RetrogeneDB ID:

retro_hsap_3621

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:81265523..81266906(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000216352
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CS
Ensembl ID:ENSG00000062485
Aliases:None
Description:citrate synthase [Source:HGNC Symbol;Acc:2422]


Retrocopy-Parental alignment summary:






>retro_hsap_3621
ATGGCTTTACTCACTACTGTCACCCAGTTCTTGGGAACAAAGGACGTATCTTGTCTTGTTCTTGCTGCCTGGCATGCCAG
TACCTCCTCCAGGAATTTGGAAGACATATCAGCTTACCTCATACCCAAGGAGCAGGCCAGAATTAAGATCTCCAGACAGC
AATGTGGCAAGAGGGTGGTGGGCCAAAACACTGTGGGCATGATGTATGGTGGCCTGAGAGGCAAGAAGGGATTGGTATAT
GAAACATCAGTTCTTGATCCTAATGAAAGCATCCATTTCTGAGGCTTTAGTGTCCCTGAGTGCCAAAAGCTGCCACCCAA
GCCTAAGGGTAAGAAAGAAACCCTGCTGGAGGGTTTATTTCAGCTGCTGGTGGCTGAACAGATCCCAACAGAGGAAACAG
GCATCTTGGCTTTCAAAAAAGTGGGCAAAGAGGACAGCTCTACCCTCCCACGTGGTCATGATGCTGGACAACTTTCCCAC
CAATATACATCCCATGTCTCAGCTCAGTGCAGCCTTTACAGCCCTCAACAGTGAAAGTAATACTGCCTGAGCATATGCAG
AGGGTATCAAGTACTGGGAGCTGATTTATGAAGACTGTGTGGATCTGATCACAAAGCTACCTGTGTTGCAGCAAAGATCT
ACCAAAATCTCTACTAAAAGGGCAAAAATGTTGGGGACATTGACTCCAAGCTGCACTGGCCCCACAATTTCACCAACATG
TTAGGCTATACTGATGCTTAGTTCACTGAGCTCATGCATCTGTATCAAACCATCCACAGTGACCATGAGGGCAGCAATGT
AAGTGCCTATATCAGCAACTTGTTGGGCAGTGCCCCTTCAAGCCCTTATCTGTCCTTTGCAACAGCCATGAATGGATTGA
CAGGCCCTCTACATGTACTAGCAAATCAGGAAGTGCTTGTCTGGCTAATTTAACTACAGAAGGCAGTTGGCAAAGATGTG
GCAGATGAGAAATTATGAGACTACACCTGGAACACACTCAACCCAAGATGAAGTTATTCCAGACTATGGCCATGTAGTGC
TAAAGAAGATTGATCCACGAGGTACCTGCTGTGAGAGTTTGCTCTGAAACACCACATAATGACCCCATGTTAACTTGGTT
GCTCAACTACACAAGATTGTGCTTAATATCCTCTTAGAGAATGGCAAGGCCAAGAATCCTTGGCCCAATGTAGACACACC
CTGGGGTACTGCTCCAGTACTATGGCATGATGGAAATGAATTACTACACTGTTCTGTTCAGAGTGTCTCAGGCATTGGGT
GTACTGGCACAGCTCATCTGAAGTCATGCACTAGGATTCCCTCTAGAAAGGCCCAAGTCCAAGACATAGATGGTCTGATA
AGTTTGTGGACTCTAAGTTGGGA

ORF - retro_hsap_3621 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.05 %
Parental protein coverage: 100. %
Number of stop codons detected: 7
Number of frameshifts detected 9


Retrocopy - Parental Gene Alignment:

ParentalMALLTAAARLLGTKNASCLVLAARHASASSTNLKDILADLIPKEQARIKTFRQQHGKTVVGQITVDMMYG
MALLT.....LGTK..SCLVLAA.HAS.SS.NL.DI.A.LIPKEQARIK..RQQ.GK.VVGQ.TV.MMYG
RetrocopyMALLTTVTQFLGTKDVSCLVLAAWHASTSSRNLEDISAYLIPKEQARIKISRQQCGKRVVGQNTVGMMYG
ParentalGMRGMKGLVYETSVLDPDEGIRFRGFSIPECQKLLPKAKGGEEPLPEGLFWLLVTGHIPTEE-QVSWLSK
G.RG.KGLVYETSVLDP.E.I.F.GFS.PECQKL.PK.KG..E.L.EGLF.LLV...IPTEE.Q.SWLSK
RetrocopyGLRGKKGLVYETSVLDPNESIHF*GFSVPECQKLPPKPKGKKETLLEGLFQLLVAEQIPTEE>QASWLSK
ParentalEWAKRAALPSHVVTMLDNFPTNLHPMSQLSAAVTALNSESNFARAYAQGISRTKYWELIYEDSMDLIAKL
.WAKR.ALPSHVV.MLDNFPTN.HPMSQLSAA.TALNSESN.A.AYA.GI...KYWELIYED..DLI.KL
RetrocopyKWAKRTALPSHVVMMLDNFPTNIHPMSQLSAAFTALNSESNTA*AYAEGI---KYWELIYEDCVDLITKL
ParentalP-CVAAKIYRNLYREGSGIGAIDSNLDWSHNFTNMLGYTDHQFTELTRLYLTIHSDHEGGNVSAHTSHLV
P.CVAAKIY.NLY..G...G.IDS.L.W.HNFTNMLGYTD..FTEL..LY.TIHSDHEG.NVSA..S.L.
RetrocopyP<CVAAKIYQNLY*KGKNVGDIDSKLHWPHNFTNMLGYTDA*FTELMHLYQTIHSDHEGSNVSAYISNLL
ParentalGSALSDPYLSFAAAMNGLAGPLHGLANQEVLVWLTQLQKEVGKDVSDEKLRDYIWNTLN-SGRVVPGYGH
GSA.S.PYLSFA.AMNGL.GPLH.LANQEVLVWL..LQK.VGKDV.DEKL.DY.WNTLN....V.P.YGH
RetrocopyGSAPSSPYLSFATAMNGLTGPLHVLANQEVLVWLI*LQKAVGKDVADEKL*DYTWNTLN>QDEVIPDYGH
ParentalAVLRKTDPRYTCQR-EFALKH-LPNDPMF-KLVAQLYKIVPNVLLEQGKAKNPWPNVDAHSG-VLLQYYG
.VL.K.DPR.TC...EFALKH...NDPM...LVAQL.KIV.N.LLE.GKAKNPWPNVD...G..L..Y.G
RetrocopyVVLKKIDPRGTCCE<EFALKH<PHNDPML<NLVAQLHKIVLNILLENGKAKNPWPNVDTPWG>LLQYY-G
ParentalMTEMNYYTVLFGVSRALGVLAQLIWSRALGFPLERPKS-MSTEGLM-KFVDSKSG
M.EMNYYTVLF.VS.ALGVLAQLI.S.ALGFPLERPKS.....GL..KFVDSK.G
RetrocopyMMEMNYYTVLFRVSQALGVLAQLI*SHALGFPLERPKS<QDIDGLI<KFVDSKLG

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 180 .81 RPM
bodymap2_adrenal 0 .00 RPM 123 .00 RPM
bodymap2_brain 0 .00 RPM 110 .78 RPM
bodymap2_breast 0 .00 RPM 292 .34 RPM
bodymap2_colon 0 .00 RPM 128 .08 RPM
bodymap2_heart 0 .00 RPM 403 .19 RPM
bodymap2_kidney 0 .00 RPM 174 .15 RPM
bodymap2_liver 0 .00 RPM 50 .49 RPM
bodymap2_lung 0 .00 RPM 116 .03 RPM
bodymap2_lymph_node 0 .00 RPM 119 .02 RPM
bodymap2_ovary 0 .00 RPM 124 .88 RPM
bodymap2_prostate 0 .00 RPM 141 .23 RPM
bodymap2_skeletal_muscle 0 .00 RPM 302 .85 RPM
bodymap2_testis 0 .00 RPM 80 .33 RPM
bodymap2_thyroid 0 .00 RPM 134 .13 RPM
bodymap2_white_blood_cells 0 .00 RPM 149 .90 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3621 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3621 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3621 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3621 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3621 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2445
Macaca mulatta retro_mmul_1840
Parental genes homology:
Parental genes homology involve 21 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000043711 retrocopy
retro_btau_386,
Canis familiaris ENSCAFG000000001151 retrocopy
retro_cfam_765,
Choloepus hoffmanni ENSCHOG000000003971 retrocopy
retro_chof_1803,
Callithrix jacchus ENSCJAG000000112751 retrocopy
retro_cjac_2031,
Dasypus novemcinctus ENSDNOG000000109072 retrocopies
retro_dnov_205, retro_dnov_468,
Echinops telfairi ENSETEG000000120351 retrocopy
retro_etel_584,
Homo sapiens ENSG00000062485 2 retrocopies
retro_hsap_1972, retro_hsap_3621 ,
Gorilla gorilla ENSGGOG000000090962 retrocopies
retro_ggor_1432, retro_ggor_2445,
Macropus eugenii ENSMEUG000000056572 retrocopies
retro_meug_1078, retro_meug_1304,
Microcebus murinus ENSMICG000000176592 retrocopies
retro_mmur_1322, retro_mmur_394,
Macaca mulatta ENSMMUG000000024832 retrocopies
retro_mmul_1502, retro_mmul_1840,
Mus musculus ENSMUSG000000056831 retrocopy
retro_mmus_258,
Nomascus leucogenys ENSNLEG000000175142 retrocopies
retro_nleu_1201, retro_nleu_809,
Oryctolagus cuniculus ENSOCUG000000072161 retrocopy
retro_ocun_1183,
Pongo abelii ENSPPYG000000046541 retrocopy
retro_pabe_2972,
Rattus norvegicus ENSRNOG000000235201 retrocopy
retro_rnor_2518,
Sorex araneus ENSSARG000000100932 retrocopies
retro_sara_360, retro_sara_628,
Sus scrofa ENSSSCG000000210911 retrocopy
retro_sscr_321,
Sus scrofa ENSSSCG000000228581 retrocopy
retro_sscr_322,
Tupaia belangeri ENSTBEG000000064251 retrocopy
retro_tbel_4652,
Tarsius syrichta ENSTSYG000000044831 retrocopy
retro_tsyr_1659,

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 ) 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 .00 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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