RetrogeneDB ID:

retro_hsap_169

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:73570489..73571964(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000229636
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:KRT8
Ensembl ID:ENSG00000170421
Aliases:KRT8, CARD2, CK-8, CK8, CYK8, K2C8, K8, KO
Description:keratin 8 [Source:HGNC Symbol;Acc:6446]


Retrocopy-Parental alignment summary:






>retro_hsap_169
GGAATCTATGCCTGGTTCAGCCTGCCTGCCTCCACTCCTGCCTCCACCATGTCCATGAGGGTGACCCAGAAGTCCTACAA
GGTGTCCACCTCCGGCCCCCGGGCCTTCAGCAGCTGCTCCTACAAGAGTGAGTCCGGTGCCTGCATCAGCTCCTCGAGCT
TCTCCCGAGTGGTCAGCAGCAGCTTCCCGGGTGGCCTGGGCAGAGGCTATGGCAGGTCCTGTGGTATGGGAAGCATCACC
ACTGTCACCGTCAACCAGAGCCTGCTGAGCCCTCTTAACCTGGAGGTGGACCCCAACATCCAGGCCATGCGCACCCAGGA
GAAGAAGCAGATCAAGACCCTCAACAACAAGTTTGCCTCCTTCATCAACAAGGAGCAGCAGAACAAGATGCTGGAGACTA
AGTGGAGCCTGCAGCACAGAAGATGCCTCGGAGCAACATGGACAACATGTTCAACAGCTACATCAACCTTCGGCAGCAGT
TGGAGACTGGGCCAGGAGAAGCTGAAGCTGAAGGCAGGGCTTGGCAACATGCAGGGGCTGGTGGAGGACTTCAAGAACAA
GTACCAGGATGAGATCAATAAGCTTACAAAGATGGAGAATGAATTTGTCCTCATCGAGAAGGATGTGGATGAAGCTTACA
CGAACAAAGTGGAGATAGAGTCTCACCTGGAACGGCTGACTGATGAGATCAGCTTCCTCAGGCAGCTGTCTGAAGAGGAG
ATCTGGGAGCTGCAGTCTCAGATCTCAGACACATCGGTGGTGCTATCCATTGACAACAGCCTCCCCCAGACATGGACGGC
ATCATTGCTGAAGTCAAGGGGCAGTACGAGGAGCTTGCCAACTGCAGCCGGGCTGAGGCTGAGAGCATGCACCAGATCAA
GTATGAGGATCTGCAGATGCTGGCAGAGAAGCACAGGGATGACCTGCAGCATACAAAGACTGAGATCTCCAAGATGAACA
GGAACATCAGCGGGCTCCAGGCTGAGACTGAGGGCCTCAAAGGCCAGAGGGCTTCCCCGGAGGCTGCCACGGCAGATTTC
GAGCAGCATGGGGAGCTGGCCCTTAACAATGCCAACACCAAGCTGTCCGAGCTGGAGGCCGCCGTGTAGCAGGCCAAGCA
GGACGCAGCGAGGCAGCTGCAGGAGTACCAGGAGCTGATAAACTTCAGGCTGGCCCTGGACGTCCAGATCGCCTCCTACA
GGAAGCTGCTGGAGGGCAAGGAGAGCTGGCTGGAGTGTGGGATGCAGAACATAAGTACCCATACGAAGACCACCAGCGGC
TAGGCAGATGGGCTGAGCTCGACCTATGGGGGCCTCACAAGCCCCGGCCTCAGCTACGTCCTGGGCTCCAGCTTTGACTC
TTGGGCGGGCTTCATCTCCTTCAACCGCACCAGCTCCACCAGGGCCATGGTTGTGAAGAAGATGGAGACCCTCGATGGGA
AGCTGGTGTCTGAGTCCTCTGACGTCCTCCCCAAG

ORF - retro_hsap_169 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.69 %
Parental protein coverage: 97.65 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalGISAWFGPPASTPASTMSIRVTQKSYKVSTSGPRAFSSRSYTSGPGSRISSSSFSRVGSSNFRGGLGGGY
GI.AWF..PASTPASTMS.RVTQKSYKVSTSGPRAFSS.SY.S..G..ISSSSFSRV.SS.F.GGLG.GY
RetrocopyGIYAWFSLPASTPASTMSMRVTQKSYKVSTSGPRAFSSCSYKSESGACISSSSFSRVVSSSFPGGLGRGY
ParentalGGASGMGGITAVTVNQSLLSPLVLEVDPNIQAVRTQEKEQIKTLNNKFASFIDKVRFLEQQNKMLETKWS
G...GMG.IT.VTVNQSLLSPL.LEVDPNIQA.RTQEK.QIKTLNNKFASFI.K....EQQNKMLETKWS
RetrocopyGRSCGMGSITTVTVNQSLLSPLNLEVDPNIQAMRTQEKKQIKTLNNKFASFINK----EQQNKMLETKWS
ParentalLLQQ-QKTARSNMDNMFESYINNLRRQLETLGQEKLKLE-AELGNMQGLVEDFKNKYEDEINKRTEMENE
.LQ..QK..RSNMDNMF.SYI.NLR.QLET.G......E.A.LGNMQGLVEDFKNKY.DEINK.T.MENE
Retrocopy-LQH<QKMPRSNMDNMFNSYI-NLRQQLET-GPGEAEAE>AGLGNMQGLVEDFKNKYQDEINKLTKMENE
ParentalFVLIKKDVDEAYMNKVELESRLEGLTDEINFLRQLYEEEIRELQSQISDTSVVLSMDNSRSL-DMDSIIA
FVLI.KDVDEAY.NKVE.ES.LE.LTDEI.FLRQL.EEEI.ELQSQISDTSVVLS.DNS....DMD.IIA
RetrocopyFVLIEKDVDEAYTNKVEIESHLERLTDEISFLRQLSEEEIWELQSQISDTSVVLSIDNSLPQ<DMDGIIA
ParentalEVKAQYEDIANRSRAEAESMYQIKYEELQSLAGKHGDDLRRTKTEISEMNRNISRLQAEIEGLKGQRASL
EVK.QYE..AN.SRAEAESM.QIKYE.LQ.LA.KH.DDL..TKTEIS.MNRNIS.LQAE.EGLKGQRAS.
RetrocopyEVKGQYEELANCSRAEAESMHQIKYEDLQMLAEKHRDDLQHTKTEISKMNRNISGLQAETEGLKGQRASP
ParentalEAAIADAEQRGELAIKDANAKLSELEAALQRAKQDMARQLREYQELMNVKLALDIEIATYRKLLEGEESR
EAA.AD.EQ.GELA...AN.KLSELEAA...AKQD.ARQL.EYQEL.N..LALD..IA.YRKLLEG.ES.
RetrocopyEAATADFEQHGELALNNANTKLSELEAAV*QAKQDAARQLQEYQELINFRLALDVQIASYRKLLEGKESW
ParentalLESGMQNMSIHTKTTSGYAGGLSSAYGGLTSPGLSYSLGSSFGSGAGSSSFSRTSSSRAVVVKKIETRDG
LE.GMQN.S.HTKTTSG.A.GLSS.YGGLTSPGLSY.LGSSF.S.AG..SF.RTSS.RA.VVKK.ET.DG
RetrocopyLECGMQNISTHTKTTSG*ADGLSSTYGGLTSPGLSYVLGSSFDSWAGFISFNRTSSTRAMVVKKMETLDG
ParentalKLVSESSDVLPK
KLVSESSDVLPK
RetrocopyKLVSESSDVLPK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 6 .86 RPM
bodymap2_adrenal 0 .00 RPM 4 .42 RPM
bodymap2_brain 0 .00 RPM 0 .56 RPM
bodymap2_breast 0 .00 RPM 56 .07 RPM
bodymap2_colon 0 .00 RPM 132 .45 RPM
bodymap2_heart 0 .00 RPM 32 .09 RPM
bodymap2_kidney 0 .00 RPM 197 .95 RPM
bodymap2_liver 0 .00 RPM 168 .59 RPM
bodymap2_lung 0 .00 RPM 176 .67 RPM
bodymap2_lymph_node 0 .00 RPM 8 .63 RPM
bodymap2_ovary 0 .00 RPM 45 .99 RPM
bodymap2_prostate 0 .00 RPM 95 .50 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .11 RPM
bodymap2_testis 0 .00 RPM 29 .77 RPM
bodymap2_thyroid 0 .00 RPM 375 .21 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .00 RPM
RNA Polymerase II actvity near the 5' end of retro_hsap_169 was not detected
No EST(s) were mapped for retro_hsap_169 retrocopy.


TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_966331543 libraries186 libraries98 libraries1 library1 library

The graphical summary, for retro_hsap_169 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

retro_hsap_169 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_169 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 16 parental genes, and 151 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000071992 retrocopies
Callithrix jacchus ENSCJAG000000181473 retrocopies
Cavia porcellus ENSCPOG000000026155 retrocopies
Dasypus novemcinctus ENSDNOG000000074003 retrocopies
Felis catus ENSFCAG000000002982 retrocopies
Homo sapiens ENSG00000170421 28 retrocopies
Gorilla gorilla ENSGGOG0000001467318 retrocopies
Macaca mulatta ENSMMUG0000000216322 retrocopies
Mustela putorius furoENSMPUG000000064417 retrocopies
Mus musculus ENSMUSG000000493821 retrocopy
Nomascus leucogenys ENSNLEG000000177338 retrocopies
Oryctolagus cuniculus ENSOCUG000000069451 retrocopy
Otolemur garnettii ENSOGAG0000001174016 retrocopies
Pongo abelii ENSPPYG0000000456231 retrocopies
Pteropus vampyrus ENSPVAG000000093603 retrocopies
Rattus norvegicus ENSRNOG000000097791 retrocopy

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:

The presence of retro_hsap_169 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_169 presence in various populations. Based on Kabza et al. 2015 (PubMed).


# Indel coordinates AFR, African AMR, Ad Mixed American EUR, European EAS, East Asian
ASW YRI LWK MXL PUR CLM CEU IBS GBR FIN TSI JPT CHB CHS
1. 1:73539134..73729800 100 100 100 100 98.18 100 100 100 100 100 100 100 100 100


Indel #1, located at the genomic coordinates 1:73539134..73729800.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 100 % Puerto Ricansfrom Puerto Rico PUR 98.18 % Colombians fromMedellin, Colombia CLM 100 % Americans of AfricanAncestry in SW USA ASW 100 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 100 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 100 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 100 % Finnish in Finland FIN 100 % Toscani in Italia TSI 100 % Han Chinese in Bejing,China CHB 100 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA





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