RetrogeneDB ID:

retro_hsap_1342

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:14:57507876..57508903(+)
Located in intron of:ENSG00000248550
Retrocopy
information
Ensembl ID:ENSG00000258758
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ZCCHC7
Ensembl ID:ENSG00000147905
Aliases:ZCCHC7, AIR1
Description:zinc finger, CCHC domain containing 7 [Source:HGNC Symbol;Acc:26209]


Retrocopy-Parental alignment summary:






>retro_hsap_1342
TCACTGTCTGATGAAGATAGTATTTATAGATGTAAAGGAAAGAATGTTAGAGCTCAAGCACAAGAAAATACCCATGGTCC
TTCTGCTTTTCTTCAATCTAATGAGCTGTTTGATAAGAAATGCAAGAGTGATATTGAAGAGAGATCAGGTGTAATCCAAG
AGGCCATGATTATAGAGGTCAGTTCAAGTGCAGAGGAAGAGAGCACCATTTCAGAAGGCAATAATGTGGAAAGCTGGATG
CTACTGGGATGTGAAATAGATGATAAAGATAATGATATCCTTCTCAACCTTCTGGGATGTGAAAACTCTGTTACTGAAGG
AGAAGATGGTATAAACTGGTTCATCAGTGACAAAGACATTGAGGCCCAGATAGCTAATAACCAATAACCTGGAAGATGGA
CCCAGCGATATTATTCAGCCAATGAAAACATTATCTGTAGAAATTGTGACAAACACGGCCATTTATCAAAAAACTGTCCC
TTACCATGAAAAGTTCGTTGCTGCTTCCTGTGCTCCTGGAGAGGACACCTCCTGTATTCCTGTCCAGCCCCCCTTTGCAA
ATACTGTCCTGTGCCTAAGATGTTGGACCACTCATGTCTTTTCAGACATTCTTGGGATAAACAGTGTGACCAATGTCATA
TGCTAGGCCACTATACAGATGCTTGCACAGAAATCTGGAGGCAATATCACCTCACGACCAAACCCAGACCACCCAAAAAG
CCAAAGACCCTTCAAAACCATCAGCCTTAGCATATTGCTGTCACTGCATGCAAAAGGCCATTATGGACACAAGTGTCCAG
AAAGAGAAGTGTATGACCTGTCTCCAGTATCTCCATTCATCTGCTACTATGATGACAAATATGAAGTTAAGGAGAGAAAA
AAGAGAGTAAAATAAAAAATAAAAGTACTCAAGAAGAGTGGGGATATCCCAGAGCCATCCAAGCTACCTTACATAAAAGC
AGCAAATGAGAACCCCCATCATGATATAAAGAAGGGCTGTGCCTCATTAAAAAGCAACAGGTGGCCT

ORF - retro_hsap_1342 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.71 %
Parental protein coverage: 64.09 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalTLSDEDSIYRCKGKNVRVQAQENAHGLSSSLQSNELVDKKCKSDIEKPKSEERSGVIREVMIIEVSSSEE
.LSDEDSIYRCKGKNVR.QAQEN.HG.S..LQSNEL.DKKCKSDIE..........I.EV.....SS.E.
RetrocopySLSDEDSIYRCKGKNVRAQAQENTHGPSAFLQSNELFDKKCKSDIEERSGVIQEAMIIEVS----SSAE-
ParentalEESTISEGDNVESWMLLGCEVDDKDDDILLNLVGCENSVTEGEDGINWSISDKDIEAQIANNRTPGRWTQ
EESTISEG.NVESWMLLGCE.DDKD.DILLNL.GCENSVTEGEDGINW.ISDKDIEAQIANN..PGRWTQ
RetrocopyEESTISEGNNVESWMLLGCEIDDKDNDILLNLLGCENSVTEGEDGINWFISDKDIEAQIANNQ*PGRWTQ
ParentalRYYSANKNIICRNCDKRGHLSKNCPLPRKVRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSW
RYYSAN.NIICRNCDK.GHLSKNCPLP.KVR.CFLCS.RGHLLYSCPAPLC.YCPVPKMLDHSCLFRHSW
RetrocopyRYYSANENIICRNCDKHGHLSKNCPLP*KVRCCFLCSWRGHLLYSCPAPLCKYCPVPKMLDHSCLFRHSW
ParentalDKQCDRCHMLGHYTDACTEIWRQYHLTTKPGPPKKPKT-PSRPSALAYCYHCAQ-KGHYGHECPEREVYD
DKQCD.CHMLGHYTDACTEIWRQYHLTTKP.PPKKPKT.PS.PSALAYC.HC.Q.KGHYGH.CPEREVYD
RetrocopyDKQCDQCHMLGHYTDACTEIWRQYHLTTKPRPPKKPKT<PSKPSALAYCCHCMQ<KGHYGHKCPEREVYD
ParentalPSPVSPFICYYDDKYEIQEREKRLKQKIKVLKKNGVIPEPSKLPYIKAANENPHHDIRKGRASWKSNRWP
.SPVSPFICYYDDKYE..E..........VLKK.G.IPEPSKLPYIKAANENPHHDI.KG.AS.KSNRWP
RetrocopyLSPVSPFICYYDDKYEVKEXXXXXXXXXXVLKKSGDIPEPSKLPYIKAANENPHHDIKKGCASLKSNRWP

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 16 .04 RPM
bodymap2_adrenal 0 .00 RPM 27 .20 RPM
bodymap2_brain 0 .00 RPM 10 .13 RPM
bodymap2_breast 0 .00 RPM 15 .51 RPM
bodymap2_colon 0 .00 RPM 23 .96 RPM
bodymap2_heart 0 .00 RPM 7 .18 RPM
bodymap2_kidney 0 .00 RPM 14 .02 RPM
bodymap2_liver 0 .00 RPM 7 .01 RPM
bodymap2_lung 0 .00 RPM 14 .64 RPM
bodymap2_lymph_node 0 .00 RPM 24 .40 RPM
bodymap2_ovary 0 .00 RPM 27 .22 RPM
bodymap2_prostate 0 .00 RPM 25 .79 RPM
bodymap2_skeletal_muscle 0 .00 RPM 10 .60 RPM
bodymap2_testis 0 .08 RPM 41 .16 RPM
bodymap2_thyroid 0 .02 RPM 22 .80 RPM
bodymap2_white_blood_cells 0 .00 RPM 34 .10 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1342 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1342 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1342 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1342 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1342 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_917
Macaca mulatta retro_mmul_2180
Parental genes homology:
Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000147905 1 retrocopy
retro_hsap_1342 ,
Macaca mulatta ENSMMUG000000074211 retrocopy
retro_mmul_2180,
Pongo abelii ENSPPYG000000297631 retrocopy
retro_pabe_1114,
Pan troglodytes ENSPTRG000000209392 retrocopies
retro_ptro_2962, retro_ptro_917,
Tursiops truncatus ENSTTRG000000060542 retrocopies
retro_ttru_1606, retro_ttru_505,

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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