RetrogeneDB ID:

retro_hsap_56

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:241797097..241799068(-)
Located in intron of:ENSG00000054277
Retrocopy
information
Ensembl ID:ENSG00000203668
Aliases:CHML, REP2
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:CHM
Ensembl ID:ENSG00000188419
Aliases:CHM, DXS540, GGTA, HSD-32, REP-1, TCD
Description:choroideremia (Rab escort protein 1) [Source:HGNC Symbol;Acc:1940]


Retrocopy-Parental alignment summary:






>retro_hsap_56
ATGGCGGACAATCTTCCCACAGAGTTTGATGTGGTTATAATAGGGACAGGTTTGCCCGAATCCATCCTTGCAGCTGCATG
TTCAAGAAGTGGTCAGAGGGTTCTGCATATTGATTCAAGAAGCTACTATGGAGGAAACTGGGCTAGTTTCAGCTTTTCAG
GATTGCTATCCTGGTTGAAGGAGTATCAGCAAAACAATGACATTGGGGAAGAAAGTACTGTTGTATGGCAGGACCTGATC
CATGAAACAGAAGAAGCCATCACTCTTCGCAAGAAGGATGAAACTATTCAACACACAGAAGCTTTTTGCTACGCCAGTCA
GGATATGGAGGACAACGTTGAAGAGATTGGTGCTCTGCAGAAAAATCCTTCTTTGGGGGTGTCTAATACCTTCACTGAAG
TTCTGGATTCTGCATTACCTGAAGAAAGCCAGTTATCGTATTTTAATAGCGACGAAATGCCTGCAAAACACACTCAGAAA
AGTGATACAGAGATTTCACTAGAAGTAACTGATGTAGAGGAATCAGTGGAGAAGGAAAAGTATTGTGGAGATAAAACTTG
TATGCACACAGTTTCAGATAAAGATGGAGATAAAGATGAAAGCAAATCTACAGTAGAAGATAAGGCCGATGAACCAATTA
GAAATAGGATTACTTACTCTCAAATAGTTAAAGAAGGCAGGAGGTTTAATATTGATTTGGTGTCAAAACTGCTGTATTCT
CAAGGATTGCTAATTGATCTTTTAATCAAATCAGATGTTAGTCGTTATGTAGAATTTAAAAATGTCACTAGGATTCTTGC
ATTTCGGGAAGGAAAGGTAGAACAAGTTCCTTGTTCCAGAGCAGATGTCTTTAATAGCAAGGAACTCACCATGGTTGAAA
AGAGGATGCTAATGAAATTTCTCACATTTTGTTTAGAGTATGAACAACATCCTGATGAATACCAAGCTTTCAGGCAGTGT
TCATTTTCAGAATACTTAAAAACTAAAAAACTAACTCCCAACCTTCAACATTTTGTACTGCACTCAATTGCAATGACATC
AGAATCATCTTGCACTACAATAGATGGTCTTAACGCAACTAAAAACTTCCTTCAGTGTCTCGGACGGTTTGGCAACACCC
CCTTTTTATTTCCCTTGTATGGCCAAGGAGAAATTCCCCAGGGTTTCTGTAGGATGTGTGCAGTTTTTGGTGGAATCTAT
TGTCTTCGTCATAAAGTACAATGCTTTGTAGTCGACAAAGAATCTGGACGATGTAAAGCAATTATAGATCACTTTGGTCA
AAGAATAAATGCTAAATATTTTATTGTGGAAGACAGTTACCTTTCTGAGGAAACATGCTCAAATGTGCAGTATAAGCAGA
TCTCTAGGGCAGTACTCATTACAGATCAGTCTATACTAAAGACAGATTTAGATCAGCAGACTTCCATTCTGATAGTTCCT
CCAGCAGAGCCAGGAGCTTGTGCTGTACGGGTCACAGAATTATGTTCTTCAACCATGACATGCATGAAGGACACCTATCT
GGTACATTTGACATGTTCATCTTCTAAAACAGCAAGAGAAGACTTAGAATCAGTGGTGAAGAAATTATTCACTCCGTATA
CTGAAACAGAAATAAACGAGGAAGAACTTACAAAGCCAAGACTCTTGTGGGCTCTTTATTTTAATATGAGAGATTCCTCG
GGAATCAGCAGAAGCTCGTATAATGGCTTGCCTTCCAATGTTTATGTCTGCTCTGGGCCTGACTGTGGCCTGGGAAATGA
GCATGCTGTCAAGCAAGCTGAAACACTTTTCCAGGAGATCTTTCCAACTGAAGAATTCTGCCCTCCACCTCCAAATCCAG
AAGACATTATCTTTGATGGTGATGATAAGCAGCCAGAGGCTCCTGGAACCAATAATGTAGTAATGGCCAAACTAGAATCC
TCTGAGGAAAGCAAAAACCTAGAAAGCCCAGAGAAGCACCTTCAAAATTAG

ORF - retro_hsap_56 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.98 %
Parental protein coverage: 99.54 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMADTLPSEFDVIVIGTGLPESIIAAACSRSGRRVLHVDSRSYYGGNWASFSFSGLLSWLKEYQENSDIVS
MAD.LP.EFDV..IGTGLPESI.AAACSRSG.RVLH.DSRSYYGGNWASFSFSGLLSWLKEYQ.N.DI..
RetrocopyMADNLPTEFDVVIIGTGLPESILAAACSRSGQRVLHIDSRSYYGGNWASFSFSGLLSWLKEYQQNNDIGE
ParentalDSPV-WQDQILENEEAIALSRKDKTIQHVEVFCYASQDLHEDVEEAGALQKNHALVTSANSTEAADSAFL
.S.V.WQD.I.E.EEAI.L..KD.TIQH.E.FCYASQD....VEE.GALQKN..L..S...TE..DSA.L
RetrocopyESTVVWQDLIHETEEAITLRKKDETIQHTEAFCYASQDMEDNVEEIGALQKNPSLGVSNTFTEVLDSA-L
ParentalPTEDESLSTMSCEMLTEQTPSSDPENALEVNGAEVTGEKENHCDDKTCVPSTSAED--MSENVPIAEDTT
P.E.......S.EM....T..SD.E..LEV...E...EKE..C.DKTC....S..D....E.....ED..
RetrocopyPEESQLSYFNSDEMPAKHTQKSDTEISLEVTDVEESVEKEKYCGDKTCMHTVSDKDGDKDESKSTVEDKA
ParentalEQPKKNRITYSQIIKEGRRFNIDLVSKLLYSRGLLIDLLIKSNVSRYAEFKNITRILAFREGRVEQVPCS
..P..NRITYSQI.KEGRRFNIDLVSKLLYS.GLLIDLLIKS.VSRY.EFKN.TRILAFREG.VEQVPCS
RetrocopyDEPIRNRITYSQIVKEGRRFNIDLVSKLLYSQGLLIDLLIKSDVSRYVEFKNVTRILAFREGKVEQVPCS
ParentalRADVFNSKQLTMVEKRMLMKFLTFCMEYEKYPDEYKGYEEITFYEYLKTQKLTPNLQYIVMHSIAMTSET
RADVFNSK.LTMVEKRMLMKFLTFC.EYE..PDEY.......F.EYLKT.KLTPNLQ..V.HSIAMTSE.
RetrocopyRADVFNSKELTMVEKRMLMKFLTFCLEYEQHPDEYQAFRQCSFSEYLKTKKLTPNLQHFVLHSIAMTSES
ParentalASSTIDGLKATKNFLHCLGRYGNTPFLFPLYGQGELPQCFCRMCAVFGGIYCLRHSVQCLVVDKESRKCK
...TIDGL.ATKNFL.CLGR.GNTPFLFPLYGQGE.PQ.FCRMCAVFGGIYCLRH.VQC.VVDKES..CK
RetrocopySCTTIDGLNATKNFLQCLGRFGNTPFLFPLYGQGEIPQGFCRMCAVFGGIYCLRHKVQCFVVDKESGRCK
ParentalAIIDQFGQRIISEHFLVEDSYFPENMCSRVQYRQISRAVLITDRSVLKTDSDQQISILTVPAEEPGTFAV
AIID.FGQRI....F.VEDSY..E..CS.VQY.QISRAVLITD.S.LKTD.DQQ.SIL.VP..EPG..AV
RetrocopyAIIDHFGQRINAKYFIVEDSYLSEETCSNVQYKQISRAVLITDQSILKTDLDQQTSILIVPPAEPGACAV
ParentalRVIELCSSTMTCMKGTYLVHLTCTSSKTAREDLESVVQKLFVPYTEMEIENEQVEKPRILWALYFNMRDS
RV.ELCSSTMTCMK.TYLVHLTC.SSKTAREDLESVV.KLF.PYTE.EI..E...KPR.LWALYFNMRDS
RetrocopyRVTELCSSTMTCMKDTYLVHLTCSSSKTAREDLESVVKKLFTPYTETEINEEELTKPRLLWALYFNMRDS
ParentalSDISRSCYNDLPSNVYVCSGPDCGLGNDNAVKQAETLFQEICPNEDFCPPPPNPEDIILDGDSLQPEASE
S.ISRS.YN.LPSNVYVCSGPDCGLGN..AVKQAETLFQEI.P.E.FCPPPPNPEDII.DGD..QPEA..
RetrocopySGISRSSYNGLPSNVYVCSGPDCGLGNEHAVKQAETLFQEIFPTEEFCPPPPNPEDIIFDGDDKQPEAPG
ParentalSSAIPEANSETFKESTNLGNLEE
......A..E...ES.NL...E.
RetrocopyTNNVVMAKLESSEESKNLESPEK

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 4 .81 RPM 19 .92 RPM
bodymap2_adrenal 1 .47 RPM 20 .69 RPM
bodymap2_brain 6 .00 RPM 43 .88 RPM
bodymap2_breast 2 .55 RPM 25 .10 RPM
bodymap2_colon 4 .10 RPM 19 .28 RPM
bodymap2_heart 3 .03 RPM 19 .73 RPM
bodymap2_kidney 3 .39 RPM 40 .93 RPM
bodymap2_liver 0 .21 RPM 11 .58 RPM
bodymap2_lung 1 .74 RPM 20 .89 RPM
bodymap2_lymph_node 3 .44 RPM 20 .92 RPM
bodymap2_ovary 9 .08 RPM 24 .46 RPM
bodymap2_prostate 2 .32 RPM 33 .15 RPM
bodymap2_skeletal_muscle 2 .16 RPM 17 .71 RPM
bodymap2_testis 10 .43 RPM 21 .21 RPM
bodymap2_thyroid 5 .33 RPM 40 .69 RPM
bodymap2_white_blood_cells 8 .35 RPM 38 .53 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_56 was not detected

EST - click to see more details

14 EST(s) were mapped to retro_hsap_56 retrocopy
EST ID Start End Identity Match Mis-match Score
AA669486 241797016 241797447 98.4 422 7 413
AL708330 241797752 241798058 98.1 304 0 300
AU123990 241797031 241797820 99.5 783 2 777
AU137744 241797713 241798416 97.9 692 3 680
AU139019 241797829 241798439 97.7 605 0 596
BP267405 241797700 241798298 97.4 581 16 564
BP268285 241797736 241798298 99.9 561 1 560
BP282990 241797241 241797823 100 581 0 581
BU569726 241797236 241797697 99 456 5 451
BX474169 241797056 241797544 100 488 0 488
BX474181 241798254 241798538 99 277 3 274
CF139504 241797545 241798085 99.9 539 1 538
N31339 241797571 241797708 100 132 0 132
R91881 241797090 241797487 97.2 388 1 380

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_917751112 libraries621 libraries94 libraries2 libraries0 libraries

The graphical summary, for retro_hsap_56 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_56 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_56 has 10 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_400
Gorilla gorilla retro_ggor_488
Pongo abelii retro_pabe_215
Macaca mulatta retro_mmul_460
Mus musculus retro_mmus_284
Rattus norvegicus retro_rnor_981
Oryctolagus cuniculus retro_ocun_893
Bos taurus retro_btau_227
Canis familiaris retro_cfam_1873
Equus caballus retro_ecab_36
Parental genes homology:
Parental genes homology involve 21 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000101901 retrocopy
retro_amel_733,
Bos taurus ENSBTAG000000095981 retrocopy
retro_btau_227,
Canis familiaris ENSCAFG000000174061 retrocopy
retro_cfam_1873,
Equus caballus ENSECAG000000192011 retrocopy
retro_ecab_36,
Felis catus ENSFCAG000000306521 retrocopy
retro_fcat_1744,
Homo sapiens ENSG00000188419 1 retrocopy
retro_hsap_56 ,
Gorilla gorilla ENSGGOG000000229121 retrocopy
retro_ggor_488,
Loxodonta africana ENSLAFG000000005231 retrocopy
retro_lafr_441,
Myotis lucifugus ENSMLUG000000112861 retrocopy
retro_mluc_138,
Macaca mulatta ENSMMUG000000167761 retrocopy
retro_mmul_460,
Monodelphis domestica ENSMODG000000143641 retrocopy
retro_mdom_1776,
Mustela putorius furoENSMPUG000000011941 retrocopy
retro_mputfur_831,
Mus musculus ENSMUSG000000255311 retrocopy
retro_mmus_284,
Nomascus leucogenys ENSNLEG000000027621 retrocopy
retro_nleu_120,
Oryctolagus cuniculus ENSOCUG000000128191 retrocopy
retro_ocun_893,
Pongo abelii ENSPPYG000000205201 retrocopy
retro_pabe_215,
Pan troglodytes ENSPTRG000000220711 retrocopy
retro_ptro_400,
Rattus norvegicus ENSRNOG000000001611 retrocopy
retro_rnor_981,
Sarcophilus harrisii ENSSHAG000000175681 retrocopy
retro_shar_127,
Ictidomys tridecemlineatus ENSSTOG000000221111 retrocopy
retro_itri_870,
Vicugna pacos ENSVPAG000000019631 retrocopy
retro_vpac_231,

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 = 20.97 RPM Legend:


Library Retrogene expression
CEU_NA11831 4 .64 RPM
CEU_NA11843 2 .33 RPM
CEU_NA11930 11 .11 RPM
CEU_NA12004 5 .58 RPM
CEU_NA12400 2 .95 RPM
CEU_NA12751 9 .18 RPM
CEU_NA12760 3 .73 RPM
CEU_NA12827 5 .66 RPM
CEU_NA12872 7 .59 RPM
CEU_NA12873 6 .57 RPM
FIN_HG00183 8 .59 RPM
FIN_HG00277 7 .17 RPM
FIN_HG00315 6 .21 RPM
FIN_HG00321 9 .40 RPM
FIN_HG00328 4 .47 RPM
FIN_HG00338 5 .43 RPM
FIN_HG00349 4 .72 RPM
FIN_HG00375 6 .31 RPM
FIN_HG00377 4 .29 RPM
FIN_HG00378 7 .27 RPM
GBR_HG00099 12 .87 RPM
GBR_HG00111 3 .20 RPM
GBR_HG00114 6 .86 RPM
GBR_HG00119 11 .54 RPM
GBR_HG00131 12 .16 RPM
GBR_HG00133 5 .35 RPM
GBR_HG00134 9 .83 RPM
GBR_HG00137 4 .01 RPM
GBR_HG00142 7 .14 RPM
GBR_HG00143 7 .69 RPM
TSI_NA20512 3 .59 RPM
TSI_NA20513 20 .97 RPM
TSI_NA20518 7 .33 RPM
TSI_NA20532 8 .98 RPM
TSI_NA20538 8 .94 RPM
TSI_NA20756 4 .77 RPM
TSI_NA20765 9 .78 RPM
TSI_NA20771 6 .67 RPM
TSI_NA20786 9 .18 RPM
TSI_NA20798 8 .26 RPM
YRI_NA18870 5 .21 RPM
YRI_NA18907 5 .65 RPM
YRI_NA18916 6 .57 RPM
YRI_NA19093 3 .93 RPM
YRI_NA19099 6 .52 RPM
YRI_NA19114 7 .47 RPM
YRI_NA19118 5 .86 RPM
YRI_NA19213 8 .08 RPM
YRI_NA19214 10 .77 RPM
YRI_NA19223 11 .74 RPM

Indel association:

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





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