RetrogeneDB ID:

retro_hsap_3385

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:126847153..126848532(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000250859
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPK
Ensembl ID:ENSG00000165119
Aliases:HNRNPK, CSBP, HNRPK, TUNP
Description:heterogeneous nuclear ribonucleoprotein K [Source:HGNC Symbol;Acc:5044]


Retrocopy-Parental alignment summary:






>retro_hsap_3385
GTGGAAACTGAACAGCCAGAAGAAAGCTTCCCTAACACTGAAACCAATGGTGAATTTGGTAAATGCCCTGCAGAAGATAT
GGAAGAGGAACAAGCATTGAAAAGATCTAGAAACACTGATGAGATGGTTGAGTTACACATTCTGCTTCAGAACAAGAATT
CTGGGGCAGTTATTGGAGAAGGAGGTAAGAATATTAAGGCTCCCTGTATAGACTACAGTGCCAGTGTTTCAGTCCCAGAC
AGCAGTGGCCCCAAGTGCATACTGAGTATCAGTGCTGGTATTGAAACAATTGGAGAAATTCTAAAGAAAATCATCCCTAC
CTTGGAAGAGGGCCTCCAGTTGCCATTACTCACTCCAACCAGCCAGCTCCTGCTGGAATCTGATGCTGTGGAATGCTTAA
ATTACCAACACTATAAAGGAAGAGACTTTGAGTGCGAGTTGAAGCTGTTGATTTATCAGAGTCTAGCAGGAGGAATATTG
GGGTCAAAGGTGCTAAAATCAAAGAACTTTGAGAGAACGCTCAAACAACCATCAAGCTTTTCTAGGAATGCTGTTCTCAT
CCCACTGACAGAGTTGTTCTTATTGGAGGAAAACCCAATAGGGTTGTAGAGTGCATAAAGATCATCCTTGATCTTATATC
TGAGTCTCCCATCAAAGGACCTGCACAGCCTTATGATCCCAGTTTTTACAATGAAACCTATGATTATGGTGGTTTTACAA
TGATGTTTGATGACCGCCCTGGATGCCCAGTGGGATTTCCAATGTGGGGAAGAGGTGGTTTTGACAGAATGCCTCCTGGT
TGGAGTGGGCGTCCCATGCCTCCATCTAGAAGAGATATGAACCCTCATCGAGGACCACCTCCTCCTCTTACTGGACGAGG
TGGCCGGGGTGGTAGCAGAGCTCGGAATCTTCCTCTTCCTCCACCACCACCACCTAGAGGGGAAGACCTAATGGCCTATG
ACAGAAGAGGGAGACCTGGAGACTGTTACGATGGCATGGTTGGTTTCAGTCCTGATGAAACTTGGAACTCTGCAATAGAT
ACATGGAGCCCATCGGAATGGCAGATGGCTTATGAACCACAGGGTGGCTCCGGATATGATTATTCCTATGCAGGGATTGG
TGGCTCATATGGTGATCTTGGTGGACCTATTACTACTGCACAAGTAACTATTCCCAAAGATTTGACTGGATCTATTATTG
GCAAAGGTGGTCAGCGGATTAAACAAATCGGTCATGAGTTGGGAGCTTCAATCAAAATTGATGAGCCTTTAGAAGGATCC
GAAGATCAGATCACTATCATTACAGGAACACAGGACCAGATACAGAATGCACAATATTTGCTGCAGAACAATGTGTAGCA
GTATTCTGGAAAGTTTTTC

ORF - retro_hsap_3385 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.85 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMETEQPEETFPNTETNGEFGKRPAEDMEEEQAFKRSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALRT
.ETEQPEE.FPNTETNGEFGK.PAEDMEEEQA.KRSRNTDEMVEL.ILLQ.KN.GAVIG.GGKNIKA...
RetrocopyVETEQPEESFPNTETNGEFGKCPAEDMEEEQALKRSRNTDEMVELHILLQNKNSGAVIGEGGKNIKAPCI
ParentalDYNASVSVPDSSGPERILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYKG
DY.ASVSVPDSSGP..ILSISA.IETIGEILKKIIPTLEEGLQLP..T.TSQL.LESDAVECLNYQHYKG
RetrocopyDYSASVSVPDSSGPKCILSISAGIETIGEILKKIIPTLEEGLQLPLLTPTSQLLLESDAVECLNYQHYKG
ParentalSDFDCELRLLIHQSLAGGI-IGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVVECIKII
.DF.CEL.LLI.QSLAGGI.IGVKGAKIKEL.EN.QTTIKLF.ECC.H.TDRVVLIGGKP.RVVECIKII
RetrocopyRDFECELKLLIYQSLAGGI<IGVKGAKIKEL*ENAQTTIKLF*ECCSHPTDRVVLIGGKPNRVVECIKII
ParentalLDLISESPIKGRAQPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRGGRPMPPSRRD
LDLISESPIKG.AQPYDP.FY.ETYDYGGFTMMFDDR.G.PVGFPM.GRGGFDRMPPG..GRPMPPSRR.
RetrocopyLDLISESPIKGPAQPYDPSFYNETYDYGGFTMMFDDRPGCPVGFPMWGRGGFDRMPPGWSGRPMPPSRR-
ParentalYDDMSPRRGPPPPPPGRGGRGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDRYDGMVGFSADETWDSAI
..DM.P.RGPPPP..GRGGRGGSRARNLPLPPPPPPRG.DLMAYDRRGRPGD.YDGMVGFS.DETW.SAI
Retrocopy--DMNPHRGPPPPLTGRGGRGGSRARNLPLPPPPPPRGEDLMAYDRRGRPGDCYDGMVGFSPDETWNSAI
ParentalDTWSPSEWQMAYEPQGGSGYDYSYAGGRGSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGA
DTWSPSEWQMAYEPQGGSGYDYSYAG..GSYGDLGGPI.T.QVTIPKDL.GSIIGKGGQRIKQI.HE.GA
RetrocopyDTWSPSEWQMAYEPQGGSGYDYSYAGIGGSYGDLGGPITTAQVTIPKDLTGSIIGKGGQRIKQIGHELGA
ParentalSIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYSGKFF
SIKIDEPLEGSED.I..ITGTQDQIQNAQYLLQN.V.QYSGKFF
RetrocopySIKIDEPLEGSEDQITIITGTQDQIQNAQYLLQNNV*QYSGKFF

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 .28 RPM 632 .24 RPM
bodymap2_adrenal 0 .25 RPM 629 .54 RPM
bodymap2_brain 0 .26 RPM 489 .31 RPM
bodymap2_breast 0 .16 RPM 490 .86 RPM
bodymap2_colon 0 .10 RPM 535 .89 RPM
bodymap2_heart 0 .02 RPM 269 .31 RPM
bodymap2_kidney 0 .15 RPM 464 .01 RPM
bodymap2_liver 0 .08 RPM 257 .46 RPM
bodymap2_lung 0 .16 RPM 592 .28 RPM
bodymap2_lymph_node 0 .00 RPM 446 .35 RPM
bodymap2_ovary 0 .10 RPM 648 .99 RPM
bodymap2_prostate 0 .23 RPM 490 .85 RPM
bodymap2_skeletal_muscle 0 .04 RPM 283 .35 RPM
bodymap2_testis 0 .04 RPM 574 .25 RPM
bodymap2_thyroid 0 .13 RPM 702 .41 RPM
bodymap2_white_blood_cells 0 .37 RPM 806 .90 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3385 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3385 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3385 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3385 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3385 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_2111
Parental genes homology:
Parental genes homology involve 14 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000211312 retrocopies
retro_btau_468, retro_btau_605,
Homo sapiens ENSG00000165119 3 retrocopies
retro_hsap_2323, retro_hsap_2674, retro_hsap_3385 ,
Homo sapiens ENSG000001971112 retrocopies
retro_hsap_4077, retro_hsap_83,
Microcebus murinus ENSMICG000000157803 retrocopies
retro_mmur_1562, retro_mmur_235, retro_mmur_448,
Myotis lucifugus ENSMLUG000000058712 retrocopies
retro_mluc_128, retro_mluc_561,
Macaca mulatta ENSMMUG000000188711 retrocopy
retro_mmul_2111,
Monodelphis domestica ENSMODG000000084021 retrocopy
retro_mdom_1666,
Mus musculus ENSMUSG000000215462 retrocopies
retro_mmus_1131, retro_mmus_2137,
Otolemur garnettii ENSOGAG000000074783 retrocopies
retro_ogar_2635, retro_ogar_2966, retro_ogar_3086,
Pongo abelii ENSPPYG000000193273 retrocopies
retro_pabe_2105, retro_pabe_2106, retro_pabe_42,
Sarcophilus harrisii ENSSHAG000000171091 retrocopy
retro_shar_820,
Tupaia belangeri ENSTBEG000000012891 retrocopy
retro_tbel_2491,
Tursiops truncatus ENSTTRG000000049061 retrocopy
retro_ttru_1622,
Tursiops truncatus ENSTTRG000000166937 retrocopies
retro_ttru_1144, retro_ttru_180, retro_ttru_1922, retro_ttru_444, retro_ttru_813, retro_ttru_930, retro_ttru_937,

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 = 0.6 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .11 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .29 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .18 RPM
CEU_NA12751 0 .15 RPM
CEU_NA12760 0 .13 RPM
CEU_NA12827 0 .14 RPM
CEU_NA12872 0 .35 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .08 RPM
FIN_HG00277 0 .37 RPM
FIN_HG00315 0 .11 RPM
FIN_HG00321 0 .24 RPM
FIN_HG00328 0 .09 RPM
FIN_HG00338 0 .15 RPM
FIN_HG00349 0 .20 RPM
FIN_HG00375 0 .29 RPM
FIN_HG00377 0 .23 RPM
FIN_HG00378 0 .23 RPM
GBR_HG00099 0 .17 RPM
GBR_HG00111 0 .11 RPM
GBR_HG00114 0 .13 RPM
GBR_HG00119 0 .14 RPM
GBR_HG00131 0 .46 RPM
GBR_HG00133 0 .43 RPM
GBR_HG00134 0 .20 RPM
GBR_HG00137 0 .19 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .32 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .07 RPM
TSI_NA20518 0 .22 RPM
TSI_NA20532 0 .17 RPM
TSI_NA20538 0 .60 RPM
TSI_NA20756 0 .09 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .14 RPM
TSI_NA20786 0 .08 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .17 RPM
YRI_NA18907 0 .49 RPM
YRI_NA18916 0 .32 RPM
YRI_NA19093 0 .21 RPM
YRI_NA19099 0 .13 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .12 RPM
YRI_NA19213 0 .22 RPM
YRI_NA19214 0 .15 RPM
YRI_NA19223 0 .14 RPM

Indel association:

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





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