RetrogeneDB ID:

retro_hsap_3487

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:73696077..73697247(+)
Located in intron of:ENSG00000185760
Retrocopy
information
Ensembl ID:ENSG00000232422
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:KNOP1
Ensembl ID:ENSG00000103550
Aliases:None
Description:lysine-rich nucleolar protein 1 [Source:HGNC Symbol;Acc:34404]


Retrocopy-Parental alignment summary:






>retro_hsap_3487
ATGATCACCAAGAAACACAAAGCAGACCTGGGCCCTGGGCTCCCAGAGAAGAAAAAGAAGAAGAAAGTGGTCAAAGAACC
AGAGACTCAATACTCAATTTTAAACAATGATGATTACTTTGCCAATGTTTCTCCTATAAGAGCCACATCCCCCTCTAAGA
GTGTGGTCCATGGGAAGGCACCTGAGATGCCTCTAGTGAAGAAAACAAGTAAAAGAAGGGTGTCAGCACCCTTTGTGAGG
AGCACGTAGAACCTGACACCACGCTGCGTGCCAGACGGTCAGAGAAGTCACCCAATCCCAGGAAGCAGGTGCTTGGCCAT
TTGGAGTTCCTCTGTGGGGAGAAGAAAAAGAAGAAGTCACCTCCAGCCATGTCCCATGCCTCTGGGGTGAAAACCTCCCC
AGACCCCAGACAGGGTGAAGAGGAAACCAGAGTTGGCAAGAAGCTCAAATAACACAAGAAGGAAACAAAGGGGGCCCAGG
ACCCCACAGCCCTCTCAGTCCAGAACCCTTGGTTCTGCGAGGCTGGGGATGCTGCGGACACTTGCTCAGTGGGGAAGAAG
GGTGAGGAACAGGCAGCCTTGGGGCAGATAACGGAAGCAGAAGAGCCCCAGGGAGCACAGTGGGAAGGTGAAGAAGAAGA
AAACAAAAATCCACCAGGAGGGAGATGCCCTCCCAGGCCACTCCAAGCCCTTCAGGTCCATGGAGAGCAGCCCTAGGAAA
GGAAGTAAAACGAAGCCAAAGTTGAGGCTCCGGAATACATCCATCCCCAAAGGAGATGGCCCTAAGGCCCCCGAGAAGAA
AAAGATGAAGTCCAAGAAGGTAGAGCAGCCAATCATTGAGGAGCCGGCTCTGAAAAGGAAGAAAAAGAACAAGAGGAAAG
AGAGTGGGGCAGCAAGAGACCCTTGGAAGGAGGAAACAGAGACGGACTTAGAGGTGGTGTTGGAAAAGAAAGGCAACATG
GACGAGGCGCACATAGACCAGGTGAGGCGAAAGGCCTTGCAAGGAGAGATCGATCGAGAGTCAGGCAAAACGGAAGCTTG
TGAAACCAGGAAGTGGACGGGAACCTAGTTTGGCCAGTGGGATACTGCTGGTTTTGACAACGAGGAACAGAAACTGAAGT
TTCTCAAACTTACTGGTGGCTTCAAAAACCTGTCCCCTTCGTTCAGCCGC

ORF - retro_hsap_3487 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.12 %
Parental protein coverage: 85.59 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMITKTHKVDLG--LPEKKKKKKVVKEPETRYSVLNNDDYFADVSPLRATSPSKSVAHGQAPEMPLVKKKK
MITK.HK.DLG..LPEKKKKKKVVKEPET.YS.LNNDDYFA.VSP.RATSPSKSV.HG.APEMPLV.KK.
RetrocopyMITKKHKADLGPGLPEKKKKKKVVKEPETQYSILNNDDYFANVSPIRATSPSKSVVHGKAPEMPLV-KKT
ParentalKK-KKGVSTLCEEHVEPETTLPARRTEKSPSLRKQVFGHLEFLSGEKKNKKSPLAMSHASGVKTSPDPRQ
.K.KKGVSTLCEEHVEP.TTL.ARR.EKSP..RKQV.GHLEFL.GEKK.KKSP.AMSHASGVKTSPDPRQ
RetrocopySK<KKGVSTLCEEHVEPDTTLRARRSEKSPNPRKQVLGHLEFLCGEKKKKKSPPAMSHASGVKTSPDPRQ
ParentalGEEETRVGKKLKKHKKEKKGAQDPTAFSVQDPWFCEAREARDVGDTCSVGKKDEEQAALGQK-RKRKSPR
GEEETRVGKKLK.HKKE.KGAQDPTA.SVQ.PWFC...EA.D..DTCSVGKK.EEQAALGQ..RK.KSPR
RetrocopyGEEETRVGKKLK*HKKETKGAQDPTALSVQNPWFC---EAGDAADTCSVGKKGEEQAALGQI>RKQKSPR
ParentalEHNGKVKKKK-KIHQEGDALPGHSKPSRSMESSPRKGSKKKPVKVEAPEYIPISDDPKASAKKKMKSKKK
EH.GKVKKKK.KIHQEGDALPGHSKP.RSMESSPRKGSK.KP........IP..D.PKA..KKKMKSKK.
RetrocopyEHSGKVKKKKTKIHQEGDALPGHSKPFRSMESSPRKGSKTKPKLRLRNTSIPKGDGPKAPEKKKMKSKK-
ParentalVEQPVIEEPALKRKKKKKRKESGVAGDPWKEETDTDLEVVLEKKGNMDEAHIDQVRRKALQEEIDRESGK
VEQP.IEEPALKRKKK.KRKESG.A.DPWKEET.TDLEVVLEKKGNMDEAHIDQVRRKALQ.EIDRESGK
RetrocopyVEQPIIEEPALKRKKKNKRKESGAARDPWKEETETDLEVVLEKKGNMDEAHIDQVRRKALQGEIDRESGK
ParentalTEASETRKWTGTQFGQWDTAGFENEDQKLKFLRLMGGFKNLSPSFSR
TEA.ETRKWTGT.FGQWDTAGF.NE.QKLKFL.L.GGFKNLSPSFSR
RetrocopyTEACETRKWTGT*FGQWDTAGFDNEEQKLKFLKLTGGFKNLSPSFSR

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 4 .77 RPM
bodymap2_adrenal 0 .10 RPM 8 .43 RPM
bodymap2_brain 0 .00 RPM 7 .81 RPM
bodymap2_breast 0 .00 RPM 6 .17 RPM
bodymap2_colon 0 .00 RPM 2 .88 RPM
bodymap2_heart 0 .00 RPM 2 .71 RPM
bodymap2_kidney 0 .00 RPM 5 .71 RPM
bodymap2_liver 0 .00 RPM 3 .67 RPM
bodymap2_lung 0 .00 RPM 1 .79 RPM
bodymap2_lymph_node 0 .00 RPM 3 .65 RPM
bodymap2_ovary 0 .00 RPM 8 .66 RPM
bodymap2_prostate 0 .00 RPM 5 .54 RPM
bodymap2_skeletal_muscle 0 .00 RPM 2 .29 RPM
bodymap2_testis 0 .00 RPM 7 .15 RPM
bodymap2_thyroid 0 .00 RPM 7 .85 RPM
bodymap2_white_blood_cells 0 .00 RPM 4 .11 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3487 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3487 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3487 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3487 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3487 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2360
Macaca mulatta retro_mmul_1771
Parental genes homology:
Parental genes homology involve 9 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000180322 retrocopies
retro_cfam_1557, retro_cfam_1763,
Callithrix jacchus ENSCJAG000000096251 retrocopy
retro_cjac_3199,
Homo sapiens ENSG00000103550 3 retrocopies
retro_hsap_3487 , retro_hsap_4007, retro_hsap_979,
Gorilla gorilla ENSGGOG000000056731 retrocopy
retro_ggor_2691,
Macaca mulatta ENSMMUG000000027072 retrocopies
retro_mmul_1771, retro_mmul_798,
Nomascus leucogenys ENSNLEG000000124962 retrocopies
retro_nleu_1618, retro_nleu_551,
Otolemur garnettii ENSOGAG000000100654 retrocopies
retro_ogar_1115, retro_ogar_1480, retro_ogar_1481, retro_ogar_2259,
Pongo abelii ENSPPYG000000071513 retrocopies
retro_pabe_3293, retro_pabe_828, retro_pabe_920,
Pan troglodytes ENSPTRG000000078363 retrocopies
retro_ptro_2360, retro_ptro_767, retro_ptro_924,

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 = 0.09 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 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .06 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .09 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .08 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .05 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .07 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .08 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .02 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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