RetrogeneDB ID:

retro_hsap_2583

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:22:34985586..34987269(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000235485
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ACO2
Ensembl ID:ENSG00000100412
Aliases:ACO2, ACONM, ICRD
Description:aconitase 2, mitochondrial [Source:HGNC Symbol;Acc:118]


Retrocopy-Parental alignment summary:






>retro_hsap_2583
ATGGTGCCCTACAGCCTACTGGTTACTTGGCTGCAGAAAGCTCTGGGTGTGCGGCAGTACCATGTGGCATCAGTCCTGTG
CCAACGGGCCAAGGTGGCGATGAGACCCTTTGAGCCTAAGTACATCCACTATGACCTGCTAGAGAAGAACATTAACATTG
TTTGCAAATGATTGAACCGGCCTCTGACCCTCTCAGAGAAGATCGTGTACAGACACCCGGATGACCCCACCAGCCAGGAA
ATTGAGCGGGGCGGGACGTACCTGCAGCAGTGGCCGGACAGCGTGACCATGCAGGATGGACGGCCCAGATGGCCATGCTG
CAGTTCATCAGCAGCAGGCTCCCAAGGTGACCATGCCATCCACCATCCACTGTGACCATCTGATTGAGGCCCAGCTCGGG
AGTGAGAAAGACCTGCACCAGGCCAAGGACATCAACCACGAAGTTTATAATTTCCTGGCAACTGGAAGTGTCAAATATGG
CTTGAGCTTCTGGAAGCCTGGATCTGGAATCATTCACCAGATTATTCTGGAAAACTATGAATATCCTGGGGTTCTTCTGA
TTGGCACTGACTCCCACACCCCCAATGGTGGCAGCCTGGGGGGCATCTGCATTGGAGTTGGGGGTGCCGAGCTGTGGATG
TCATGACTGGGATCCCCTGGGAGCTGAAGTGCCCCAAGGTGATTGGCGTGAAGCTGATGGGCTCCCTCTCTGGTTGGACC
TCACCCAAAGATGTGATCCTGAAGGTGGCAGGCATCCTCACCATGAAAGGTGGCACAGGTGCAATCGTGGAATACCACGG
GCCTGTTGTAGACTCCATCTCCTGCACTGGCATGGTGACAGTCTGCAACATGGGCTTAGAAATTGGGACCACCACTTCCG
TGTTCCATTACAACCTCAGGATGAAGAAGTACATGAGCAAGACCTGCCAGGCAGACATTGCCAATCTAGCTGATGAATTC
AAAGATCACTTGGTGCCTGACCCTGGGTGCCATTATGACCAACTAATTGAAGTTAACCCCAGTGAACTGAAGCTGCACAT
CAATGGGCCCTTCACCCCTGACCTGGCTCACCCTGTGGCAGAAGTGGGCAAGGTGGCAGAGAAGGAAGAATGGCCTCTGG
ACATCTGAGTGGGTCTGTGGGGCAGCTGCACCAATTCAAGCTATGAAGATATGGGGTGCTCAGCAGGTGTGGCCAAGCAG
GCACTGGCCCATGGCCTCAAGTGCAAGTCCCAGTTCACTATTACTCCATGCTCCGAGCAGATCCGTGCCTCCATTGAGCA
GGATGGCTATGCACAGACCTTGAGGGATGTGGGTGGCATCGTCCTGGCCAATGCTTGTGGCCCCTGCATTGGTCAGTTGC
ACAGAAAGGACATCAACAAGCAGGAGAAGAACATAATTGTCACCTCCTACAACAGGAACTTCATGGGCCACAATGACACG
AACCCCGAGACCCATGCCTTCATCACATCCCCAGAGACTGTCACAGCCCTGGCCATTGTGGGAACCCTCAAGTTCAACCC
AGAGACCAACTACCTGACAGGCAAGGATGGCAAGAAGTTCAAGCTGGAGGCTCCGGATGCAGATGAGCTTCCCCAAGCAG
AGTTTGGCCCAGGGCAGGACACCTACCAGCACCCCCGCATGGGGTACCACTGACCACATCTCAGCTGCCGGCCCCTGACT
CAA

ORF - retro_hsap_2583 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.86 %
Parental protein coverage: 72.18 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMAPYSLLVTRLQKALGVRQYHVASVLCQRAKVAMSHFEPNEYIHYDLLEKNINIVRKRLNRPLTLSEKIV
M.PYSLLVT.LQKALGVRQYHVASVLCQRAKVAM..FEP..YIHYDLLEKNINIV.K.LNRPLTLSEKIV
RetrocopyMVPYSLLVTWLQKALGVRQYHVASVLCQRAKVAMRPFEP-KYIHYDLLEKNINIVCK*LNRPLTLSEKIV
ParentalYGHLDDPASQEIERGKSYLRLRPDRVAMQDA-TAQMAMLQFISSGLS-KVAVPSTIHCDHLIEAQVGGEK
Y.H.DDP.SQEIERG..YL...PD.V.MQD..TAQMAMLQFISS.L..KV..PSTIHCDHLIEAQ.G.EK
RetrocopyYRHPDDPTSQEIERGGTYLQQWPDSVTMQDG<TAQMAMLQFISSRLP<KVTMPSTIHCDHLIEAQLGSEK
ParentalDLRRAKDINQEVYNFLATAGAKYGVGFWKPGSGIIHQIILENYAYPGVLLIGTDSHTPNGGGLGGICIGV
DL..AKDIN.EVYNFLAT...KYG..FWKPGSGIIHQIILENY.YPGVLLIGTDSHTPNGG.LGGICIGV
RetrocopyDLHQAKDINHEVYNFLATGSVKYGLSFWKPGSGIIHQIILENYEYPGVLLIGTDSHTPNGGSLGGICIGV
ParentalGGAD-AVDVMAGIPWELKCPKVIGVKLTGSLSGWSSPKDVILKVAGILTVKGGTGAIVEYHGPGVDSISC
GGA..AVDVM.GIPWELKCPKVIGVKL.GSLSGW.SPKDVILKVAGILT.KGGTGAIVEYHGP.VDSISC
RetrocopyGGAE<AVDVMTGIPWELKCPKVIGVKLMGSLSGWTSPKDVILKVAGILTMKGGTGAIVEYHGPVVDSISC
ParentalTGMATICNMGAEIGATTSVFPYNHRMKKYLSKTGREDIANLADEFKDHLVPDPGCHYDQLIEINLSELKP
TGM.T.CNMG.EIG.TTSVF.YN.RMKKY.SKT...DIANLADEFKDHLVPDPGCHYDQLIE.N.SELK.
RetrocopyTGMVTVCNMGLEIGTTTSVFHYNLRMKKYMSKTCQADIANLADEFKDHLVPDPGCHYDQLIEVNPSELKL
ParentalHINGPFTPDLAHPVAEVGKVAEKEGWPLDIRVGLIGSCTNSSYEDMGRSAAVAKQALAHGLKCKSQFTIT
HINGPFTPDLAHPVAEVGKVAEKE.WPLDI.VGL.GSCTNSSYEDMG.SA.VAKQALAHGLKCKSQFTIT
RetrocopyHINGPFTPDLAHPVAEVGKVAEKEEWPLDI*VGLWGSCTNSSYEDMGCSAGVAKQALAHGLKCKSQFTIT
ParentalPGSEQIRATIERDGYAQILRDLGGIVLANACGPCIGQWDRKDIKKGEKNTIVTSYNRNFTGRNDANPETH
P.SEQIRA.IE.DGYAQ.LRD.GGIVLANACGPCIGQ..RKDI.K.EKN.IVTSYNRNF.G.ND.NPETH
RetrocopyPCSEQIRASIEQDGYAQTLRDVGGIVLANACGPCIGQLHRKDINKQEKNIIVTSYNRNFMGHNDTNPETH
ParentalAFVTSPEIVTALAIAGTLKFNPETDYLTGTDGKKFRLEAPDADELPKGEFDPGQDTYQHPPKDSSGQHVD
AF.TSPE.VTALAI.GTLKFNPET.YLTG.DGKKF.LEAPDADELP..EF.PGQDTYQHP.......H..
RetrocopyAFITSPETVTALAIVGTLKFNPETNYLTGKDGKKFKLEAPDADELPQAEFGPGQDTYQHPRMGYH*PHLS
ParentalVSPTSQ
..P..Q
RetrocopyCRPLTQ

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 59 .51 RPM
bodymap2_adrenal 0 .00 RPM 44 .95 RPM
bodymap2_brain 0 .00 RPM 94 .65 RPM
bodymap2_breast 0 .00 RPM 86 .95 RPM
bodymap2_colon 0 .00 RPM 41 .32 RPM
bodymap2_heart 0 .00 RPM 314 .65 RPM
bodymap2_kidney 0 .02 RPM 98 .54 RPM
bodymap2_liver 0 .00 RPM 32 .40 RPM
bodymap2_lung 0 .00 RPM 35 .02 RPM
bodymap2_lymph_node 0 .00 RPM 35 .62 RPM
bodymap2_ovary 0 .00 RPM 33 .54 RPM
bodymap2_prostate 0 .00 RPM 54 .23 RPM
bodymap2_skeletal_muscle 0 .00 RPM 272 .38 RPM
bodymap2_testis 0 .02 RPM 44 .38 RPM
bodymap2_thyroid 0 .00 RPM 104 .76 RPM
bodymap2_white_blood_cells 0 .00 RPM 44 .61 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2583 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2583 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2583 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2583 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2583 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_647
Parental genes homology:
Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000100412 2 retrocopies
retro_hsap_2583 , retro_hsap_324,
Myotis lucifugus ENSMLUG000000024721 retrocopy
retro_mluc_2566,
Macaca mulatta ENSMMUG000000014542 retrocopies
retro_mmul_647, retro_mmul_694,
Mus musculus ENSMUSG000000224771 retrocopy
retro_mmus_535,
Nomascus leucogenys ENSNLEG000000154822 retrocopies
retro_nleu_1519, retro_nleu_1767,
Pongo abelii ENSPPYG000000118711 retrocopy
retro_pabe_1903,
Pan troglodytes ENSPTRG000000144281 retrocopy
retro_ptro_260,
Drosophila melanogaster FBgn00101001 retrocopy
retro_dmel_56,

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 = 0.03 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 .03 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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