RetrogeneDB ID:

retro_hsap_3947

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:36952667..36953889(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SMARCE1
Ensembl ID:ENSG00000073584
Aliases:SMARCE1, BAF57
Description:SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Source:HGNC Symbol;Acc:11109]


Retrocopy-Parental alignment summary:






>retro_hsap_3947
GAAAGACCGTCTTATGCTCCACCTCTCACCCCAGCTCCTGCAACACAAATGCCCAGCACACCAGGGTTTGTGAGATACAA
TCCATACAGTCATCTCACCTACAACAACTACAGGCTTGAAGGGAACCCAGGCACCAACAGCCAGGTCACAGCATCCTCTG
CTATTACCATACCAAAACCCCCAAAGCCACCAGATAAGCCGCTGATGCCCTACGTGAGGTACAGGCAGAAAGGTCTGGGA
CCAAGTAAAGACTTCCAACCCTGACTTAAAGTTGTGGGAGATTGGCAAGATTATTGGTGGCATGTGGTGAGATCTCACTG
GTGAAGAAAAGCAAGAATATTTAAATGAATACGAAGCAGAAAAGACAGAATACAATGAATCTATGAAGGCCTATCATAAA
TCCCCCATATACCTTGCTTACATAAATGCAAAAAGTCGTGCAGAAGCTGCTTTAGAGGAAGAAAGTTGACAGAGACAGTC
TTGCGTGGAGAAAGGAGAACCGTACATGAACATTTAGCCTCCTGAAGATCCAGATGATTATGACGATGGCTTTTCAATGA
AGCATACAGCCACCGCCCATTTCCAGAGAAACCACTGCCTCATCAGTGAAATCCTTAGTGAGAGTGTGGTGCCAGACGTT
CGGTCAGTTGTCACAACAGCTAGAATGTGGATCATCAAATGACAGGTCCAGTCCTTAATTATTCATCAGCGAAAACTAGA
AGCTGAACTTCTTCAGATAGAGGAAATGACACCAGGAGAAGAGGAGGAAATACTTGGAAAGCACAGATTCATTTAATGAT
GAACTTAAAAGTTTGTGTGGTCTGAAAGTAGAAGTGGATATGAAGAAAATTGCAGGTGAGATTGCACAGGCAGAGGAACA
GGCCCGCAAAAGGCAGGAGAAAAGGGAGAAGGAGGCAGCAGAGCAAGCTGAGCACAGAGCAGCATTGTTCCTAAGGAAAA
GCAAGCAGCCAGCAAAGGCGAGGAGAAGAAAGATGACAAGAACATTCCAATGGAGATGGAGGAGGCACGCTTTGAAGAAA
TGACAGAGAGCCAACAGAACAGTGAAGAAGGCACGTCTACTCCTGAGGACAAGGAGAGTGGGCAGGAGTGGGTAGACAGT
ATGGCAGAGGAAGGAACCAGTGATAGTAACATTGGATCGGACAGCAACAGCACAATAGTGCAGGAGCCACCAAAAGATCC
CATACCAGAAGATGAGAAAAAA

ORF - retro_hsap_3947 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.43 %
Parental protein coverage: 99.27 %
Number of stop codons detected: 4
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalKRPSYAPPPTPAPATQMPSTPGFVGYNPYSHLAYNNYRLGGNPGTNSRVTASSGITIPKPPKPPDKPLMP
.RPSYAPP.TPAPATQMPSTPGFV.YNPYSHL.YNNYRL.GNPGTNS.VTASS.ITIPKPPKPPDKPLMP
RetrocopyERPSYAPPLTPAPATQMPSTPGFVRYNPYSHLTYNNYRLEGNPGTNSQVTASSAITIPKPPKPPDKPLMP
ParentalYMRY-SRKVWDQVKASNPDLKLWEIGKIIGGMWRDLTDEEKQEYLNEYEAEKIEYNESMKAYHNSPAYLA
Y.RY..RKVWDQVK.SNPDLKLWEIGKIIGGMW.DLT.EEKQEYLNEYEAEK.EYNESMKAYH.SP.YLA
RetrocopyYVRY>GRKVWDQVKTSNPDLKLWEIGKIIGGMW*DLTGEEKQEYLNEYEAEKTEYNESMKAYHKSPIYLA
ParentalYINAKSRAEAALEEESRQRQSRMEKGEPYMSIQPAEDPDDYDDGFSMKHTATARFQRNHRLISEILSESV
YINAKSRAEAALEEES.QRQS..EKGEPYM.I.P.EDPDDYDDGFSMKHTATA.FQRNH.LISEILSESV
RetrocopyYINAKSRAEAALEEES*QRQSCVEKGEPYMNI*PPEDPDDYDDGFSMKHTATAHFQRNHCLISEILSESV
ParentalVPDVRSVVTTARMQVLKRQVQSLMVHQRKLEAELLQIEER-HQEKKRKFLESTDSFNNELKRLCGLKVEV
VPDVRSVVTTARM...K.QVQSL..HQRKLEAELLQIEE..HQEK.RK.LESTDSFN.ELK.LCGLKVEV
RetrocopyVPDVRSVVTTARMWIIK*QVQSLIIHQRKLEAELLQIEEM>HQEKRRKYLESTDSFNDELKSLCGLKVEV
ParentalDMEKIAAEIAQAEEQARKRQEEREKEAAEQAER-SQSSIVPEEEQAANKGEEKKDDENIPMETEETHLEE
DM.KIA.EIAQAEEQARKRQE.REKEAAEQAE....S....E..QAA.KGEEKKDD.NIPME.EE...EE
RetrocopyDMKKIAGEIAQAEEQARKRQEKREKEAAEQAEH<QSSIVPKEK-QAASKGEEKKDDKNIPMEMEEARFEE
ParentalTTESQQNGEEGTSTPEDKESGQEGVDSMAEEGTSDSNTGSESNSATVEEPPTDPIPEDEKK
.TESQQN.EEGTSTPEDKESGQE.VDSMAEEGTSDSN.GS.SNS..V.EPP.DPIPEDEKK
RetrocopyMTESQQNSEEGTSTPEDKESGQEWVDSMAEEGTSDSNIGSDSNSTIVQEPPKDPIPEDEKK

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 56 .08 RPM
bodymap2_adrenal 0 .00 RPM 94 .61 RPM
bodymap2_brain 0 .00 RPM 46 .83 RPM
bodymap2_breast 0 .00 RPM 71 .79 RPM
bodymap2_colon 0 .00 RPM 76 .98 RPM
bodymap2_heart 0 .00 RPM 35 .19 RPM
bodymap2_kidney 0 .00 RPM 63 .37 RPM
bodymap2_liver 0 .00 RPM 26 .45 RPM
bodymap2_lung 0 .00 RPM 43 .13 RPM
bodymap2_lymph_node 0 .00 RPM 65 .71 RPM
bodymap2_ovary 0 .00 RPM 110 .88 RPM
bodymap2_prostate 0 .00 RPM 90 .20 RPM
bodymap2_skeletal_muscle 0 .00 RPM 32 .34 RPM
bodymap2_testis 0 .00 RPM 73 .21 RPM
bodymap2_thyroid 0 .00 RPM 79 .05 RPM
bodymap2_white_blood_cells 0 .00 RPM 71 .60 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3947 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3947 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3947 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3947 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3947 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2678
Pongo abelii retro_pabe_3251
Macaca mulatta retro_mmul_2286
Parental genes homology:
Parental genes homology involve 17 parental genes, and 68 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000135734 retrocopies
retro_cjac_1107, retro_cjac_2109, retro_cjac_50, retro_cjac_854,
Homo sapiens ENSG00000073584 5 retrocopies
retro_hsap_1195, retro_hsap_1304, retro_hsap_3623, retro_hsap_3947 , retro_hsap_922,
Gorilla gorilla ENSGGOG000000118032 retrocopies
retro_ggor_1020, retro_ggor_931,
Microcebus murinus ENSMICG000000098214 retrocopies
retro_mmur_1408, retro_mmur_1592, retro_mmur_608, retro_mmur_928,
Myotis lucifugus ENSMLUG000000046091 retrocopy
retro_mluc_1209,
Macaca mulatta ENSMMUG000000040053 retrocopies
retro_mmul_1284, retro_mmul_2159, retro_mmul_2286,
Mustela putorius furoENSMPUG000000146604 retrocopies
retro_mputfur_1411, retro_mputfur_1482, retro_mputfur_1499, retro_mputfur_739,
Mus musculus ENSMUSG000000379355 retrocopies
retro_mmus_1111, retro_mmus_1127, retro_mmus_2437, retro_mmus_2618, retro_mmus_3194,
Nomascus leucogenys ENSNLEG000000019574 retrocopies
retro_nleu_1060, retro_nleu_2051, retro_nleu_2083, retro_nleu_286,
Oryctolagus cuniculus ENSOCUG000000089811 retrocopy
retro_ocun_59,
Otolemur garnettii ENSOGAG000000016527 retrocopies
retro_ogar_1734, retro_ogar_2059, retro_ogar_3199, retro_ogar_402, retro_ogar_454, retro_ogar_682, retro_ogar_760,
Ochotona princeps ENSOPRG000000009851 retrocopy
retro_opri_731,
Pongo abelii ENSPPYG000000084564 retrocopies
retro_pabe_2973, retro_pabe_3251, retro_pabe_794, retro_pabe_994,
Pan troglodytes ENSPTRG000000229025 retrocopies
retro_ptro_2451, retro_ptro_2678, retro_ptro_3039, retro_ptro_639, retro_ptro_894,
Pteropus vampyrus ENSPVAG000000113551 retrocopy
retro_pvam_237,
Rattus norvegicus ENSRNOG000000106767 retrocopies
retro_rnor_1278, retro_rnor_1311, retro_rnor_1456, retro_rnor_1507, retro_rnor_1599, retro_rnor_2383, retro_rnor_2593,
Tupaia belangeri ENSTBEG0000000077010 retrocopies
retro_tbel_1246, retro_tbel_1554, retro_tbel_2208, retro_tbel_2955, retro_tbel_4035, retro_tbel_4629, retro_tbel_4656, retro_tbel_658, retro_tbel_821, retro_tbel_844,

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 = 0.04 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .03 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 .02 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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





Copyright © RetrogeneDB 2014-2017