RetrogeneDB ID:

retro_hsap_1708

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:16:78082961..78083841(-)
Located in intron of:ENSG00000261540
Retrocopy
information
Ensembl ID:ENSG00000260731
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_1708
GGAATCTCCACTTGGTTCAGCCTGCCTACCTCCACTCTGCCTCCACTATGTCCATCAAGGTGACCCAGAAGTCCTACAAG
GTGTCCACCTCTGACCCCTGGGCCTTCAGCAGCCTCTCCTACACAAGTGGGCCCGGTGCCCCCATCAGCTTCTCTAGCTT
CTCCCGAGTGGGCAGCAGCAGCTTCCGGGGTGGCCAGGGTGGAGGCTATGCTGGGGCCAGTGGAATGGGAGGCATCACCA
TCATCACAGTCAACCAGAGCCTACTGAGCCCCCTTAACCTGGAGGTGGACCCCAACATCCAGGCCGTGCACACCCAGGAG
AAGGAGCAGGTCAAGACTCTCAACAAGTTTGCTTCCTTCATAGAGAAGGTACGGTTCCTGGAGCAGCAGAACAAGATGCT
TGGAGACCAAGTGGAGCCTCCTGCAGCAGCAGCAGATGGCTTGGAGCAACATGGACAAACATGTTCGAGAGCTACATCAA
TAACCTTAGGTGGCAGCTGGAGACTCTGGGCCAGGAGAAGCTGAAGCTGGAGGCAGAGTTTGGCAACATGAAGGGGCTGG
TGGAGAACTTCAAGAACAAGTATGAGGATGAGATCAATAAGCGTACAGAGGTGGGGAATGAATTTGTCCTCATCAAGAAG
GATGTGGATGAAGCTTACATGAACAAGGTAGAGCTGGAGTCTTGCCTGGAAGTCCTGACTGACGAGATCAACTTCTTCAG
TCAGCTATATGAAGAGGACATCCAGGAGCTGCAGTCCCAGATATCGGACACGTTTGTGGTGCTGTCCATGGACAACAGCC
GCACCCTGGACATGGACAGCATCATCACTGAGGTCAGGGCGCAGTATGAGGAGATCGCCAACTGCAGCCAGGCTGAGGCT

ORF - retro_hsap_1708 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.18 %
Parental protein coverage: 57.53 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalGISAWFGPPAST-PASTMSIRVTQKSYKVSTSGPRAFSSRSYTSGPGSRISSSSFSRVGSSNFRGGLGGG
GIS.WF..P.ST..ASTMSI.VTQKSYKVSTS.P.AFSS.SYTSGPG..IS.SSFSRVGSS.FRGG.GGG
RetrocopyGISTWFSLPTST<SASTMSIKVTQKSYKVSTSDPWAFSSLSYTSGPGAPISFSSFSRVGSSSFRGGQGGG
ParentalYGGASGMGGITAVTVNQSLLSPLVLEVDPNIQAVRTQEKEQIKTLNNKFASFIDKVRFLEQQNKML-ETK
Y.GASGMGGIT..TVNQSLLSPL.LEVDPNIQAV.TQEKEQ.KTLN.KFASFI.KVRFLEQQNKML.ETK
RetrocopyYAGASGMGGITIITVNQSLLSPLNLEVDPNIQAVHTQEKEQVKTLN-KFASFIEKVRFLEQQNKML>ETK
ParentalWSLLQQQKTARSNMD-NMFESYINNLRRQLETLGQEKLKLEAELGNMQGLVEDFKNKYEDEINKRTEMEN
WSLLQQQ..A.SNMD.NMFESYINNLR.QLETLGQEKLKLEAE.GNM.GLVE.FKNKYEDEINKRTE..N
RetrocopyWSLLQQQQMAWSNMD>NMFESYINNLRWQLETLGQEKLKLEAEFGNMKGLVENFKNKYEDEINKRTEVGN
ParentalEFVLIKKDVDEAYMNKVELESRLEGLTDEINFLRQLYEEEIRELQSQISDTSVVLSMDNSRSLDMDSIIA
EFVLIKKDVDEAYMNKVELES.LE.LTDEINF..QLYEE.I.ELQSQISDT.VVLSMDNSR.LDMDSII.
RetrocopyEFVLIKKDVDEAYMNKVELESCLEVLTDEINFFSQLYEEDIQELQSQISDTFVVLSMDNSRTLDMDSIIT
ParentalEVKAQYEDIANRSRAEA
EV.AQYE.IAN.S.AEA
RetrocopyEVRAQYEEIANCSQAEA

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 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

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1708 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1708 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1708 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1708 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1708 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
retro_cfam_1036, retro_cfam_1590,
Callithrix jacchus ENSCJAG000000181473 retrocopies
retro_cjac_124, retro_cjac_167, retro_cjac_216,
Cavia porcellus ENSCPOG000000026155 retrocopies
retro_cpor_1269, retro_cpor_1459, retro_cpor_233, retro_cpor_302, retro_cpor_516,
Dasypus novemcinctus ENSDNOG000000074003 retrocopies
retro_dnov_1267, retro_dnov_1886, retro_dnov_2358,
Felis catus ENSFCAG000000002982 retrocopies
retro_fcat_1142, retro_fcat_891,
Homo sapiens ENSG00000170421 28 retrocopies
retro_hsap_1012, retro_hsap_1024, retro_hsap_1324, retro_hsap_1513, retro_hsap_1557, retro_hsap_1599, retro_hsap_169, retro_hsap_1708 , retro_hsap_235, retro_hsap_2354, retro_hsap_2669, retro_hsap_2731, retro_hsap_2768, retro_hsap_2797, retro_hsap_2842, retro_hsap_3069, retro_hsap_3359, retro_hsap_3379, retro_hsap_3433, retro_hsap_371, retro_hsap_3963, retro_hsap_4203, retro_hsap_4688, retro_hsap_4691, retro_hsap_4775, retro_hsap_644, retro_hsap_844, retro_hsap_932,
Gorilla gorilla ENSGGOG0000001467318 retrocopies
retro_ggor_1160, retro_ggor_1787, retro_ggor_1862, retro_ggor_1897, retro_ggor_1900, retro_ggor_2320, retro_ggor_2662, retro_ggor_2913, retro_ggor_2918, retro_ggor_297, retro_ggor_2975, retro_ggor_382, retro_ggor_564, retro_ggor_66, retro_ggor_691, retro_ggor_751, retro_ggor_803, retro_ggor_809,
Macaca mulatta ENSMMUG0000000216322 retrocopies
retro_mmul_1069, retro_mmul_1122, retro_mmul_1178, retro_mmul_1349, retro_mmul_1351, retro_mmul_1412, retro_mmul_1697, retro_mmul_1753, retro_mmul_1810, retro_mmul_1855, retro_mmul_1866, retro_mmul_2097, retro_mmul_2137, retro_mmul_2357, retro_mmul_2431, retro_mmul_2546, retro_mmul_289, retro_mmul_488, retro_mmul_58, retro_mmul_766, retro_mmul_816, retro_mmul_886,
Mustela putorius furoENSMPUG000000064417 retrocopies
retro_mputfur_1101, retro_mputfur_1208, retro_mputfur_1271, retro_mputfur_1557, retro_mputfur_1587, retro_mputfur_556, retro_mputfur_895,
Mus musculus ENSMUSG000000493821 retrocopy
retro_mmus_2905,
Nomascus leucogenys ENSNLEG000000177338 retrocopies
retro_nleu_1913, retro_nleu_225, retro_nleu_2285, retro_nleu_2421, retro_nleu_2485, retro_nleu_2727, retro_nleu_2787, retro_nleu_672,
Oryctolagus cuniculus ENSOCUG000000069451 retrocopy
retro_ocun_313,
Otolemur garnettii ENSOGAG0000001174016 retrocopies
retro_ogar_1076, retro_ogar_1162, retro_ogar_1256, retro_ogar_1572, retro_ogar_1874, retro_ogar_1898, retro_ogar_1952, retro_ogar_2004, retro_ogar_2149, retro_ogar_2177, retro_ogar_2261, retro_ogar_2500, retro_ogar_3198, retro_ogar_3318, retro_ogar_339, retro_ogar_664,
Pongo abelii ENSPPYG0000000456231 retrocopies
retro_pabe_1102, retro_pabe_1261, retro_pabe_1289, retro_pabe_1460, retro_pabe_1743, retro_pabe_2063, retro_pabe_2077, retro_pabe_2129, retro_pabe_2142, retro_pabe_2214, retro_pabe_2270, retro_pabe_2352, retro_pabe_2544, retro_pabe_2741, retro_pabe_2763, retro_pabe_2787, retro_pabe_2842, retro_pabe_2926, retro_pabe_2943, retro_pabe_3138, retro_pabe_332, retro_pabe_3439, retro_pabe_3644, retro_pabe_3716, retro_pabe_417, retro_pabe_460, retro_pabe_569, retro_pabe_605, retro_pabe_701, retro_pabe_803, retro_pabe_851,
Pteropus vampyrus ENSPVAG000000093603 retrocopies
retro_pvam_1299, retro_pvam_1396, retro_pvam_45,
Rattus norvegicus ENSRNOG000000097791 retrocopy
retro_rnor_807,

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 .03 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 .03 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_1708 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_1708 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. 16:78079278..78095600 100 100 100 100 100 100 99.41 100 99.44 99.46 100 100 100 100

Indel #1, located at the genomic coordinates 16:78079278..78095600.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 100 % Puerto Ricansfrom Puerto Rico PUR 100 % 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 99.41 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 99.44 % Finnish in Finland FIN 99.46 % 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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