RetrogeneDB ID:

retro_hsap_4268

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:68370651..68370975(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000226020
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CDK2AP2
Ensembl ID:ENSG00000167797
Aliases:CDK2AP2, DOC-1R, p14
Description:cyclin-dependent kinase 2 associated protein 2 [Source:HGNC Symbol;Acc:30833]


Retrocopy-Parental alignment summary:






>retro_hsap_4268
ATGTCCTACAAACCTACCACCCCTGCCCCCAGCAGCACCCCCGGCTTCAGCACCCCTGGGCCAGGCACTCGGGTCCCTAC
AGGAAGCGTCCCGTCGCCGTCGGGCTCAGGGCCGGGAGCCACTGCCCCTTGCAGACCGCTGTTTAAAGACTTTGGACCGC
CTACCGTCGGTTGTGTGCAGGCCATGAAACCACCTGGTGCCCAGGGCTCCCAGAGCACCTACACAGAACTGCTGTTGGTC
ACAGGGGAGATGGGCAAAGGGATCCGGCCCACCTATGCTGGCAGCAAGAGCGCCGCGGAGCGCCTGAAGACAGGTATCAT
CCAT

ORF - retro_hsap_4268 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.33 %
Parental protein coverage: 85.71 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSYKPIAPAPSSTPGSSTPGPGTPVPTGSVPSPSGSVPGAGAPFRPLFNDFGPPSMGYVQAMKPPGAQGS
MSYKP..PAPSSTPG.STPGPGT.VPTGSVPSPSGS.PGA.AP.RPLF.DFGPP..G.VQAMKPPGAQGS
RetrocopyMSYKPTTPAPSSTPGFSTPGPGTRVPTGSVPSPSGSGPGATAPCRPLFKDFGPPTVGCVQAMKPPGAQGS
ParentalQSTYTDLLSVIEEMGKEIRPTYAGSKSAMERLKRGIIH
QSTYT.LL.V..EMGK.IRPTYAGSKSA.ERLK.GIIH
RetrocopyQSTYTELLLVTGEMGKGIRPTYAGSKSAAERLKTGIIH

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 16 .24 RPM
bodymap2_adrenal 0 .00 RPM 12 .36 RPM
bodymap2_brain 0 .00 RPM 3 .33 RPM
bodymap2_breast 0 .00 RPM 11 .93 RPM
bodymap2_colon 0 .00 RPM 30 .26 RPM
bodymap2_heart 0 .00 RPM 9 .34 RPM
bodymap2_kidney 0 .00 RPM 63 .32 RPM
bodymap2_liver 0 .00 RPM 24 .86 RPM
bodymap2_lung 0 .00 RPM 30 .24 RPM
bodymap2_lymph_node 0 .00 RPM 41 .17 RPM
bodymap2_ovary 0 .00 RPM 14 .80 RPM
bodymap2_prostate 0 .07 RPM 25 .27 RPM
bodymap2_skeletal_muscle 0 .00 RPM 9 .73 RPM
bodymap2_testis 0 .09 RPM 19 .38 RPM
bodymap2_thyroid 0 .00 RPM 11 .94 RPM
bodymap2_white_blood_cells 0 .00 RPM 36 .88 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4268 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4268 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4268 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4268 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4268 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 11 parental genes, and 33 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000113701 retrocopy
retro_cfam_55,
Equus caballus ENSECAG000000200792 retrocopies
retro_ecab_180, retro_ecab_579,
Echinops telfairi ENSETEG000000064283 retrocopies
retro_etel_257, retro_etel_334, retro_etel_437,
Homo sapiens ENSG000001113282 retrocopies
retro_hsap_2227, retro_hsap_2834,
Homo sapiens ENSG00000167797 4 retrocopies
retro_hsap_3699, retro_hsap_4172, retro_hsap_4176, retro_hsap_4268 ,
Gorilla gorilla ENSGGOG000000101593 retrocopies
retro_ggor_2502, retro_ggor_2799, retro_ggor_2800,
Macaca mulatta ENSMMUG000000118275 retrocopies
retro_mmul_1712, retro_mmul_640, retro_mmul_728, retro_mmul_730, retro_mmul_763,
Nomascus leucogenys ENSNLEG000000064381 retrocopy
retro_nleu_176,
Otolemur garnettii ENSOGAG000000082751 retrocopy
retro_ogar_1584,
Pan troglodytes ENSPTRG000000039669 retrocopies
retro_ptro_2508, retro_ptro_2973, retro_ptro_2976, retro_ptro_3002, retro_ptro_3003, retro_ptro_3004, retro_ptro_3005, retro_ptro_3008, retro_ptro_3009,
Tupaia belangeri ENSTBEG000000054762 retrocopies
retro_tbel_439, retro_tbel_612,

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 = 0.03 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 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 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 .02 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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