RetrogeneDB ID:

retro_hsap_585

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:70020368..70021256(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000234102
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:KRT19
Ensembl ID:ENSG00000171345
Aliases:KRT19, CK19, K19, K1CS
Description:keratin 19 [Source:HGNC Symbol;Acc:6436]


Retrocopy-Parental alignment summary:






>retro_hsap_585
CTGGCCTCCTACCTGGCCAAGGTGAACGCCCTGGAAGAGGTCACCTGAGAGCTGGGGGTGAAGGTCCATGGCTGGTACCA
GAAGCAAGGGCCTGGGCCCTCCTGTGGCTTACACCCACTACTTCAAGCCCATCAGGGACCTATGGGACAAGATTCTCACT
GCCACCATTGAGAACTTCAGGATTGTCCTGATGACCAACAGCACCCATCTGGCTGCAGATGACTTCTGAACCAAGTTTAA
GGAGCTGGCCCCGGGTCTGAGCCTGGAGATCCACATCAACGTTCTGTGCAGGGTGCTGGGCGAGCTGAGCCTGGCCAGGA
CTGACCTGGAGATGGGGATGGAAAGCCTGAAGGAGGAGCTGGCCTACCTGAAGAAAAATTGCCAGAAAGGAATTGTTGCC
CTGAGGGGCCAGGTGGGAGGCCTAGTCAGTGTGGTGATAGATTCCCCTCCAGGCATCAACCCAGCCTAGATCCTGAACAA
CGACTTGAGAAGCAAATAGGAAGTCATGGCTGAGCAGAACTAGGAGGGTGCTGAAGCCTGGTTAACCAGCCAGTCCCAGG
AGCTGAATCAGGAGGTTACCAGCCACATGAGCAGCTCCAGATGAGCAAATTCAAGGTCACTGACCTGCGGTGAACCCCCC
AGGGTTTTGACATTGAGCTGCAGCAGCTCAGCATGAAAGCCGCCCTGGAAGGCACACTGGAAGAAACAAGGGCCCTCTTT
GGAGCCAAGCTGGCACAGATCCAGGCGCTGGTCAGGGGTGTTGAAGCCCAGCAGGGTGACGTGGGTGCTGACAGCCAGCA
GCAGAACCAGCACCAGTGGTTCATGGACATCAAGTCTCAGCTGGAGGAGGAGATTACTATCTACTGAAGCCTGTCCTTGG
GCCAGGAT

ORF - retro_hsap_585 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.12 %
Parental protein coverage: 74.5 %
Number of stop codons detected: 7
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLASYLDKVRALEAANGELEVKIRDWYQKQGPGPSRD-YSHYYTTIQDLRDKILGATIENSRIVLQIDNAR
LASYL.KV.ALE....EL.VK...WYQKQGPGPS...Y.HY...I.DL.DKIL.ATIEN.RIVL......
RetrocopyLASYLAKVNALEEVT*ELGVKVHGWYQKQGPGPSCG>YTHYFKPIRDLWDKILTATIENFRIVLMTNSTH
ParentalLAADDFRTKFETEQALRMSVEADINGLRRVLDELTLARTDLEMQIEGLKEELAYLKKNHEEEISTLRGQV
LAADDF.TKF..E.A...S.E..IN.L.RVL.EL.LARTDLEM..E.LKEELAYLKKN....I..LRGQV
RetrocopyLAADDF*TKFK-ELAPGLSLEIHINVLCRVLGELSLARTDLEMGMESLKEELAYLKKNCQKGIVALRGQV
ParentalGGQVSVEVDSAPGTDLAKIL-SDMRSQYEVMAEQNRKDAEAWFTSRTEELNREVAGHT-EQLQMSRSEVT
GG.VSV..DS.PG...A.IL..D.RS..EVMAEQN...AEAW.TS...ELN.EV..H..EQLQMS...VT
RetrocopyGGLVSVVIDSPPGINPA*ILNNDLRSK*EVMAEQN*EGAEAWLTSQSQELNQEVTSHM<EQLQMSKFKVT
ParentalDLRRTLQGLEIELQSQLSMKAALEDTLAETEARFGAQLAHIQALISGIEAQLGDVRADSERQNQEYQRLM
DLR.T.QG..IELQ.QLSMKAALE.TL.ET.A.FGA.LA.IQAL..G.EAQ.GDV.ADS..QNQ..Q..M
RetrocopyDLR*TPQGFDIELQ-QLSMKAALEGTLEETRALFGAKLAQIQALVRGVEAQQGDVGADSQQQNQ-HQWFM
ParentalDIKSRLEQEIATYRSLLEGQE
DIKS.LE.EI..Y.SL..GQ.
RetrocopyDIKSQLEEEITIY*SLSLGQD

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 1 .75 RPM
bodymap2_adrenal 0 .00 RPM 0 .18 RPM
bodymap2_brain 0 .00 RPM 0 .21 RPM
bodymap2_breast 0 .02 RPM 62 .24 RPM
bodymap2_colon 0 .02 RPM 22 .85 RPM
bodymap2_heart 0 .00 RPM 0 .39 RPM
bodymap2_kidney 0 .00 RPM 89 .65 RPM
bodymap2_liver 0 .00 RPM 1 .54 RPM
bodymap2_lung 0 .00 RPM 87 .20 RPM
bodymap2_lymph_node 0 .00 RPM 7 .36 RPM
bodymap2_ovary 0 .00 RPM 69 .28 RPM
bodymap2_prostate 0 .00 RPM 113 .19 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .11 RPM
bodymap2_testis 0 .00 RPM 19 .17 RPM
bodymap2_thyroid 0 .00 RPM 20 .96 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .04 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_585 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_585 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_585 retrocopy 5' end.

Lab - click to see more details

retro_hsap_585 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_585 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_430
Gorilla gorilla retro_ggor_518
Pongo abelii retro_pabe_603
Parental genes homology:
Parental genes homology involve 14 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000297569 retrocopies
retro_cjac_1151, retro_cjac_1812, retro_cjac_2347, retro_cjac_2646, retro_cjac_3108, retro_cjac_3198, retro_cjac_3237, retro_cjac_3358, retro_cjac_633,
Equus caballus ENSECAG000000140862 retrocopies
retro_ecab_76, retro_ecab_931,
Echinops telfairi ENSETEG000000078816 retrocopies
retro_etel_1217, retro_etel_1319, retro_etel_191, retro_etel_480, retro_etel_685, retro_etel_95,
Homo sapiens ENSG00000171345 3 retrocopies
retro_hsap_3486, retro_hsap_585 , retro_hsap_959,
Gorilla gorilla ENSGGOG000000169013 retrocopies
retro_ggor_2352, retro_ggor_518, retro_ggor_773,
Macropus eugenii ENSMEUG000000161583 retrocopies
retro_meug_1860, retro_meug_403, retro_meug_826,
Macaca mulatta ENSMMUG000000186534 retrocopies
retro_mmul_1770, retro_mmul_717, retro_mmul_774, retro_mmul_790,
Nomascus leucogenys ENSNLEG000000107873 retrocopies
retro_nleu_1609, retro_nleu_2204, retro_nleu_800,
Oryctolagus cuniculus ENSOCUG000000161321 retrocopy
retro_ocun_1884,
Otolemur garnettii ENSOGAG000000243061 retrocopy
retro_ogar_1301,
Ochotona princeps ENSOPRG000000079082 retrocopies
retro_opri_337, retro_opri_673,
Pongo abelii ENSPPYG000000084163 retrocopies
retro_pabe_2880, retro_pabe_603, retro_pabe_820,
Pan troglodytes ENSPTRG000000091683 retrocopies
retro_ptro_2074, retro_ptro_2359, retro_ptro_430,
Ictidomys tridecemlineatus ENSSTOG000000144032 retrocopies
retro_itri_1514, retro_itri_697,

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:

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





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