RetrogeneDB ID:

retro_hsap_1191

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:13:42499733..42501331(+)
Located in intron of:ENSG00000102763
Retrocopy
information
Ensembl ID:ENSG00000229696
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:KARS
Ensembl ID:ENSG00000065427
Aliases:KARS, CMTRIB, DFNB89, KARS1, KARS2, KRS
Description:lysyl-tRNA synthetase [Source:HGNC Symbol;Acc:6215]


Retrocopy-Parental alignment summary:






>retro_hsap_1191
GTGGCAGTGGTACAGGGGGCTGAGGTGAAAGTGGATGGCAGCAAGCCAAAACTGAGCAAGAATGAGCTGAAGAGATCCCT
GAAAGCCAAGAAGAAAGTGGCAGAGAAGGAGGCCAAGCAGGAAGAACTCAGTGAGAAAGTTAAACCAGGCCACAGCTGCT
GTCACCAACCATACCACTGACAGTGGTGTGGGTACTGAGGAGAAGAGCCTGGACCCAAATCAACACTACAAGATCCATAG
TCAGGCAGTTTATCAACTGAATGTCAATGGGGAACACCCATACCCACACAAGTTCCATGCAGACATCTCATTCAATGACT
TCATCCAAGAATATAGTCACCAGCAGCCTGGGGGTCACCTGAATGATGTCACCTTAAAGGTGGCAGGTAGGATCCATGCT
AAAAGAGCTTCTGAGGGAAAGTTCATCTTCTATGACCTTCAAGGAGAGGGGGTCAAGTTGCAAGTCATGGTGAATCCCAG
AAATTATAAATCAGAAGAATTTATTCATATTAGTAAGAAACTGCATCAAGGAGACATAATTGGAGTTCAGGGGAACCCTG
GGAAAACCAAGAAGGGTGAGCTGAGCATCATTCCTTATGAGATCACACTGCTGTCTCCCCACATGCATATGTTACCTCAT
CTTCACTGTGGCCTCAAAGACCAGGAAACAAGGTATCATCAGAAATACTTGGACTTGATACTAAATGATTTTGTGAGGCA
GAAATTTATCATCTGCTCTAAGATCATCACATGTATAAGAAGTTTCTTGGATGAACTGGGATTCCTAAAGATTGAAACTC
CCATGGTGAACATCATCCCGGGGGAGCTGTGGCCAAGCTTTTCATCACTTATGACAATGCGCTGGACATGAGAATTGCTC
CGGAACTCTATCATAAGATGCTAGTGGTTGGTGGCACCAAGCAGATTTATGAAACTGGATGCCAGTTCCAGAATGAAGGG
ATTGATTTGAGGCACAATCCTGAGTTCACCACCTGCGAGTTCTATATGGCCTATGCAGACTACCACAATCTCTTGGAAAT
CACAGAGAAGATGGTTTCAGGGATGGTAAAGCATATTACAGGCAGTTACAAGGTCAGCTACCACCCAGATGGCCCATAGG
GCCAGGCCTATGATACTGACTTCACCCCACCCTTCCAGAGAATCAGCATGGTAGAAGAACTTGAGAAAGCCCTGGGGGGT
AAAGCTGCCAGAAACTAACCTCTTTGAAACTGATGAAACTTGCAAACTTCTTAATGATATCTGTGTGGCAAAAGCTGTTG
AATGCCCTCTACCTTGGACCACAGCCAGGCTCCTTGACAAGCTTGTAGGGGAGTTCCTGGAAATGATTTGCATCAATCCT
ACATTAATCTGTGATCATCCACAGATAATGAGCGCTATGGCAAATGGCACCGCTCTAAAGAGAATCTGTCCAAGCACTTT
GAGCTGCTTGTCATGAAGAAAGAGATAAGCGATGCCTAAACTAAGCTGAATAATCCTGTGCCGCAGCAGCGGGTTTTTGA
ACAACAGGCCAAAGCCAAGGCCACAGGTGATGATGAGGCCATTTCACAGATGAAAACTTCTGTACTGCCCTGGAATAC

ORF - retro_hsap_1191 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.31 %
Parental protein coverage: 90.28 %
Number of stop codons detected: 2
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMAAVQAAEVKVDGSEPKLSKNELKRRLKAE-KKVAEKEAKQKELSEKQLSQATAAATNHTTDNGVGPEEE
.A.VQ.AEVKVDGS.PKLSKNELKR.LKA...K........K..S...L.QATAA.TNHTTD.GVG.EE.
RetrocopyVAVVQGAEVKVDGSKPKLSKNELKRSLKAK>RKWQRRRPSRKN-SVRKLNQATAAVTNHTTDSGVGTEEK
ParentalSVDPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHLTDITLKVAGRIHAKRASG
S.DPNQ.YKI.SQA..QL.VNGE.PYPHKFH.DIS..DFIQ.YSH.QPG.HL.D.TLKVAGRIHAKRAS.
RetrocopySLDPNQHYKIHSQAVYQLNVNGEHPYPHKFHADISFNDFIQEYSHQQPGGHLNDVTLKVAGRIHAKRASE
ParentalGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPC
GK.IFYDL.GEGVKLQVM.N.RNYKSEE.FIHI..KL..GDIIGVQGNPGKTKKGELSIIPYEITLLSP.
RetrocopyGKFIFYDLQGEGVKLQVMVNPRNYKSEE-FIHISKKLHQGDIIGVQGNPGKTKKGELSIIPYEITLLSPH
ParentalLHMLPHLHFGLKDKETRYRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMMNIIPG-GA
.HMLPHLH.GLKD.ETRY.Q.YLDLILNDFVRQKFII.SKIIT.IRSFLDELGFL.IETPM.NIIPG.GA
RetrocopyMHMLPHLHCGLKDQETRYHQKYLDLILNDFVRQKFIICSKIITCIRSFLDELGFLKIETPMVNIIPG<GA
ParentalVAKPFITYHNELDMNLYMRIAPELYHKMLVVGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYH
VAK.FITY.N.LD....MRIAPELYHKMLVVGG....YE.G.QF.NEGIDL.HNPEFTTCEFYMAYADYH
RetrocopyVAKLFITYDNALD----MRIAPELYHKMLVVGGTKQIYETGCQFQNEGIDLRHNPEFTTCEFYMAYADYH
ParentalDLMEITEKMVSGMVKHITGSYKVTYHPDGPEGQAYDVDFTPPFRRINMVEELEKAL-GMKLPETNLFETE
.L.EITEKMVSGMVKHITGSYKV.YHPDGP.GQAYD.DFTPPF.RI.MVEELEKAL.G.KLPETNLFET.
RetrocopyNLLEITEKMVSGMVKHITGSYKVSYHPDGP*GQAYDTDFTPPFQRISMVEELEKAL>GVKLPETNLFETD
ParentalETRKILDDICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLA-KWHRSKEGLTERF
ET.K.L.DICVAKAVECP.P.TTARLLDKLVGEFLE..CINPT.ICDHPQIMS..A.KWHRSKE.L...F
RetrocopyETCKLLNDICVAKAVECPLPWTTARLLDKLVGEFLEMICINPTLICDHPQIMSAMA<KWHRSKENLSKHF
ParentalELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEAM-FIDENFCTALEY
EL.VMKKEI..A.T.LN.P..Q...FE.QAKAKA.GDDEA..F.DENFCTALEY
RetrocopyELLVMKKEISDA*TKLNNPVPQQRVFEQQAKAKATGDDEAI<FTDENFCTALEY

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 136 .54 RPM
bodymap2_adrenal 0 .04 RPM 138 .50 RPM
bodymap2_brain 0 .09 RPM 64 .74 RPM
bodymap2_breast 0 .00 RPM 94 .88 RPM
bodymap2_colon 0 .00 RPM 141 .93 RPM
bodymap2_heart 0 .09 RPM 91 .84 RPM
bodymap2_kidney 0 .08 RPM 90 .89 RPM
bodymap2_liver 0 .00 RPM 59 .10 RPM
bodymap2_lung 0 .14 RPM 95 .64 RPM
bodymap2_lymph_node 0 .00 RPM 94 .62 RPM
bodymap2_ovary 0 .00 RPM 126 .82 RPM
bodymap2_prostate 0 .00 RPM 134 .58 RPM
bodymap2_skeletal_muscle 0 .00 RPM 321 .82 RPM
bodymap2_testis 0 .00 RPM 203 .33 RPM
bodymap2_thyroid 0 .00 RPM 129 .28 RPM
bodymap2_white_blood_cells 0 .00 RPM 144 .41 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1191 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1191 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1191 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1191 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1191 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3036
Gorilla gorilla retro_ggor_930
Pongo abelii retro_pabe_992
Parental genes homology:
Parental genes homology involve 10 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000134471 retrocopy
retro_chof_2324,
Callithrix jacchus ENSCJAG000000142132 retrocopies
retro_cjac_4104, retro_cjac_608,
Homo sapiens ENSG00000065427 1 retrocopy
retro_hsap_1191 ,
Gorilla gorilla ENSGGOG000000055151 retrocopy
retro_ggor_930,
Mus musculus ENSMUSG000000319488 retrocopies
retro_mmus_3536, retro_mmus_3537, retro_mmus_3538, retro_mmus_3539, retro_mmus_3540, retro_mmus_3541, retro_mmus_3542, retro_mmus_3543,
Nomascus leucogenys ENSNLEG000000130721 retrocopy
retro_nleu_2080,
Pongo abelii ENSPPYG000000075671 retrocopy
retro_pabe_992,
Pan troglodytes ENSPTRG000000083641 retrocopy
retro_ptro_3036,
Pteropus vampyrus ENSPVAG000000067462 retrocopies
retro_pvam_1301, retro_pvam_723,
Sorex araneus ENSSARG000000114931 retrocopy
retro_sara_415,

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 = 0.06 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 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 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 .02 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .06 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .02 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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