATTCTGCTGCCGGTTATCCTCCTTGCTGAGGTGATCTTGGCCATCCTGCACTTTGTTTACGAACGGAAGCTG
AATGTATAGGTAGCTGAGGGCCTGACGGACAGCATCTACCATTACCACTGGGACAACAGCACCAAGGCGATGTGGGACTC
CATCCAGTCATTTCTGCACTGCTGTGGCGTAAATGGCATGAGTGATTGGTCCAGCGGATAGCAAGCATCTTGCCCCTCAG
ATCCAAAAGTGAAAGGTTGCTATGCAAAAGCGAGACTGTAGTTTCACGCCAATTTCCTGTATATCAGAATCATCACCATC
TGTGTATATGTG

ORF - retro_hsap_2960 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.22 %
Parental protein coverage: 74.89 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGIYLLIHNNFGVLFHNLPSLTLGNVFVIVGSIIMVVAFLGCMGSIKENKCLLMSFFILLLIILLAEVTLA
G.Y.LIHN..GVLFH.LPSL..GNV.VIV.SII.VVAFLGC.GS.K.N.CLLMS.FILL..ILLAEV.LA
RetrocopyGMYPLIHNSLGVLFHKLPSLMPGNVLVIVVSIITVVAFLGCIGSVKKNRCLLMSLFILLPVILLAEVILA
ParentalILLFVYEQKLNEYVAKGLTDSIHRYHSDNSTKAAWDSIQSFLQCCGINGTSDWTSGPPASCPSDRKVEGC
IL.FVYE.KLN..VA.GLTDSI..YH.DNSTKA.WDSIQSFL.CCG.NG.SDW.SG..ASCPSD.KV.GC
RetrocopyILHFVYERKLNV*VAEGLTDSIYHYHWDNSTKAMWDSIQSFLHCCGVNGMSDWSSG*QASCPSDPKVKGC
ParentalYAKARLWFHSNFLYIGIITICVCV
YAKARL.FH.NFLYI.IITICV.V
RetrocopyYAKARL*FHANFLYIRIITICVYV

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 26 .58 RPM
bodymap2_adrenal 0 .08 RPM 140 .73 RPM
bodymap2_brain 0 .05 RPM 11 .20 RPM
bodymap2_breast 0 .02 RPM 17 .39 RPM
bodymap2_colon 0 .00 RPM 8 .06 RPM
bodymap2_heart 0 .18 RPM 12 .24 RPM
bodymap2_kidney 0 .04 RPM 23 .06 RPM
bodymap2_liver 0 .00 RPM 15 .76 RPM
bodymap2_lung 0 .00 RPM 79 .18 RPM
bodymap2_lymph_node 0 .00 RPM 280 .61 RPM
bodymap2_ovary 0 .08 RPM 15 .94 RPM
bodymap2_prostate 0 .17 RPM 16 .58 RPM
bodymap2_skeletal_muscle 0 .11 RPM 1 .20 RPM
bodymap2_testis 0 .09 RPM 7 .35 RPM
bodymap2_thyroid 0 .26 RPM 8 .30 RPM
bodymap2_white_blood_cells 0 .00 RPM 661 .31 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2960 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2960 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2960 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2960 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2960 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2004
Gorilla gorilla retro_ggor_2050
Parental genes homology:
Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000107602 retrocopies
retro_chof_116, retro_chof_307,
Homo sapiens ENSG00000143119 1 retrocopy
retro_hsap_2960 ,
Gorilla gorilla ENSGGOG000000054681 retrocopy
retro_ggor_2050,
Macaca mulatta ENSMMUG000000008111 retrocopy
retro_mmul_1894,
Nomascus leucogenys ENSNLEG000000036491 retrocopy
retro_nleu_1643,
Otolemur garnettii ENSOGAG000000167132 retrocopies
retro_ogar_2407, retro_ogar_469,
Pan troglodytes ENSPTRG000000010851 retrocopy
retro_ptro_2004,

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 = 0.14 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .09 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .13 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .09 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .06 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .09 RPM
GBR_HG00114 0 .08 RPM
GBR_HG00119 0 .07 RPM
GBR_HG00131 0 .14 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .07 RPM
GBR_HG00137 0 .14 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .14 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .06 RPM

Indel association:

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



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