RetrogeneDB ID:

retro_hsap_521

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:227598341..227599020(-)
Located in intron of:ENSG00000234277
Retrocopy
information
Ensembl ID:ENSG00000232864
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NUCKS1
Ensembl ID:ENSG00000069275
Aliases:NUCKS1, NUCKS
Description:nuclear casein kinase and cyclin-dependent kinase substrate 1 [Source:HGNC Symbol;Acc:29923]


Retrocopy-Parental alignment summary:






>retro_hsap_521
ATGTCGCGATTCTTCAGAACTAGGAAGGTTTGTTGATTACTCACAGTTTCAGGAATCTGGTGATGCAAATGAAGATTATG
GAAGAGATTCGGGCCCTATCACTAAGAAAATTTCATCATCTCCCCTAGAAGCTAAAAATAAGGCAATCTGGAAAGAATTC
ACAGGAAGATAGTGAGGACTCAGAAGAAAAAGATCTGAAGACAAAGAAGGATGATTTTCACTGAGCAGAGGATAATGAAG
ATGAAAATGAAGATGATAAAAATGTACGCCAGCACAGCAGGCAGCATCTAAAGCAGCTTCCAAACAGAGCTCATGGAAGA
TGTGGGCATGAGGAAGAACAAGAAGAGGATGAGACACCCTTCCAGGAGAATTCCAGCAGCAATGAAGATTTCCTGATGGA
AGATGATGACAATAGTGACTATGGCAATTCAAAAAAGAAAAACAAAAAGATGGTTAAGAAGTCCAAACCTGAGAGAAAAG
AAAAGAAAATGTCCAAACCCAGGCTAAAGGCTACAGTGACGCCAAGTCCAGTGAAAGGCAAAGGGAATGTGGGTCGCCCC
ACAGCTTCAAAGCCATCGAAGGAAAAGATTACTTCTCCCAAGGAAGATGAGGTACCAGAAAGCCCGCCAGAAAAGAAAAC
ATCTACAAGCCCCCACCCAAGAAATCTGGTGATGAAGGC

ORF - retro_hsap_521 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.45 %
Parental protein coverage: 95.88 %
Number of stop codons detected: 3
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMSRPVRNRKV-VDYSQFQESDDADEDYGRDSGPPT-KKIRSSPREAKNKRRSGKNSQEDSEDSEDKDVKT
MSR..R.RKV.VDYSQFQES.DA.EDYGRDSGP.T..K....P...K..R.SGKNSQEDSEDSE.KD.KT
RetrocopyMSRFFRTRKV>VDYSQFQESGDANEDYGRDSGPIT>RKFHHLP*KLKI-RQSGKNSQEDSEDSEEKDLKT
ParentalKKDDSHSAEDSEDEKEDHKNVRQQRQ-AASKAASKQREMLMEDV-GSEEEQEEEDEAPFQEKDSGSDEDF
KKDD.H.A...ED...........RQ..A....S.....LMEDV.G.EEEQEE.DE.PFQE..S.S.EDF
RetrocopyKKDDFH*A---EDNEDENEDDKNVRQ>TAGSI*SSFQTELMEDV<GHEEEQEE-DETPFQE-NSSSNEDF
ParentalLMEDDDDSDYGSSKKKNKKMVKKSKPERKEKKMPKPRLKATVTPSPVKGKGKVGRPTASKASKEKTPSPK
LMEDDD.SDYG.....................M.KPRLKATVTPSPVKGKG.VGRPTASK.SKEK..SPK
RetrocopyLMEDDDNSDYGNXXXXXXXXXXXXXXXXXXXXMSKPRLKATVTPSPVKGKGNVGRPTASKPSKEKITSPK
ParentalEEDEEPESPPEKKTSTS-PPPEKSGDEG
.EDE.PESPPEKKTSTS.PPP.KSGDEG
Retrocopy-EDEVPESPPEKKTSTS<PPPKKSGDEG

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 342 .97 RPM
bodymap2_adrenal 0 .00 RPM 267 .11 RPM
bodymap2_brain 0 .00 RPM 485 .80 RPM
bodymap2_breast 0 .00 RPM 299 .17 RPM
bodymap2_colon 0 .00 RPM 266 .45 RPM
bodymap2_heart 0 .00 RPM 314 .63 RPM
bodymap2_kidney 0 .00 RPM 190 .96 RPM
bodymap2_liver 0 .00 RPM 115 .27 RPM
bodymap2_lung 0 .00 RPM 270 .36 RPM
bodymap2_lymph_node 0 .00 RPM 147 .94 RPM
bodymap2_ovary 0 .00 RPM 517 .81 RPM
bodymap2_prostate 0 .00 RPM 284 .93 RPM
bodymap2_skeletal_muscle 0 .00 RPM 135 .75 RPM
bodymap2_testis 0 .06 RPM 268 .83 RPM
bodymap2_thyroid 0 .00 RPM 400 .56 RPM
bodymap2_white_blood_cells 0 .00 RPM 170 .42 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_521 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_521 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_521 retrocopy 5' end.

Lab - click to see more details

retro_hsap_521 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_521 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_389
Gorilla gorilla retro_ggor_480
Macaca mulatta retro_mmul_422
Parental genes homology:
Parental genes homology involve 16 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000129501 retrocopy
retro_amel_339,
Bos taurus ENSBTAG000000080011 retrocopy
retro_btau_541,
Choloepus hoffmanni ENSCHOG000000018551 retrocopy
retro_chof_437,
Dasypus novemcinctus ENSDNOG000000172122 retrocopies
retro_dnov_348, retro_dnov_6,
Dipodomys ordii ENSDORG000000031831 retrocopy
retro_dord_688,
Homo sapiens ENSG00000069275 1 retrocopy
retro_hsap_521 ,
Gorilla gorilla ENSGGOG000000266551 retrocopy
retro_ggor_480,
Macropus eugenii ENSMEUG000000078292 retrocopies
retro_meug_2015, retro_meug_372,
Macaca mulatta ENSMMUG000000056451 retrocopy
retro_mmul_422,
Monodelphis domestica ENSMODG000000018321 retrocopy
retro_mdom_980,
Nomascus leucogenys ENSNLEG000000145641 retrocopy
retro_nleu_2576,
Pan troglodytes ENSPTRG000000019041 retrocopy
retro_ptro_389,
Rattus norvegicus ENSRNOG000000472872 retrocopies
retro_rnor_2337, retro_rnor_2338,
Tupaia belangeri ENSTBEG000000156411 retrocopy
retro_tbel_2591,
Tarsius syrichta ENSTSYG000000009101 retrocopy
retro_tsyr_987,
Vicugna pacos ENSVPAG000000037511 retrocopy
retro_vpac_313,

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 .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 .03 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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