RetrogeneDB ID:

retro_hsap_64

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:57020603..57021380(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000204271
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:SPIN1
Ensembl ID:ENSG00000106723
Aliases:SPIN1, SPIN
Description:spindlin 1 [Source:HGNC Symbol;Acc:11243]


Retrocopy-Parental alignment summary:






>retro_hsap_64
ATGAAGACCCCGTTTGGAAAGGCAGCTGCAGGGCAGCGGTCCAGGACGGGCGCTGGCCACGGCAGTGTGTCTGTTACCAT
GATAAAGAGGAAGGCTGCACACAAGAAGCATAGGAGCCGACCCACCTCCCAGCCTCGGGGGAACATCGTGGGCTGCAGAA
TTCAGCACGGATGGAAAGATGGAGATGAACCTCTAACACAGTGGAAAGGAACCGTTCTGGATCAGGTACCTGTAAATCCC
TCTCTGTATCTTATCAAATATGATGGATTTGACTGTGTTTATGGATTGGAACTTCACAGAGATGAAAGAGTGTCATCACT
TGAAGTCCTTCCTAATAGAGTTGCATCATCTAGAATCAGTGATACACACTTGGCAGAAATAATGGTTGGCAAAGCAGTGG
AACATATTTTTGAGACAGAGGAAGGTTCCAAAAATGAATGGAGGGGGATGGTCTTAGCTCAGGCACCTGTCATGAACACA
TGGTTTTACATTACCTATGAGAAAGATCCTGTATTATATATGTACCAGCTCTTAGATGATTATAAAGATGGTGACCTCCG
CATCCTTCAAGATTCCAATGATTCTCCTCTGGCAGAGAGGGAGCCAGGAGAAGTCATAGACAGCCTGGTAGGCAAACAGG
TGGAATACGCCAAAGACGATGGCTCCAAGAGAACTGGCATGGTCATTCATCAGGTAGAAGCAAAACCCTCTGTGTACTTC
ATCAAATTTGATGATGATTTCCATATCTATGTCTACGATTTGGTAAAAACATCTTAG

ORF - retro_hsap_64 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.1 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMKTPFGKTPGQRSRADAGHAGVSANMMKKRTSHKKHRSSVGPSKPVSQPRRNIVGCRIQHGWKEGNGPVT
MKTPF....G..........G.............K.......S.P.SQPR.NIVGCRIQHGWK.G..P.T
RetrocopyMKTPF----GKAAAGQRSRTGAGHGSVSVTMIKRKAAHKKHRSRPTSQPRGNIVGCRIQHGWKDGDEPLT
ParentalQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELNKDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHM
QWKGTVLDQVPVNPSLYLIKYDGFDCVYGLEL..DERVS.LEVLP.RVA.SRISD.HLA..M.GKAVEH.
RetrocopyQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELHRDERVSSLEVLPNRVASSRISDTHLAEIMVGKAVEHI
ParentalFETEDGSKDEWRGMVLARAPVMNTWFYITYEKDPVLYMYQLLDDYKEGDLRIMPDSNDSPPAEREPGEVV
FETE.GSK.EWRGMVLA.APVMNTWFYITYEKDPVLYMYQLLDDYK.GDLRI..DSNDSP.AEREPGEV.
RetrocopyFETEEGSKNEWRGMVLAQAPVMNTWFYITYEKDPVLYMYQLLDDYKDGDLRILQDSNDSPLAEREPGEVI
ParentalDSLVGKQVEYAKEDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLVKTS
DSLVGKQVEYAK.DGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLVKTS
RetrocopyDSLVGKQVEYAKDDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLVKTS

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 1 .23 RPM 112 .71 RPM
bodymap2_adrenal 1 .39 RPM 82 .70 RPM
bodymap2_brain 3 .35 RPM 222 .99 RPM
bodymap2_breast 1 .05 RPM 126 .09 RPM
bodymap2_colon 1 .12 RPM 132 .51 RPM
bodymap2_heart 0 .66 RPM 70 .69 RPM
bodymap2_kidney 1 .08 RPM 138 .17 RPM
bodymap2_liver 0 .23 RPM 28 .07 RPM
bodymap2_lung 0 .56 RPM 98 .00 RPM
bodymap2_lymph_node 0 .82 RPM 85 .01 RPM
bodymap2_ovary 3 .24 RPM 291 .62 RPM
bodymap2_prostate 2 .25 RPM 142 .53 RPM
bodymap2_skeletal_muscle 0 .51 RPM 12 .73 RPM
bodymap2_testis 1 .56 RPM 234 .36 RPM
bodymap2_thyroid 1 .88 RPM 129 .35 RPM
bodymap2_white_blood_cells 1 .10 RPM 65 .48 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_64 in 42 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A X:57021712..57022310
ENCFF002CFX POLR2A X:57021723..57022294
ENCFF002CGN POLR2A X:57021808..57022261
ENCFF002CHO POLR2A X:57021683..57022375
ENCFF002CIH POLR2A X:57021985..57022253
ENCFF002CIO POLR2A X:57021751..57022300
ENCFF002CJE POLR2A X:57021666..57022278
ENCFF002CJZ POLR2A X:57021764..57022300
ENCFF002CKX POLR2A X:57021717..57022297
ENCFF002CLM POLR2A X:57021672..57022212
ENCFF002CMI POLR2A X:57021752..57022279
ENCFF002CPG POLR2A X:57021862..57022352
ENCFF002CPH POLR2A X:57021912..57022302
ENCFF002CQA POLR2A X:57022009..57022185
ENCFF002CQC POLR2A X:57021818..57022053
ENCFF002CQC POLR2A X:57021974..57022229
ENCFF002CQE POLR2A X:57021779..57022075
ENCFF002CQG POLR2A X:57021644..57022168
ENCFF002CQG POLR2A X:57021858..57022382
ENCFF002CQI POLR2A X:57021795..57022049
ENCFF002CQI POLR2A X:57022033..57022233
ENCFF002CQK POLR2A X:57021739..57022240
ENCFF002CQM POLR2A X:57021791..57022040
ENCFF002CQM POLR2A X:57022029..57022252
ENCFF002CQO POLR2A X:57021750..57022232
ENCFF002CRK POLR2A X:57021642..57022166
ENCFF002CRK POLR2A X:57021856..57022380
ENCFF002CRO POLR2A X:57021687..57022107
ENCFF002CSY POLR2A X:57021739..57022260
ENCFF002CUP POLR2A X:57021808..57022124
ENCFF002CUQ POLR2A X:57022005..57022246
ENCFF002CXM POLR2A X:57021870..57022360
ENCFF002CXO POLR2A X:57021910..57022334
ENCFF002CXP POLR2A X:57021874..57022354
ENCFF002CXR POLR2A X:57021839..57021960
ENCFF002CZC POLR2A X:57021888..57022227
ENCFF002CZD POLR2A X:57021949..57022206
ENCFF002DAE POLR2A X:57021806..57022026
ENCFF002DAE POLR2A X:57021990..57022300
ENCFF002DAH POLR2A X:57021878..57021993
ENCFF002DAK POLR2A X:57021860..57022360
ENCFF002DAV POLR2A X:57021743..57022287
ENCFF002DAY POLR2A X:57021581..57022217
ENCFF002DBB POLR2A X:57021843..57022043
ENCFF002DBO POLR2A X:57021753..57022271
ENCFF002DBP POLR2A X:57021788..57022029
ENCFF002DBP POLR2A X:57021995..57022245
ENCFF002DBQ POLR2A X:57022039..57022202
ENCFF002DBT POLR2A X:57021734..57022104

EST - click to see more details

No EST(s) were mapped for retro_hsap_64 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_64 retrocopy 5' end.

Lab - click to see more details

retro_hsap_64 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_64 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 23 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000033014 retrocopies
retro_amel_1831, retro_amel_1879, retro_amel_38, retro_amel_41,
Bos taurus ENSBTAG000000030444 retrocopies
retro_btau_1678, retro_btau_1841, retro_btau_187, retro_btau_553,
Canis familiaris ENSCAFG000000022083 retrocopies
retro_cfam_153, retro_cfam_2095, retro_cfam_59,
Choloepus hoffmanni ENSCHOG000000069832 retrocopies
retro_chof_1343, retro_chof_1852,
Callithrix jacchus ENSCJAG000000174521 retrocopy
retro_cjac_227,
Cavia porcellus ENSCPOG000000007431 retrocopy
retro_cpor_123,
Echinops telfairi ENSETEG000000137191 retrocopy
retro_etel_28,
Felis catus ENSFCAG000000071972 retrocopies
retro_fcat_32, retro_fcat_70,
Homo sapiens ENSG00000106723 1 retrocopy
retro_hsap_64 ,
Loxodonta africana ENSLAFG000000274972 retrocopies
retro_lafr_18, retro_lafr_58,
Microcebus murinus ENSMICG000000145101 retrocopy
retro_mmur_8,
Myotis lucifugus ENSMLUG000000085162 retrocopies
retro_mluc_132, retro_mluc_1626,
Mustela putorius furoENSMPUG000000085851 retrocopy
retro_mputfur_139,
Mus musculus ENSMUSG000000213953 retrocopies
retro_mmus_112, retro_mmus_16, retro_mmus_3351,
Oryctolagus cuniculus ENSOCUG000000118801 retrocopy
retro_ocun_63,
Otolemur garnettii ENSOGAG000000021662 retrocopies
retro_ogar_2327, retro_ogar_9,
Procavia capensis ENSPCAG000000158001 retrocopy
retro_pcap_14,
Pongo abelii ENSPPYG000000193551 retrocopy
retro_pabe_33,
Pan troglodytes ENSPTRG000000210882 retrocopies
retro_ptro_116, retro_ptro_95,
Pteropus vampyrus ENSPVAG000000133913 retrocopies
retro_pvam_2, retro_pvam_22, retro_pvam_858,
Rattus norvegicus ENSRNOG000000111194 retrocopies
retro_rnor_1483, retro_rnor_1531, retro_rnor_281, retro_rnor_2818,
Ictidomys tridecemlineatus ENSSTOG000000291071 retrocopy
retro_itri_136,
Tursiops truncatus ENSTTRG000000056026 retrocopies
retro_ttru_1061, retro_ttru_13, retro_ttru_1452, retro_ttru_1506, retro_ttru_1669, retro_ttru_1698,

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 = 3.79 RPM Legend:


Library Retrogene expression
CEU_NA11831 1 .80 RPM
CEU_NA11843 1 .56 RPM
CEU_NA11930 2 .25 RPM
CEU_NA12004 1 .18 RPM
CEU_NA12400 1 .02 RPM
CEU_NA12751 2 .77 RPM
CEU_NA12760 1 .66 RPM
CEU_NA12827 1 .27 RPM
CEU_NA12872 2 .34 RPM
CEU_NA12873 2 .30 RPM
FIN_HG00183 2 .99 RPM
FIN_HG00277 2 .74 RPM
FIN_HG00315 1 .60 RPM
FIN_HG00321 3 .32 RPM
FIN_HG00328 1 .47 RPM
FIN_HG00338 1 .96 RPM
FIN_HG00349 1 .48 RPM
FIN_HG00375 2 .47 RPM
FIN_HG00377 0 .93 RPM
FIN_HG00378 2 .40 RPM
GBR_HG00099 1 .63 RPM
GBR_HG00111 0 .90 RPM
GBR_HG00114 1 .79 RPM
GBR_HG00119 3 .30 RPM
GBR_HG00131 3 .79 RPM
GBR_HG00133 1 .86 RPM
GBR_HG00134 2 .93 RPM
GBR_HG00137 1 .51 RPM
GBR_HG00142 3 .56 RPM
GBR_HG00143 1 .88 RPM
TSI_NA20512 0 .71 RPM
TSI_NA20513 2 .32 RPM
TSI_NA20518 2 .28 RPM
TSI_NA20532 1 .94 RPM
TSI_NA20538 2 .53 RPM
TSI_NA20756 1 .69 RPM
TSI_NA20765 2 .03 RPM
TSI_NA20771 2 .35 RPM
TSI_NA20786 1 .91 RPM
TSI_NA20798 1 .84 RPM
YRI_NA18870 2 .03 RPM
YRI_NA18907 2 .32 RPM
YRI_NA18916 1 .98 RPM
YRI_NA19093 1 .98 RPM
YRI_NA19099 1 .78 RPM
YRI_NA19114 2 .52 RPM
YRI_NA19118 1 .80 RPM
YRI_NA19213 1 .84 RPM
YRI_NA19214 2 .31 RPM
YRI_NA19223 2 .27 RPM

Indel association:

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



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