RetrogeneDB ID:

retro_hsap_3541

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:160514579..160514963(+)
Located in intron of:ENSG00000197081
Retrocopy
information
Ensembl ID:ENSG00000213073
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CHP1
Ensembl ID:ENSG00000187446
Aliases:CHP1, CHP, SLC9A1BP, Sid470p, p22, p24
Description:calcineurin-like EF-hand protein 1 [Source:HGNC Symbol;Acc:17433]


Retrocopy-Parental alignment summary:






>retro_hsap_3541
CAGGACGATTTCCAGGGGATTCCAGAACTTGCCATCAACCCAGTGGGGGACTGGATCATCAATGCCTTCCTTCCAGAGGG
AGAGGACCAGGTAAACTTCCGTGGATTCCTGCAAACTCTGGCTCATTTCCAAACCATTGAGGATAATGAAAAGAGCAAAG
TTGTGAATGGACCTGAACCACTCAACAGCCGAAGCAACAAACTGCAGTTTGCTTTTCGACTATATGATTTGGATAAAGAT
AACAAGATCTCTCGTGATGAGCTGTTAAGGGTGCTGTGCATGATGGTCCAAATAAATATCTCAGATAAGCAGCTGGGCAG
TATCGCAGACAGGACCATTCAGGAGGCTGATCAGCATGGGGACAGTGCCATATCTTTATCACAG

ORF - retro_hsap_3541 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.81 %
Parental protein coverage: 65.64 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalREDFQRIPELAINPLGDRIINAFFPEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLHF
..DFQ.IPELAINP.GD.IINAF.PEGEDQVNFRGF..TLAHF..IEDNEKSK.VNGPEPLNSRSNKL.F
RetrocopyQDDFQGIPELAINPVGDWIINAFLPEGEDQVNFRGFLQTLAHFQTIEDNEKSKVVNGPEPLNSRSNKLQF
ParentalAFRLYDLDKDEKISRDELLQVLRMMVGVNISDEQLGSIADRTIQEADQDGDSAISFTE
AFRLYDLDKD.KISRDELL.VL.MMV..NISD.QLGSIADRTIQEADQ.GDSAIS...
RetrocopyAFRLYDLDKDNKISRDELLRVLCMMVQINISDKQLGSIADRTIQEADQHGDSAISLSQ

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 .10 RPM 245 .75 RPM
bodymap2_adrenal 0 .49 RPM 63 .78 RPM
bodymap2_brain 0 .09 RPM 127 .14 RPM
bodymap2_breast 0 .16 RPM 241 .40 RPM
bodymap2_colon 0 .27 RPM 136 .98 RPM
bodymap2_heart 0 .30 RPM 100 .74 RPM
bodymap2_kidney 0 .39 RPM 197 .37 RPM
bodymap2_liver 0 .28 RPM 308 .93 RPM
bodymap2_lung 0 .18 RPM 189 .28 RPM
bodymap2_lymph_node 0 .26 RPM 90 .84 RPM
bodymap2_ovary 0 .42 RPM 94 .30 RPM
bodymap2_prostate 0 .14 RPM 116 .17 RPM
bodymap2_skeletal_muscle 0 .05 RPM 237 .62 RPM
bodymap2_testis 0 .06 RPM 89 .36 RPM
bodymap2_thyroid 0 .21 RPM 124 .31 RPM
bodymap2_white_blood_cells 0 .45 RPM 196 .15 RPM
RNA Polymerase II actvity near the 5' end of retro_hsap_3541 was not detected
No EST(s) were mapped for retro_hsap_3541 retrocopy.
No TSS is located nearby retro_hsap_3541 retrocopy 5' end.
retro_hsap_3541 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3541 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2392

Parental genes homology:
Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000095251 retrocopy
Cavia porcellus ENSCPOG000000105772 retrocopies
Homo sapiens ENSG00000187446 2 retrocopies
retro_hsap_3334, retro_hsap_3541 ,
Homo sapiens ENSG000002218231 retrocopy
Gorilla gorilla ENSGGOG000000073122 retrocopies
Macaca mulatta ENSMMUG000000170922 retrocopies
Mus musculus ENSMUSG000000140774 retrocopies
Nomascus leucogenys ENSNLEG000000034654 retrocopies
Procavia capensis ENSPCAG000000054191 retrocopy
Pongo abelii ENSPPYG000000063702 retrocopies
Pan troglodytes ENSPTRG000000069422 retrocopies
Rattus norvegicus ENSRNOG000000047422 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000145031 retrocopy

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 = 1.11 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .26 RPM
CEU_NA11843 0 .20 RPM
CEU_NA11930 0 .42 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .67 RPM
CEU_NA12751 0 .73 RPM
CEU_NA12760 0 .54 RPM
CEU_NA12827 0 .61 RPM
CEU_NA12872 0 .38 RPM
CEU_NA12873 0 .38 RPM
FIN_HG00183 0 .52 RPM
FIN_HG00277 1 .11 RPM
FIN_HG00315 0 .22 RPM
FIN_HG00321 0 .79 RPM
FIN_HG00328 0 .07 RPM
FIN_HG00338 0 .23 RPM
FIN_HG00349 0 .31 RPM
FIN_HG00375 0 .20 RPM
FIN_HG00377 0 .33 RPM
FIN_HG00378 0 .47 RPM
GBR_HG00099 0 .29 RPM
GBR_HG00111 0 .43 RPM
GBR_HG00114 0 .34 RPM
GBR_HG00119 0 .38 RPM
GBR_HG00131 0 .55 RPM
GBR_HG00133 0 .65 RPM
GBR_HG00134 0 .31 RPM
GBR_HG00137 0 .58 RPM
GBR_HG00142 0 .89 RPM
GBR_HG00143 0 .26 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .56 RPM
TSI_NA20518 0 .50 RPM
TSI_NA20532 0 .44 RPM
TSI_NA20538 0 .83 RPM
TSI_NA20756 0 .38 RPM
TSI_NA20765 0 .39 RPM
TSI_NA20771 0 .17 RPM
TSI_NA20786 0 .29 RPM
TSI_NA20798 0 .28 RPM
YRI_NA18870 0 .34 RPM
YRI_NA18907 0 .28 RPM
YRI_NA18916 0 .48 RPM
YRI_NA19093 0 .42 RPM
YRI_NA19099 0 .37 RPM
YRI_NA19114 0 .18 RPM
YRI_NA19118 0 .35 RPM
YRI_NA19213 0 .69 RPM
YRI_NA19214 0 .69 RPM
YRI_NA19223 0 .34 RPM


Indel association:

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




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