RetrogeneDB ID:

retro_hsap_18

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:154393419..154397124(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000226650
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:KIF4A
Ensembl ID:ENSG00000090889
Aliases:KIF4A, KIF4, KIF4G1
Description:kinesin family member 4A [Source:HGNC Symbol;Acc:13339]


Retrocopy-Parental alignment summary:






>retro_hsap_18
ATGAAGGAAGAGGTGAAGGGAATTCCTGTAAGAGTGGCACTGCGTTGTCGCCCTCTGGTCCCCAAAGAGATTAGCGAGGG
CTGCCAGATGTGCCTTTCCTTCGTGCCCGGGGAGACTCAGGTGGTGGTTGGTACTGATAAATCCTTCACCTACGATTTTG
TGTTTGACCCCTGTACTGAGCAGGAAGAAGTCTTCAATAAAGCAGTAGCGCCGCTCATAAAAGGCATATTTAAAGGATAT
AATGCAACGGTCCTGGCCTATGGGCAGACTGGCTCTGGAAAAACCTATTCAATGGGAGGTGCATACACTGCGGAGCAGGA
GAATGAACCAACAGTTGGCATTATTCCTAGGGTAATACAACTGCTCTTCAAAGAAATTGATAAAAAGAGTGACTTTGAAT
TTACTCTGAAAGTGTCTTACTTAGAGATTTACAATGAAGAAATTTTGGATCTTCTATGCCCATCTCGTGAGAAAGCTCAA
ATAAATATACGGGAGGATCCTAAGGAAGGCATAAAGATTGTGGGACTCACTGAGAAGACTGTTTTAGTTGCCTTGGATAC
TGTTTCCTGTTTGGAGCAGGGCAACAACTCTAGGACTGTGGCCTCCACAGCTATGAACTCCCAGTCGTCCCGATCTCATG
CCATCTTTACAATCTCCATAGAGCAAAGAAAGAAAAGTGACAAGAATTGCAGCTTTCGCTCCAAGCTGCATCTTGTAGAT
CTCGCTGGATCAGAAAGACAGAAGAAAACCAAGGCTGAAGGGGATCGTCTAAAAGAGGGTATTAATATTAACCGAGGCCT
CCTATGCTTGGGAAATGTAATCAGTGCTCTTGGAGATGACAAAAAGGGTAGCTTTGTGCCCTACAGAGATTCCAAGTTAA
CTCGACTGCTGCAAGATTCTCTAGGAGGTAACAGCCACACTCTTATGATAGCCTGTGTGAGTCCTGCTGACTCCAATCTA
GAGGAAACATTAAGTACCCTTCGCTATGCTGACAGAGCAAGAAAAATCAAGAACAAACCTATTGTTAATATTGATCCCCA
CACAGCTGAACTTAATCATCTAAAGCAACAGGTACAACAGCTACAAGTCTTGTTGCTACAAGCCCATGGAGGTACCCTGC
CTGGATCTATAAATGCAGAACCATCAGAGAATCTACAATCCCTGATGGAGAAGAATCAGTCCCTGGTAGAGGAGAATGAA
AAATTAAGTCGTTGTCTGAGCAAGGCAGCTGGTCAGACAGCCCAGATGTTGGAGAGGATCATTTTGACAGAGCAAGTGAA
TGAAAAACTGAACGCCAAGCTAGAAGAGCTCAGGCAGCATGTGGCCTGCAAGCTGGATCTTCAAAAGCTAGTGGAGACTT
TGGAAGACCAGGAATTGAAAGAAAATGTAGAGATAATTTGTAACCTGCAGCAACTGATTACCCAGTTATCAGATGAAACT
GTTGCTTGCACGGCTGCAGCCATTGATACTGCGGTAGAAGAAGAAGCTCAAGTGGAAACCAGTCCAGAGACAAGCAGGTC
TTCTGACGCTTTTACCACTCAGCATGCTCTCCATCAAGCTCAGATGTCTAAGGAGGTGGTTGAGTTGAATAACGCCCTTG
CACTGAAAGAGGCCCTAGTTAGGAAGATGACTCAGAACGACAACCAACTACAGCCCATTCAGTTTCAATACCAGGATAAC
ATAAAAAATCTAGAATTAGAAGTCATCAATCTGCAAAAGGAAAAGGAAGAATTGGTTCGTGAACTTCAGACAGCAAAGAA
GAATGTCAACCAAGCCAAGCTGAGTGAGCACCGCCACAAACTTCTCCAGGAGCTGGAGGGTCAAATAGCTGATCTGAAGA
AGAAACTGAATGAGCAGTCCAAACTTCTGAAACTAAAGGAATCCACAGAGCGTACTGTCTCCAAGCTGAACCAAGAGATA
TGGATGATGAAAAACCAGCGGGTACAGTTAATGCGTCAAATGAAAGAGGATGCTGAGAAGTTTAGACAATGGAAGCAGAA
AAAAGACAAAGAAGTAATACAGTTGAAAGAACGAGACCGTAAGAGGCAATATGAGCTGCTCAAACTTGAAAGAAACTTCC
AGAAACAATCCAGTGTGCTCAGACGTAAAACGGAAGAGGCAGCAGCTGCCAACAAGCGACTCAAGGATGCTCTCCAGAAA
CAACGAGAGGTCACAGATAAGCGGAAAGAGACTCAGAGCCATGGAAAGGAAGGTATTGCAGCTCGAGTGAGGAATTGGCT
TGGAAATGAAATTGAGGTTATGGTCAGTACTGAGGAAGCCAAACGCCATCTGAATGACCTCCTTGAAGACAGAAAGATCC
TGGCTCAGGATGTGGTTCAACTCAAAGAAAAAAAGGAATCTCGGGAGAATCCACCTCCTAAACTCCGGAAGTGTACATTC
TCCCTTTCTGAGGTGCATGGTCAAGTTTTGGAGTCAGAAGATTGTATTACAAAACAGATTGAAAGCCTAGAGACTGAAAT
GGAACTCAGGAGTGCTCAGATTGCTGACCTACAGCAGAAGCTGCTGGATGCAGAAAGTGAAGATAGGCCAAAACAATGCT
GGGAGAATATTGCCACCATTCTGGAAGCCAAGTGTGCCCTGAAATATTTGATTGGAGAGCTGGTCTCCTCCAAAATACAT
GTCACCAAACTTGAAAACAGCCTGAGACAGAGCAAGGCCAGCTGTGCTGACATGCAGAAGATGCTATTTGAGGAACAAAA
TCATTTTTCTGAGATAGAGACAGAGTTACAAGCTGAGCTGGTCAGAATGGAGCAACAGCACCAAGAGAAGGTGCTATACC
TTGTCAGCCAGCTGCAGGAAAGCCAAATGGCAGAGAAGCAGTTAGAGAAATCAGCCAGTGAAAAGGAACAACAGCTGGTG
AGCACACTGCAGTGTCAGGATGAAGAACTTGAGAAGATGCGAGAAGTGTGTGAGCAAAATCAGCAGCTTCTCCAAGAGAA
TGAAATCATCAAGCAGAAACTGATCCTCCTCCAGGTAGCCAGCAGACAGAAACATCTTCCTAATGATACCCTTCTATCTC
CAGACTCTTCTTTTGAATATATCCCACCTAAGCCAAAACCTTCTCGTGTTAAAGAAAAGTTTCTGGAGCAAAGCATGGAC
ATCGAGGATCTAAAATATTGTTCAGAGCATTCTGTGAATGAGCATGAAGATGGTGATGGTGATGGCGACAGTGATGAGGG
GGATGATGAGGAATGGAAGCCAACAAAATTAGTCAAGGTGTCCAGGAAGAACATCCAAGGGTGTTCCTGCAAGGGCTGGT
GTGGGAACAAGCAGTGTGGGTGCAGGAAGCAAAAGTCAGACTGTGGTGTGGACTGTAGCTGTGACCCCACAAAGTGTCGG
AACCGCCAGCAAGGCAAGGATAGCTTGGGCACTGTTGAACAGACCCAGGATTCCGAAGGCTCCTTCAAACTGGAGGATCC
TACCGAGGTGACCCCAGGATTGAGCTTCTTTAACCCTGTCTGTGCCACCCCCAATAGCAAGATCCTGAAAGAGATGTGTG
ACATGGAGCAGGTGCTGTCAAAGAAGACTGCTCCAGCTCCCTCCCCTTTTGACCTCCCAGAGTCGAAACATGGAGCAACA
GAATACCAACAAAATAAGCCTCCAGGGAAGAAAAAGAAACGAGCTCTGGCTAGCAACACCAGCTTCTTCTCTGGCTGCTC
CCCTATCGAAGAAGAGGCCCACTGA

ORF - retro_hsap_18 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.76 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMKEEVKGIPVRVALRCRPLVPKEISEGCQMCLSFVPGEPQVVVGTDKSFTYDFVFDPSTEQEEVFNTAVA
MKEEVKGIPVRVALRCRPLVPKEISEGCQMCLSFVPGE.QVVVGTDKSFTYDFVFDP.TEQEEVFN.AVA
RetrocopyMKEEVKGIPVRVALRCRPLVPKEISEGCQMCLSFVPGETQVVVGTDKSFTYDFVFDPCTEQEEVFNKAVA
ParentalPLIKGVFKGYNATVLAYGQTGSGKTYSMGGAYTAEQENEPTVGVIPRVIQLLFKEIDKKSDFEFTLKVSY
PLIKG.FKGYNATVLAYGQTGSGKTYSMGGAYTAEQENEPTVG.IPRVIQLLFKEIDKKSDFEFTLKVSY
RetrocopyPLIKGIFKGYNATVLAYGQTGSGKTYSMGGAYTAEQENEPTVGIIPRVIQLLFKEIDKKSDFEFTLKVSY
ParentalLEIYNEEILDLLCPSREKAQINIREDPKEGIKIVGLTEKTVLVALDTVSCLEQGNNSRTVASTAMNSQSS
LEIYNEEILDLLCPSREKAQINIREDPKEGIKIVGLTEKTVLVALDTVSCLEQGNNSRTVASTAMNSQSS
RetrocopyLEIYNEEILDLLCPSREKAQINIREDPKEGIKIVGLTEKTVLVALDTVSCLEQGNNSRTVASTAMNSQSS
ParentalRSHAIFTISLEQRKKSDKNSSFRSKLHLVDLAGSERQKKTKAEGDRLKEGININRGLLCLGNVISALGDD
RSHAIFTIS.EQRKKSDKN.SFRSKLHLVDLAGSERQKKTKAEGDRLKEGININRGLLCLGNVISALGDD
RetrocopyRSHAIFTISIEQRKKSDKNCSFRSKLHLVDLAGSERQKKTKAEGDRLKEGININRGLLCLGNVISALGDD
ParentalKKGGFVPYRDSKLTRLLQDSLGGNSHTLMIACVSPADSNLEETLNTLRYADRARKIKNKPIVNIDPQTAE
KKG.FVPYRDSKLTRLLQDSLGGNSHTLMIACVSPADSNLEETL.TLRYADRARKIKNKPIVNIDP.TAE
RetrocopyKKGSFVPYRDSKLTRLLQDSLGGNSHTLMIACVSPADSNLEETLSTLRYADRARKIKNKPIVNIDPHTAE
ParentalLNHLKQQVQQLQVLLLQAHGGTLPGSITVEPSENLQSLMEKNQSLVEENEKLSRGLSEAAGQTAQMLERI
LNHLKQQVQQLQVLLLQAHGGTLPGSI..EPSENLQSLMEKNQSLVEENEKLSR.LS.AAGQTAQMLERI
RetrocopyLNHLKQQVQQLQVLLLQAHGGTLPGSINAEPSENLQSLMEKNQSLVEENEKLSRCLSKAAGQTAQMLERI
ParentalILTEQANEKMNAKLEELRQHAACKLDLQKLVETLEDQELKENVEIICNLQQLITQLSDETVACMAAAIDT
ILTEQ.NEK.NAKLEELRQH.ACKLDLQKLVETLEDQELKENVEIICNLQQLITQLSDETVAC.AAAIDT
RetrocopyILTEQVNEKLNAKLEELRQHVACKLDLQKLVETLEDQELKENVEIICNLQQLITQLSDETVACTAAAIDT
ParentalAVEQEAQVETSPETSRSSDAFTTQHALRQAQMSKELVELNKALALKEALARKMTQNDSQLQPIQYQYQDN
AVE.EAQVETSPETSRSSDAFTTQHAL.QAQMSKE.VELN.ALALKEAL.RKMTQND.QLQPIQ.QYQDN
RetrocopyAVEEEAQVETSPETSRSSDAFTTQHALHQAQMSKEVVELNNALALKEALVRKMTQNDNQLQPIQFQYQDN
ParentalIKELELEVINLQKEKEELVLELQTAKKDANQAKLSERRRKRLQELEGQIADLKKKLNEQSKLLKLKESTE
IK.LELEVINLQKEKEELV.ELQTAKK..NQAKLSE.R.K.LQELEGQIADLKKKLNEQSKLLKLKESTE
RetrocopyIKNLELEVINLQKEKEELVRELQTAKKNVNQAKLSEHRHKLLQELEGQIADLKKKLNEQSKLLKLKESTE
ParentalRTVSKLNQEIRMMKNQRVQLMRQMKEDAEKFRQWKQKKDKEVIQLKERDRKRQYELLKLERNFQKQSNVL
RTVSKLNQEI.MMKNQRVQLMRQMKEDAEKFRQWKQKKDKEVIQLKERDRKRQYELLKLERNFQKQS.VL
RetrocopyRTVSKLNQEIWMMKNQRVQLMRQMKEDAEKFRQWKQKKDKEVIQLKERDRKRQYELLKLERNFQKQSSVL
ParentalRRKTEEAAAANKRLKDALQKQREVADKRKETQSRGMEGTAARVKNWLGNEIEVMVSTEEAKRHLNDLLED
RRKTEEAAAANKRLKDALQKQREV.DKRKETQS.G.EG.AARV.NWLGNEIEVMVSTEEAKRHLNDLLED
RetrocopyRRKTEEAAAANKRLKDALQKQREVTDKRKETQSHGKEGIAARVRNWLGNEIEVMVSTEEAKRHLNDLLED
ParentalRKILAQDVAQLKEKKESGENPPPKLRRRTFSLTEVRGQVSESEDSITKQIESLETEMEFRSAQIADLQQK
RKILAQDV.QLKEKKES.ENPPPKLR..TFSL.EV.GQV.ESED.ITKQIESLETEME.RSAQIADLQQK
RetrocopyRKILAQDVVQLKEKKESRENPPPKLRKCTFSLSEVHGQVLESEDCITKQIESLETEMELRSAQIADLQQK
ParentalLLDAESEDRPKQRWENIATILEAKCALKYLIGELVSSKIQVSKLESSLKQSKTSCADMQKMLFEERNHFA
LLDAESEDRPKQ.WENIATILEAKCALKYLIGELVSSKI.V.KLE.SL.QSK.SCADMQKMLFEE.NHF.
RetrocopyLLDAESEDRPKQCWENIATILEAKCALKYLIGELVSSKIHVTKLENSLRQSKASCADMQKMLFEEQNHFS
ParentalEIETELQAELVRMEQQHQEKVLYLLSQLQQSQMAEKQLEESVSEKEQQLLSTLKCQDEELEKMREVCEQN
EIETELQAELVRMEQQHQEKVLYL.SQLQ.SQMAEKQLE.S.SEKEQQL.STL.CQDEELEKMREVCEQN
RetrocopyEIETELQAELVRMEQQHQEKVLYLVSQLQESQMAEKQLEKSASEKEQQLVSTLQCQDEELEKMREVCEQN
ParentalQQLLRENEIIKQKLTLLQVASRQKHLPKDTLLSPDSSFEYVPPKPKPSRVKEKFLEQSMDIEDLKYCSEH
QQLL.ENEIIKQKL.LLQVASRQKHLP.DTLLSPDSSFEY.PPKPKPSRVKEKFLEQSMDIEDLKYCSEH
RetrocopyQQLLQENEIIKQKLILLQVASRQKHLPNDTLLSPDSSFEYIPPKPKPSRVKEKFLEQSMDIEDLKYCSEH
ParentalSVNEHE--DGDGDDDEGDDEEWKPTKLVKVSRKNIQGCSCKGWCGNKQCGCRKQKSDCGVDCCCDPTKCR
SVNEHE..DGDGD.DEGDDEEWKPTKLVKVSRKNIQGCSCKGWCGNKQCGCRKQKSDCGVDC.CDPTKCR
RetrocopySVNEHEDGDGDGDSDEGDDEEWKPTKLVKVSRKNIQGCSCKGWCGNKQCGCRKQKSDCGVDCSCDPTKCR
ParentalNRQQGKDSLGTVERTQDSEGSFKLEDPTEVTPGLSFFNPVCATPNSKILKEMCDVEQVLSKKTPPAPSPF
NRQQGKDSLGTVE.TQDSEGSFKLEDPTEVTPGLSFFNPVCATPNSKILKEMCD.EQVLSKKT.PAPSPF
RetrocopyNRQQGKDSLGTVEQTQDSEGSFKLEDPTEVTPGLSFFNPVCATPNSKILKEMCDMEQVLSKKTAPAPSPF
ParentalDLPELKHVATEYQENKAPGKKKKRALASNTSFFSGCSPIEEEAH
DLPE.KH.ATEYQ.NK.PGKKKKRALASNTSFFSGCSPIEEEAH
RetrocopyDLPESKHGATEYQQNKPPGKKKKRALASNTSFFSGCSPIEEEAH

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 0 .85 RPM
bodymap2_adrenal 0 .00 RPM 0 .88 RPM
bodymap2_brain 0 .05 RPM 0 .94 RPM
bodymap2_breast 0 .00 RPM 0 .62 RPM
bodymap2_colon 0 .00 RPM 1 .57 RPM
bodymap2_heart 0 .00 RPM 0 .55 RPM
bodymap2_kidney 0 .00 RPM 0 .45 RPM
bodymap2_liver 0 .00 RPM 0 .21 RPM
bodymap2_lung 0 .00 RPM 0 .25 RPM
bodymap2_lymph_node 0 .00 RPM 1 .86 RPM
bodymap2_ovary 0 .00 RPM 2 .14 RPM
bodymap2_prostate 0 .00 RPM 0 .21 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .20 RPM
bodymap2_testis 7 .67 RPM 5 .28 RPM
bodymap2_thyroid 0 .00 RPM 0 .66 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .33 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_18 was not detected

EST - click to see more details

6 EST(s) were mapped to retro_hsap_18 retrocopy
EST ID Start End Identity Match Mis-match Score
AL044084 154395387 154395804 99.8 416 1 415
DB060480 154393314 154393883 99.5 569 0 568
DB065349 154393323 154393861 100 538 0 538
DB072048 154393313 154393869 99.5 556 0 555
DB083049 154393315 154393864 99.9 548 1 547
DB094835 154393314 154393873 99.7 557 2 555

TSS - click to see more details

No TSS is located nearby retro_hsap_18 retrocopy 5' end.

Lab - click to see more details

retro_hsap_18 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_18 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000155661 retrocopy
retro_cjac_2142,
Cavia porcellus ENSCPOG000000002111 retrocopy
retro_cpor_681,
Homo sapiens ENSG00000090889 1 retrocopy
retro_hsap_18 ,
Gorilla gorilla ENSGGOG000000066311 retrocopy
retro_ggor_2218,
Myotis lucifugus ENSMLUG000000110481 retrocopy
retro_mluc_114,
Mus musculus ENSMUSG000000343111 retrocopy
retro_mmus_268,
Pongo abelii ENSPPYG000000204381 retrocopy
retro_pabe_2700,
Rattus norvegicus ENSRNOG000000380351 retrocopy
retro_rnor_2330,

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 = 0.21 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .06 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .10 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 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 .03 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .11 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 .07 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .10 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .09 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .08 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .17 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .21 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .14 RPM
YRI_NA19214 0 .05 RPM
YRI_NA19223 0 .08 RPM

Indel association:

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



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