RetrogeneDB ID:

retro_hsap_27

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:61808069..61808309(-)
Located in intron of:ENSG00000068796
Retrocopy
information
Ensembl ID:ENSG00000268942
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:CKS1B
Ensembl ID:ENSG00000173207
Aliases:CKS1B, CKS1, PNAS-16, PNAS-18, ckshs1
Description:CDC28 protein kinase regulatory subunit 1B [Source:HGNC Symbol;Acc:19083]


Retrocopy-Parental alignment summary:






>retro_hsap_27
ATGTCGCACAAACAAATTTACTATTCGGACAAATACGATGACGAGGAGTTTGAGTATCGACATGTCATGCTGCCCAAGGA
CATAGCCAAGCTGGTCCCTAAAACCCATCTGATGTCTGAATCTGAATGGAGGAATCTTGGCGTTCAGCAGAGTCAGGGAT
GGGTCCATTATATGATCCATGAACCAGAACCTCACATCTTGCTGTTCCGGCGCCCACTACCCAAGAAACCAAAGAAATGA

ORF - retro_hsap_27 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 100. %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSHKQIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEPHILLFR
MSHKQIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEPHILLFR
RetrocopyMSHKQIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEPHILLFR
ParentalRPLPKKPKK
RPLPKKPKK
RetrocopyRPLPKKPKK

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 11 .69 RPM
bodymap2_adrenal 0 .00 RPM 8 .39 RPM
bodymap2_brain 0 .00 RPM 4 .01 RPM
bodymap2_breast 0 .00 RPM 19 .69 RPM
bodymap2_colon 0 .00 RPM 9 .63 RPM
bodymap2_heart 0 .00 RPM 2 .97 RPM
bodymap2_kidney 0 .00 RPM 9 .55 RPM
bodymap2_liver 0 .00 RPM 6 .30 RPM
bodymap2_lung 0 .00 RPM 9 .88 RPM
bodymap2_lymph_node 0 .00 RPM 10 .12 RPM
bodymap2_ovary 0 .00 RPM 11 .05 RPM
bodymap2_prostate 0 .00 RPM 7 .33 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .82 RPM
bodymap2_testis 0 .02 RPM 19 .93 RPM
bodymap2_thyroid 0 .00 RPM 5 .10 RPM
bodymap2_white_blood_cells 0 .00 RPM 5 .22 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_27 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_27 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_27 retrocopy 5' end.

Lab - click to see more details

retro_hsap_27 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_27 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 23 parental genes, and 62 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG0000003363510 retrocopies
retro_cjac_13, retro_cjac_1441, retro_cjac_1478, retro_cjac_1779, retro_cjac_2040, retro_cjac_2212, retro_cjac_2649, retro_cjac_276, retro_cjac_57, retro_cjac_876,
Cavia porcellus ENSCPOG000000240612 retrocopies
retro_cpor_859, retro_cpor_941,
Dipodomys ordii ENSDORG000000037646 retrocopies
retro_dord_25, retro_dord_290, retro_dord_599, retro_dord_64, retro_dord_647, retro_dord_739,
Equus caballus ENSECAG000000034601 retrocopy
retro_ecab_975,
Erinaceus europaeus ENSEEUG000000158951 retrocopy
retro_eeur_302,
Echinops telfairi ENSETEG000000033374 retrocopies
retro_etel_1246, retro_etel_1938, retro_etel_239, retro_etel_497,
Felis catus ENSFCAG000000013471 retrocopy
retro_fcat_1041,
Homo sapiens ENSG000001239751 retrocopy
retro_hsap_4183,
Homo sapiens ENSG00000173207 1 retrocopy
retro_hsap_27 ,
Gorilla gorilla ENSGGOG000000134194 retrocopies
retro_ggor_10, retro_ggor_1070, retro_ggor_2739, retro_ggor_659,
Loxodonta africana ENSLAFG000000322131 retrocopy
retro_lafr_243,
Myotis lucifugus ENSMLUG000000024081 retrocopy
retro_mluc_1303,
Mus musculus ENSMUSG000000280441 retrocopy
retro_mmus_280,
Nomascus leucogenys ENSNLEG000000115323 retrocopies
retro_nleu_1098, retro_nleu_2592, retro_nleu_411,
Oryctolagus cuniculus ENSOCUG000000162042 retrocopies
retro_ocun_1389, retro_ocun_18,
Otolemur garnettii ENSOGAG0000000638410 retrocopies
retro_ogar_1673, retro_ogar_1703, retro_ogar_1713, retro_ogar_1983, retro_ogar_2317, retro_ogar_245, retro_ogar_3310, retro_ogar_450, retro_ogar_530, retro_ogar_877,
Pongo abelii ENSPPYG000000007683 retrocopies
retro_pabe_1143, retro_pabe_3625, retro_pabe_717,
Pan troglodytes ENSPTRG000000013984 retrocopies
retro_ptro_2769, retro_ptro_3100, retro_ptro_558, retro_ptro_944,
Rattus norvegicus ENSRNOG000000425611 retrocopy
retro_rnor_97,
Sorex araneus ENSSARG000000123832 retrocopies
retro_sara_667, retro_sara_77,
Sarcophilus harrisii ENSSHAG000000047961 retrocopy
retro_shar_786,
Sus scrofa ENSSSCG000000297371 retrocopy
retro_sscr_730,
Vicugna pacos ENSVPAG000000121821 retrocopy
retro_vpac_532,

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 = 0.16 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .06 RPM
FIN_HG00349 0 .11 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .09 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .16 RPM
YRI_NA18870 0 .07 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .11 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .12 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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





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