RetrogeneDB ID:

retro_hsap_407

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:76209105..76210440(-)
Located in intron of:ENSG00000117054
Retrocopy
information
Ensembl ID:ENSG00000181227
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DLST
Ensembl ID:ENSG00000119689
Aliases:DLST, DLTS
Description:dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex) [Source:HGNC Symbol;Acc:2911]


Retrocopy-Parental alignment summary:






>retro_hsap_407
GTGTCCCGGGCGTTCAGCCACTCGCTCTCTGCCTTCCAGAAGGGGAACTGCCCTCTAGGGAGACATTCCCTGCCTGGGGT
CTCCTTATGCCAGGGACCAGGTTACCCTAACAGCAGGAAGGTTGTCATTAACAACAGTGTCTTCAGTGTTCGCTTCTTCA
GAACTACAACTGTATGCAAGTATGACTTGGTTACAGTCAAAACCCCAGCGTTTGCAGAACCTGTCACAGAGGGAGATGTC
AGGTGGGAGAAAGCTGTTGGAGACACAGTTGCAGAAGATGAAGTGGTTTGTGAGATTGAAACTGACAAGACATTGGTGCA
GGTTCCATCACCAGCAAATGGCATGATTGAAGCTCTTTTCGTACCTGATGGGGGAAAAGTCGAAGGAGGCACTCCGCTTT
TCACACTCAGGAAAACTGGTGCTGCTCCTGCTAAGGCCAAGCCGGCTGAAGCTCCTGCTGCTGCAGCCCCAAAAGCAGAA
CCTATAGCAGCGGCAGTTCCTCCCCATGCAGCACCCATACCCACTCGATGCCACCAGTGCCCTCGCCCTCACAACCTCCT
TCTAGCAAACCTGTGTCTGCAGTAAAACCCACTGCTGTCCCACCACTAGCTGAGCCAGGAGCTGGCAAAGGTCTGCATTC
AGAACATCAGGAGAAAATGAACAGGATGCGGCAGTGCATTGCTCAGCGTCTGAAGGAGGCCCAGAATACATGTGCCAATG
CTGACAATTTTTAATGAGATTGATGTGAGTAACATCCAGAAGATGAGGGCTCGGCACAAAGAGGCTTTTTTGAAGAAACA
TAACCTCAAACTAGGCTTCATGTCGGCATCTGTGAAGGCCTCAGCCTTTGCCTTGCAGGAACAGCCTGTTGTAAACGCAG
TGATTGATGATATAACCAAAGAGGTGGTATATAGGGATTATATTGACATCAGTGTTGCAGTGGCCACCCCACAGGGTCTG
GTGGTTCCAGTCATCAGGAATGTGGAAGCTATGAATTATGCAGATATTGAACAGACCATCACTGAACTGGGAGAGAAGGC
CCGAAAGAATGAATTTGCCATTGAAGATATGGATGGTGGTACCTTCACCATTAGCAATGGAGGTGTTTTTGGCTCACTCT
TTGAACACCCATTATCAACCCCCCTGTCTGCCATCCTGGGGATGCATGGCATCTTTGACAAGCCAGTGGCTATAGGAGGC
AAGGTAGAGGTGCAGCCCATGATGTACGTGGCACTGACCTATGATCACCGGCTGATTGATGGCAGAGAGGCTGTGACTTT
CCTCCGCAAAATCAAGGCAGCGGTAGAGGATCCCAGAGTCCTCCTCTTTGATCTT

ORF - retro_hsap_407 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.52 %
Parental protein coverage: 98.45 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVSRAFSRSLSAFQKGNCPLGRRSLPGVSLCQGPGYPNSRKVVINNSVFSVRFFRTTAVCKDDLVTVKTPA
VSRAFS.SLSAFQKGNCPLGR.SLPGVSLCQGPGYPNSRKVVINNSVFSVRFFRTT.VCK.DLVTVKTPA
RetrocopyVSRAFSHSLSAFQKGNCPLGRHSLPGVSLCQGPGYPNSRKVVINNSVFSVRFFRTTTVCKYDLVTVKTPA
ParentalFAESVTEGDVRWEKAVGDTVAEDEVVCEIETDKTSVQVPSPANGVIEALLVPDGGKVEGGTPLFTLRKTG
FAE.VTEGDVRWEKAVGDTVAEDEVVCEIETDKT.VQVPSPANG.IEAL.VPDGGKVEGGTPLFTLRKTG
RetrocopyFAEPVTEGDVRWEKAVGDTVAEDEVVCEIETDKTLVQVPSPANGMIEALFVPDGGKVEGGTPLFTLRKTG
ParentalAAPAKAKPAEAPAAAAPKAEPTAAAVPPPAAPIPTQ-MPPVPSPSQPPSGKPVSAVKPTVAPPLAEPGAG
AAPAKAKPAEAPAAAAPKAEP.AAAVPP.AAPIPT..MPPVPSPSQPPS.KPVSAVKPT..PPLAEPGAG
RetrocopyAAPAKAKPAEAPAAAAPKAEPIAAAVPPHAAPIPTR<MPPVPSPSQPPSSKPVSAVKPTAVPPLAEPGAG
ParentalKGLRSEHREKMNRMRQRIAQRLKEAQNTCA-MLTTFNEIDMSNIQEMRARHKEAFLKKHNLKLGFMSAFV
KGL.SEH.EKMNRMRQ.IAQRLKEAQNTCA.MLT.FNEID.SNIQ.MRARHKEAFLKKHNLKLGFMSA.V
RetrocopyKGLHSEHQEKMNRMRQCIAQRLKEAQNTCA>MLTIFNEIDVSNIQKMRARHKEAFLKKHNLKLGFMSASV
ParentalKASAFALQEQPVVNAVIDDTTKEVVYRDYIDISVAVATPRGLVVPVIRNVEAMNFADIERTITELGEKAR
KASAFALQEQPVVNAVIDD.TKEVVYRDYIDISVAVATP.GLVVPVIRNVEAMN.ADIE.TITELGEKAR
RetrocopyKASAFALQEQPVVNAVIDDITKEVVYRDYIDISVAVATPQGLVVPVIRNVEAMNYADIEQTITELGEKAR
ParentalKNELAIEDMDGGTFTISNGGVFGSLFGTPIINPPQSAILGMHGIFDRPVAIGGKVEVRPMMYVALTYDHR
KNE.AIEDMDGGTFTISNGGVFGSLF..P....P.SAILGMHGIFD.PVAIGGKVEV.PMMYVALTYDHR
RetrocopyKNEFAIEDMDGGTFTISNGGVFGSLFEHPL-STPLSAILGMHGIFDKPVAIGGKVEVQPMMYVALTYDHR
ParentalLIDGREAVTFLRKIKAAVEDPRVLLLDL
LIDGREAVTFLRKIKAAVEDPRVLL.DL
RetrocopyLIDGREAVTFLRKIKAAVEDPRVLLFDL

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 .08 RPM 84 .06 RPM
bodymap2_adrenal 0 .78 RPM 76 .97 RPM
bodymap2_brain 0 .38 RPM 37 .13 RPM
bodymap2_breast 0 .10 RPM 74 .28 RPM
bodymap2_colon 0 .06 RPM 67 .56 RPM
bodymap2_heart 0 .31 RPM 120 .55 RPM
bodymap2_kidney 0 .58 RPM 119 .10 RPM
bodymap2_liver 0 .08 RPM 63 .67 RPM
bodymap2_lung 0 .07 RPM 69 .41 RPM
bodymap2_lymph_node 0 .18 RPM 77 .57 RPM
bodymap2_ovary 0 .44 RPM 60 .64 RPM
bodymap2_prostate 0 .03 RPM 102 .02 RPM
bodymap2_skeletal_muscle 0 .00 RPM 105 .58 RPM
bodymap2_testis 0 .11 RPM 55 .35 RPM
bodymap2_thyroid 0 .77 RPM 84 .74 RPM
bodymap2_white_blood_cells 0 .18 RPM 76 .88 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_407 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_407 retrocopy
EST ID Start End Identity Match Mis-match Score
DA949096 76209174 76209716 100 542 0 542

TSS - click to see more details

No TSS is located nearby retro_hsap_407 retrocopy 5' end.

Lab - click to see more details

retro_hsap_407 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_407 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_312
Gorilla gorilla retro_ggor_403
Parental genes homology:
Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000093161 retrocopy
retro_cpor_1089,
Homo sapiens ENSG00000119689 1 retrocopy
retro_hsap_407 ,
Gorilla gorilla ENSGGOG000000115911 retrocopy
retro_ggor_403,
Nomascus leucogenys ENSNLEG000000163301 retrocopy
retro_nleu_1006,
Oryctolagus cuniculus ENSOCUG000000156061 retrocopy
retro_ocun_322,
Pan troglodytes ENSPTRG000000065431 retrocopy
retro_ptro_312,
Tursiops truncatus ENSTTRG000000019151 retrocopy
retro_ttru_681,
Xenopus tropicalis ENSXETG000000132641 retrocopy
retro_xtro_46,

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 = 2.07 RPM Legend:


Library Retrogene expression
CEU_NA11831 1 .28 RPM
CEU_NA11843 0 .74 RPM
CEU_NA11930 1 .63 RPM
CEU_NA12004 0 .46 RPM
CEU_NA12400 0 .74 RPM
CEU_NA12751 1 .48 RPM
CEU_NA12760 1 .08 RPM
CEU_NA12827 1 .23 RPM
CEU_NA12872 1 .47 RPM
CEU_NA12873 1 .02 RPM
FIN_HG00183 1 .46 RPM
FIN_HG00277 1 .66 RPM
FIN_HG00315 0 .99 RPM
FIN_HG00321 1 .42 RPM
FIN_HG00328 1 .28 RPM
FIN_HG00338 0 .72 RPM
FIN_HG00349 0 .51 RPM
FIN_HG00375 1 .64 RPM
FIN_HG00377 0 .50 RPM
FIN_HG00378 0 .93 RPM
GBR_HG00099 0 .58 RPM
GBR_HG00111 0 .64 RPM
GBR_HG00114 0 .97 RPM
GBR_HG00119 1 .63 RPM
GBR_HG00131 1 .55 RPM
GBR_HG00133 1 .45 RPM
GBR_HG00134 1 .22 RPM
GBR_HG00137 0 .99 RPM
GBR_HG00142 1 .69 RPM
GBR_HG00143 0 .45 RPM
TSI_NA20512 0 .45 RPM
TSI_NA20513 1 .55 RPM
TSI_NA20518 1 .14 RPM
TSI_NA20532 1 .60 RPM
TSI_NA20538 1 .24 RPM
TSI_NA20756 0 .44 RPM
TSI_NA20765 2 .07 RPM
TSI_NA20771 1 .16 RPM
TSI_NA20786 0 .58 RPM
TSI_NA20798 1 .00 RPM
YRI_NA18870 1 .35 RPM
YRI_NA18907 0 .73 RPM
YRI_NA18916 1 .28 RPM
YRI_NA19093 0 .68 RPM
YRI_NA19099 0 .67 RPM
YRI_NA19114 0 .71 RPM
YRI_NA19118 1 .08 RPM
YRI_NA19213 1 .12 RPM
YRI_NA19214 0 .76 RPM
YRI_NA19223 1 .59 RPM

Indel association:

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



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