RetrogeneDB ID:

retro_hsap_4266

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:66081967..66083335(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000242301
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FKBP4
Ensembl ID:ENSG00000004478
Aliases:None
Description:FK506 binding protein 4, 59kDa [Source:HGNC Symbol;Acc:3720]


Retrocopy-Parental alignment summary:






>retro_hsap_4266
ATGACAGCCAAGGAGATGAAGGCGACCGAGAGTGCGGCGCAGCCAGCGCCGCTGCCCAAGAAGGAAGTGGACGTCAGCCC
CAAACAGGATGAAGGAGTGCTGAAGGTCATCAAGAGAGAGGGCACAGGTACAGAGATGCCCATGACTGGGGACCTAGTCT
TTGTCCACTACACTGGCTGGCTGTTAGAGGGCACAAAGTTTGACTCCAGCGTGGATCGCAAGGACAAATTCTCCTTTGAC
CTGGGAAAAGGGGAGGTCATCAAGGCTTGGGACATTGCCGTAGCAACCATGAAGGTGGGGGAGGTGGGCCACATCACCTG
CAAACCAGGATATGCCTAGGGTTCAGCAGACAGTCCTCCAACGATCCCCCCATAACGCCACGCTTGTGTTTGAGGTGGAA
TTGTTTAAGGAAGAAGATCTGACGGAAGAGGAAGATGGGGGAATCATCCGCAGAATAGGGACTCGCGGTGAAGGCTATGT
CAAGCCCGATGAGGGCGCTATGGTGGAGGTTGCGCTGGAAGGGTGCTGCAAGGACCAGCTCTTTGACCAACGGGCGCTCC
GCTTTGAGGTTAGCGAGGGGGAGAACCTGGATCTGCCTTATGATCTGGAGAGGGCCATTCAGCACTTGGAGAAAGGAGAA
CATTCCACTGTGTACCTCAAGCCCAGCTATGCTTTTGGCAGTGTTGGGAAGGAAAAGTTCCAAATCCCACCAAATGCCGA
GCTGAAATATGAATTACATCTCAAGAGTTTTGAAAAGGCCAAGGAATCTTGGGAGATGATTTCAGAAGAGAAGCTGGAAC
AGAACACCATAGTGAAAGAGCAGGGCAGTGTGTACTTCAAGGAAGGCAAATACAAGCAAGCTTTACTACAGTGTAAGAAG
ATTGTGTCCTGGCTGGAATATGAGTCTAGTTTTTCCAATGAGGAAGCACAGAAGGCACAGGCCCTTCGACTGGCCTCTCA
CCTCGACCTGGCCATGTGTCAGCTGAAACTACAGGCCTTCTCTGCTGCCATTGAAAGTTGTAACAATGCCCTAGAACTGG
GCAGCAACAACGAGAAGGGCCCCTTCCGCCGGGGAGAGGCCCACCTGGCGGTGAATGACTTTGAACTGGCATGGGCTGAC
TTCCAGAAGGTCCTGCAGCTCTACCCCAACGACAAAGCCGCCAGGGCCCAGCTGGCTGTGGGTCAGCAGCGGATCCACAG
GCAGCTTGCCTGGGAGAAGTTCTATGCCAAAATGTTTGAGAGGCTGGCTGAGGAGGAGAACAAGGCCAAGGCAGAGGCTT
GCTCAGGAGACCATCCCACTGACACAGAGATGAAGGCGGAGTGCAAGAGCAACACGGCGGGAGCCAGTCTCAGGTGGAGA
CAGAAGCA

ORF - retro_hsap_4266 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.2 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMTAEEMKATESGAQSAPLPMEGVDISPKQDEGVLKVIKREGTGTEMPMIGDRVFVHYTGWLLDGTKFDSS
MTA.EMKATES.AQ.APLP...VD.SPKQDEGVLKVIKREGTGTEMPM.GD.VFVHYTGWLL.GTKFDSS
RetrocopyMTAKEMKATESAAQPAPLPKKEVDVSPKQDEGVLKVIKREGTGTEMPMTGDLVFVHYTGWLLEGTKFDSS
ParentalLDRKDKFSFDLGKGEVIKAWDIAIATMKVGEVCHITCKPEYAYGSAGSPPKIPP-NATLVFEVELFEFKG
.DRKDKFSFDLGKGEVIKAWDIA.ATMKVGEV.HITCKP.YA.GSA.SPP.IPP.NATLVFEVELF..K.
RetrocopyVDRKDKFSFDLGKGEVIKAWDIAVATMKVGEVGHITCKPGYA*GSADSPPTIPP>NATLVFEVELF--KE
ParentalEDLTEEEDGGIIRRIQTRGEGYAKPNEGAIVEVALEGYYKDKLFDQRELRFEIGEGENLDLPYGLERAIQ
EDLTEEEDGGIIRRI.TRGEGY.KP.EGA.VEVALEG..KD.LFDQR.LRFE..EGENLDLPY.LERAIQ
RetrocopyEDLTEEEDGGIIRRIGTRGEGYVKPDEGAMVEVALEGCCKDQLFDQRALRFEVSEGENLDLPYDLERAIQ
ParentalRMEKGEHSIVYLKPSYAFGSVGKEKFQIPPNAELKYELHLKSFEKAKESWEMNSEEKLEQSTIVKERGTV
..EKGEHS.VYLKPSYAFGSVGKEKFQIPPNAELKYELHLKSFEKAKESWEM.SEEKLEQ.TIVKE.G.V
RetrocopyHLEKGEHSTVYLKPSYAFGSVGKEKFQIPPNAELKYELHLKSFEKAKESWEMISEEKLEQNTIVKEQGSV
ParentalYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD
YFKEGKYKQALLQ.KKIVSWLEYESSFSNEEAQKAQALRLASHL.LAMC.LKLQAFSAAIESCN.ALEL.
RetrocopyYFKEGKYKQALLQCKKIVSWLEYESSFSNEEAQKAQALRLASHLDLAMCQLKLQAFSAAIESCNNALELG
ParentalSNNEKGLFRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQRIRRQLAREKKLYANMFERLA
SNNEKG.FRRGEAHLAVNDFELA.ADFQKVLQLYPN.KAA..QLAV.QQRI.RQLA.E.K.YA.MFERLA
RetrocopySNNEKGPFRRGEAHLAVNDFELAWADFQKVLQLYPNDKAARAQLAVGQQRIHRQLAWE-KFYAKMFERLA
ParentalEEENKAKAEASSGDHPTDTEMKEEQKSNTA-GSQSQVETEA
EEENKAKAEA.SGDHPTDTEMK.E.KSNTA.GSQSQVETEA
RetrocopyEEENKAKAEACSGDHPTDTEMKAECKSNTA<GSQSQVETEA

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 71 .84 RPM
bodymap2_adrenal 0 .00 RPM 38 .75 RPM
bodymap2_brain 0 .00 RPM 89 .26 RPM
bodymap2_breast 0 .00 RPM 49 .36 RPM
bodymap2_colon 0 .00 RPM 286 .02 RPM
bodymap2_heart 0 .00 RPM 43 .48 RPM
bodymap2_kidney 0 .00 RPM 223 .20 RPM
bodymap2_liver 0 .00 RPM 75 .69 RPM
bodymap2_lung 0 .00 RPM 106 .05 RPM
bodymap2_lymph_node 0 .00 RPM 227 .74 RPM
bodymap2_ovary 0 .00 RPM 160 .08 RPM
bodymap2_prostate 0 .00 RPM 152 .17 RPM
bodymap2_skeletal_muscle 0 .00 RPM 199 .27 RPM
bodymap2_testis 0 .00 RPM 224 .41 RPM
bodymap2_thyroid 0 .00 RPM 287 .93 RPM
bodymap2_white_blood_cells 0 .00 RPM 57 .86 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4266 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4266 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4266 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4266 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4266 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 12 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000076051 retrocopy
retro_btau_561,
Callithrix jacchus ENSCJAG000000187461 retrocopy
retro_cjac_436,
Dasypus novemcinctus ENSDNOG000000112441 retrocopy
retro_dnov_894,
Homo sapiens ENSG00000004478 5 retrocopies
retro_hsap_3085, retro_hsap_4162, retro_hsap_4165, retro_hsap_4264, retro_hsap_4266 ,
Homo sapiens ENSG000000888321 retrocopy
retro_hsap_1198,
Homo sapiens ENSG000000960604 retrocopies
retro_hsap_4255, retro_hsap_4260, retro_hsap_4262, retro_hsap_4318,
Homo sapiens ENSG000001197821 retrocopy
retro_hsap_1329,
Gorilla gorilla ENSGGOG000000104714 retrocopies
retro_ggor_2120, retro_ggor_2852, retro_ggor_2854, retro_ggor_2855,
Macaca mulatta ENSMMUG000000074051 retrocopy
retro_mmul_1969,
Nomascus leucogenys ENSNLEG000000028351 retrocopy
retro_nleu_2291,
Pongo abelii ENSPPYG000000041494 retrocopies
retro_pabe_2607, retro_pabe_2611, retro_pabe_3383, retro_pabe_3518,
Pan troglodytes ENSPTRG000000045293 retrocopies
retro_ptro_2083, retro_ptro_3000, retro_ptro_3001,

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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