RetrogeneDB ID:

retro_hsap_14

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:40235373..40236927(-)
Located in intron of:ENSG00000116985
Retrocopy
information
Ensembl ID:ENSG00000198754
Aliases:OXCT2, SCOTT
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:OXCT1
Ensembl ID:ENSG00000083720
Aliases:OXCT1, OXCT, SCOT
Description:3-oxoacid CoA transferase 1 [Source:HGNC Symbol;Acc:8527]


Retrocopy-Parental alignment summary:






>retro_hsap_14
ATGGCGGCGCTGCGGCTCCTGGCGTCAGTGCTCGGGCGCGGGGTCCCCGCCGGCGGCTCAGGGCTCGCGCTGTCCCAGGG
CTGCGCCCGCTGCTTTGCCACCAGTCCCCGGCTCCGTGCCAAGTTCTACGCGGACCCGGTGGAGATGGTGAAGGACATCT
CTGACGGGGCGACCGTCATGATCGGGGGCTTCGGGCTCTGCGGGATCCCCGAGAACCTGATCGCCGCGCTGCTCAGGACC
CGCGTGAAAGACCTGCAGGTGGTCAGCAGCAACGTGGGCGTGGAGGACTTCGGCCTGGGCCTCCTGCTGGCCGCCAGGCA
GGTCCGTCGCATCGTCTGTTCCTACGTGGGCGAGAACACCCTGTGCGAGAGCCAGTACCTGGCAGGAGAGCTGGAGCTGG
AGCTCACGCCCCAGGGCACCCTGGCCGAGCGCATCCGCGCGGGGGGCGCCGGGGTGCCCGCCTTCTACACCCCCACGGGC
TACGGGACCCTGGTCCAGGAAGGGGGCGCCCCCATCCGCTACACCCCGGACGGCCACCTGGCGCTCATGAGCCAGCCCCG
AGAGGTGAGGGAGTTCAACGGCGACCACTTCCTTTTGGAGCGCGCCATCCGGGCAGACTTCGCCCTGGTGAAAGGGTGGA
AGGCCGACCGGGCAGGAAACGTGGTCTTCAGGAGAAGCGCCCGCAATTTCAACGTGCCCATGTGCAAAGCTGCAGACGTC
ACGGCGGTGGAGGTGGAAGAGATCGTGGAGGTGGGGGCTTTCCCCCCAGAAGACATCCACGTTCCTAACATTTATGTAGA
TCGCGTGATAAAGGGGCAGAAATACGAGAAACGAATTGAGCGCTTAACGATCCTGAAAGAGGAAGATGGAGACGCTGGAA
AGGAAGAGGACGCCAGGACGCGCATCATCAGACGCGCAGCTCTGGAATTTGAGGACGGCATGTACGCCAATCTGGGCATA
GGCATCCCCCTGCTGGCCAGCAACTTCATCAGTCCCAGCATGACTGTCCATCTTCACAGTGAGAACGGGATCCTGGGCCT
GGGCCCGTTTCCCACGGAAGATGAGGTGGATGCCGACCTCATCAATGCAGGCAAGCAGACGGTCACGGTGCTTCCCGGGG
GCTGCTTCTTCGCCAGCGACGACTCCTTCGCCATGATCCGAGGGGGACACATCCAACTAACCATGCTTGGAGCCATGCAG
GTTTCCAAATACGGCGACCTGGCGAACTGGATGATCCCTGGCAAGAAGGTGAAAGGCATGGGCGGTGCCATGGACTTGGT
GTCCAGTCAGAAGACCAGAGTGGTGGTCACCATGCAGCACTGCACAAAGGACAACACCCCCAAGATCATGGAGAAATGCA
CCATGCCGCTGACCGGGAAGCGGTGCGTGGACCGCATCATCACCGAGAAGGCCGTGTTTGACGTGCACAGGAAGAAAGAG
CTGACGCTGAGGGAGCTCTGGGAGGGCCTGACGGTGGACGACATCAAAAAGAGCACGGGGTGTGCCTTTGCTGTGTCCCC
GAACCTCAGGCCCATGCAGCAGGTGGCACCCTGA

ORF - retro_hsap_14 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.37 %
Parental protein coverage: 99.81 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAALKLLSSGLRLCASARGSGATWYKGCVCSFSTSAHRHTKFYTDPVEAVKDIPDGATVLVGGFGLCGIP
MAAL.LL.S.L.....A.GSG.....GC...F.TS.....KFY.DPVE.VKDI.DGATV..GGFGLCGIP
RetrocopyMAALRLLASVLGRGVPAGGSGLALSQGCARCFATSPRLRAKFYADPVEMVKDISDGATVMIGGFGLCGIP
ParentalENLIDALLKTGVKGLTAVSNNAGVDNFGLGLLLRSKQIKRMVSSYVGENAEFERQYLSGELEVELTPQGT
ENLI.ALL.T.VK.L..VS.N.GV..FGLGLLL...Q..R.V.SYVGEN...E.QYL.GELE.ELTPQGT
RetrocopyENLIAALLRTRVKDLQVVSSNVGVEDFGLGLLLAARQVRRIVCSYVGENTLCESQYLAGELELELTPQGT
ParentalLAERIRAGGAGVPAFYTPTGYGTLVQEGGSPIKYNKDGSVAIASKPREVREFNGQHFILEEAITGDFALV
LAERIRAGGAGVPAFYTPTGYGTLVQEGG.PI.Y..DG..A..S.PREVREFNG.HF.LE.AI..DFALV
RetrocopyLAERIRAGGAGVPAFYTPTGYGTLVQEGGAPIRYTPDGHLALMSQPREVREFNGDHFLLERAIRADFALV
ParentalKAWKADRAGNVIFRKSARNFNLPMCKAAETTVVEVEEIVDIGAFAPEDIHIPQIYVHRLIKGEKYEKRIE
K.WKADRAGNV.FR.SARNFN.PMCKAA..T.VEVEEIV..GAF.PEDIH.P.IYV.R.IKG.KYEKRIE
RetrocopyKGWKADRAGNVVFRRSARNFNVPMCKAADVTAVEVEEIVEVGAFPPEDIHVPNIYVDRVIKGQKYEKRIE
ParentalRLSIRKEGDGEAKSAKPGDDVRERIIKRAALEFEDGMYANLGIGIPLLASNFISPNITVHLQSENGVLGL
RL.I.KE.DG.A.......D.R.RII.RAALEFEDGMYANLGIGIPLLASNFISP..TVHL.SENG.LGL
RetrocopyRLTILKEEDGDAGKE---EDARTRIIRRAALEFEDGMYANLGIGIPLLASNFISPSMTVHLHSENGILGL
ParentalGPYPRQHEADADLINAGKETVTILPGASFFSSDESFAMIRGGHVDLTMLGAMQVSKYGDLANWMIPGKMV
GP.P...E.DADLINAGK.TVT.LPG..FF.SD.SFAMIRGGH..LTMLGAMQVSKYGDLANWMIPGK.V
RetrocopyGPFPTEDEVDADLINAGKQTVTVLPGGCFFASDDSFAMIRGGHIQLTMLGAMQVSKYGDLANWMIPGKKV
ParentalKGMGGAMDLVSSAKTKVVVTMEHSAKGNAHKIMEKCTLPLTGKQCVNRIITEKAVFDVDKKKGLTLIELW
KGMGGAMDLVSS.KT.VVVTM.H..K.N..KIMEKCT.PLTGK.CV.RIITEKAVFDV..KK.LTL.ELW
RetrocopyKGMGGAMDLVSSQKTRVVVTMQHCTKDNTPKIMEKCTMPLTGKRCVDRIITEKAVFDVHRKKELTLRELW
ParentalEGLTVDDVQKSTGCDFAVSPKLMPMQQIA
EGLTVDD..KSTGC.FAVSP.L.PMQQ.A
RetrocopyEGLTVDDIKKSTGCAFAVSPNLRPMQQVA

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 .08 RPM 27 .17 RPM
bodymap2_adrenal 0 .41 RPM 35 .96 RPM
bodymap2_brain 0 .49 RPM 183 .25 RPM
bodymap2_breast 0 .00 RPM 110 .66 RPM
bodymap2_colon 0 .14 RPM 43 .95 RPM
bodymap2_heart 0 .18 RPM 247 .43 RPM
bodymap2_kidney 0 .00 RPM 69 .49 RPM
bodymap2_liver 0 .06 RPM 1 .03 RPM
bodymap2_lung 0 .05 RPM 12 .38 RPM
bodymap2_lymph_node 0 .11 RPM 28 .80 RPM
bodymap2_ovary 0 .33 RPM 29 .40 RPM
bodymap2_prostate 0 .19 RPM 51 .49 RPM
bodymap2_skeletal_muscle 0 .00 RPM 29 .79 RPM
bodymap2_testis 7 .18 RPM 44 .17 RPM
bodymap2_thyroid 0 .26 RPM 71 .75 RPM
bodymap2_white_blood_cells 0 .00 RPM 28 .59 RPM
RNA Polymerase II actvity near the 5' end of retro_hsap_14 was not detected
1 EST(s) were mapped to retro_hsap_14 retrocopy
EST ID Start End Identity Match Mis-match Score
HY047427 40235455 40235865 99.6 405 2 403
No TSS is located nearby retro_hsap_14 retrocopy 5' end.
retro_hsap_14 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_14 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_336

Parental genes homology:
Parental genes homology involve 16 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000331862 retrocopies
Dipodomys ordii ENSDORG000000163181 retrocopy
Equus caballus ENSECAG000000183121 retrocopy
Homo sapiens ENSG00000083720 1 retrocopy
retro_hsap_14 ,
Gorilla gorilla ENSGGOG000000250871 retrocopy
Myotis lucifugus ENSMLUG000000094311 retrocopy
Nomascus leucogenys ENSNLEG000000166561 retrocopy
Oryctolagus cuniculus ENSOCUG000000092311 retrocopy
Otolemur garnettii ENSOGAG000000099092 retrocopies
Pongo abelii ENSPPYG000000154282 retrocopies
Pan troglodytes ENSPTRG000000168291 retrocopy
Rattus norvegicus ENSRNOG000000430942 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000082711 retrocopy
Tarsius syrichta ENSTSYG000000136411 retrocopy
Tursiops truncatus ENSTTRG000000043311 retrocopy
Vicugna pacos ENSVPAG000000025501 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 ) > 0 RPM = 2.85 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .79 RPM
CEU_NA11843 0 .91 RPM
CEU_NA11930 1 .21 RPM
CEU_NA12004 2 .85 RPM
CEU_NA12400 0 .39 RPM
CEU_NA12751 1 .60 RPM
CEU_NA12760 0 .81 RPM
CEU_NA12827 0 .28 RPM
CEU_NA12872 1 .85 RPM
CEU_NA12873 1 .24 RPM
FIN_HG00183 0 .88 RPM
FIN_HG00277 0 .59 RPM
FIN_HG00315 0 .83 RPM
FIN_HG00321 1 .63 RPM
FIN_HG00328 1 .66 RPM
FIN_HG00338 1 .34 RPM
FIN_HG00349 1 .14 RPM
FIN_HG00375 2 .40 RPM
FIN_HG00377 2 .27 RPM
FIN_HG00378 0 .57 RPM
GBR_HG00099 0 .46 RPM
GBR_HG00111 1 .20 RPM
GBR_HG00114 2 .50 RPM
GBR_HG00119 1 .20 RPM
GBR_HG00131 0 .75 RPM
GBR_HG00133 0 .46 RPM
GBR_HG00134 0 .44 RPM
GBR_HG00137 1 .59 RPM
GBR_HG00142 0 .89 RPM
GBR_HG00143 0 .73 RPM
TSI_NA20512 2 .03 RPM
TSI_NA20513 0 .99 RPM
TSI_NA20518 2 .08 RPM
TSI_NA20532 0 .51 RPM
TSI_NA20538 2 .12 RPM
TSI_NA20756 1 .37 RPM
TSI_NA20765 0 .95 RPM
TSI_NA20771 0 .48 RPM
TSI_NA20786 0 .84 RPM
TSI_NA20798 1 .34 RPM
YRI_NA18870 0 .44 RPM
YRI_NA18907 1 .35 RPM
YRI_NA18916 1 .18 RPM
YRI_NA19093 1 .04 RPM
YRI_NA19099 1 .01 RPM
YRI_NA19114 1 .21 RPM
YRI_NA19118 1 .24 RPM
YRI_NA19213 1 .15 RPM
YRI_NA19214 0 .81 RPM
YRI_NA19223 0 .16 RPM


Indel association:

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




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