RetrogeneDB ID:

retro_hsap_3810

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:152064603..152065743(+)
Located in intron of:ENSG00000055609
Retrocopy
information
Ensembl ID:ENSG00000241007
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SEPT7
Ensembl ID:ENSG00000122545
Aliases:None
Description:septin 7 [Source:HGNC Symbol;Acc:1717]


Retrocopy-Parental alignment summary:






>retro_hsap_3810
GGCGAACCTGGATTGGGAAAGTCGACATTAATCAACTCATTATTCCTTACAGATTTGTATGCTCCAGAGTATCCAGGTCC
TTCTCATAGAATTAAAAAGACTATACAGGTGGACAATCCAAAGTTTTAATCAAAGAAGGTGGTGTTCAGTTGCTGCTCAC
AATAGCTGACACCCCAGGATTTGGAGATGTAGTGGATAATAGTAATTGCTGGCAGCCTCTTATCGATTACATTGATAGTA
AATCTGAGGACTACCTAAATGCAGAATCACGAGTGAACAGACGTCAGATGCCTAATAGCAGGGTGCAGTGTTGTTTATAC
TTCATTGCTCCTTCAGGACATGAACTTAAACCATTGGATATTGAGTTTATGAAGCGTTCGCATGAAAAAGTGATTATCAT
CCAACTTATTGCCAAAGCAGACACACTTATACCAGAGGAATGCCAACAGTTTAAAAAACAGATAATGAAAGAAATCCAAG
AACATAAAATTAAGATATATGATTTTCCAGAAATAGATGATGAAGAAGAAAATAAACTTGCTAAAAAGGTAAAGGACTGT
TTACCTCTTGCTGTGGTAAGCTAGTAATACTATCATTGAAGTTAATGGCAAAAGGGTCAAAGGAAGGCAGTATCCTTGGG
GTGCTGCTGAAGTTGAAAATGGTGAACATTGTGATTTTACAATTCTAAGAAATATGCTGATAAAAACACACACTCAGGAC
TTGAAAGATGTTACTAATAATGTCCACTATGAGAACTACAGAAGCAGAAAACTGGCAGCTGTGACTTATAATGGAGTTGA
TAACAACAAGAATAAAGGGCAGCTGACTAAGAGCCCTCTGGCACAAATGGAAGAAGAAAGAAGGGAGTATGCAGCTAAAA
TGAAGAAGATAGAGATGGAGATGGAGCAGGTGTTAGAGATGAAGGTCAAATAAAAAGTTCAAAAACTAAAGGACTCTGAA
GCTGAGCTCCAGTGGCGCCGTGAGCTAATGAAAAAGAATTTGGAAGCACAGCACAAAGAATTAGAGGAAAAACGTCGTCA
GTTTGAGGATGAGAAGGCAAACTGGGAAGCTCAACAACATATTTTAGAACAGAACTCTTCGAGAACCTTGGAAAAGAACA
AGAAGAAAGGGAAGATCTTT

ORF - retro_hsap_3810 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.34 %
Parental protein coverage: 99.22 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalGESGLGKSTLINSLFLTDLYSPEYPGPSHRIKKTVQVE-QSKVLIKEGGVQLLLTIVDTPGFGDAVDNSN
GE.GLGKSTLINSLFLTDLY.PEYPGPSHRIKKT.QV..QSKVLIKEGGVQLLLTI.DTPGFGD.VDNSN
RetrocopyGEPGLGKSTLINSLFLTDLYAPEYPGPSHRIKKTIQVD<QSKVLIKEGGVQLLLTIADTPGFGDVVDNSN
ParentalCWQPVIDYIDSKFEDYLNAESRVNRRQMPDNRVQCCLYFIAPSGHGLKPLDIEFMKRLHEKVNIIPLIAK
CWQP.IDYIDSK.EDYLNAESRVNRRQMP..RVQCCLYFIAPSGH.LKPLDIEFMKR.HEKV.II.LIAK
RetrocopyCWQPLIDYIDSKSEDYLNAESRVNRRQMPNSRVQCCLYFIAPSGHELKPLDIEFMKRSHEKVIIIQLIAK
ParentalADTLTPEECQQFKKQIMKEIQEHKIKIYEFPETDDEEENKLVKKIKDRLPLAVVG-SNTIIEVNGKRVRG
ADTL.PEECQQFKKQIMKEIQEHKIKIY.FPE.DDEEENKL.KK.KD.LPLAVV..SNTIIEVNGKRV.G
RetrocopyADTLIPEECQQFKKQIMKEIQEHKIKIYDFPEIDDEEENKLAKKVKDCLPLAVVS>SNTIIEVNGKRVKG
ParentalRQYPWGVAEVENGEHCDFTILRNMLIRTHMQDLKDVTNNVHYENYRSRKLAAVTYNGVDNNKNKGQLTKS
RQYPWG.AEVENGEHCDFTILRNMLI.TH.QDLKDVTNNVHYENYRSRKLAAVTYNGVDNNKNKGQLTKS
RetrocopyRQYPWGAAEVENGEHCDFTILRNMLIKTHTQDLKDVTNNVHYENYRSRKLAAVTYNGVDNNKNKGQLTKS
ParentalPLAQMEEERREHVAKMKKMEMEMEQVFEMKVKEKVQKLKDSEAELQRRHEQMKKNLEAQHKELEEKRRQF
PLAQMEEERRE..AKMKK.EMEMEQV.EMKVK.KVQKLKDSEAELQ.R.E.MKKNLEAQHKELEEKRRQF
RetrocopyPLAQMEEERREYAAKMKKIEMEMEQVLEMKVK*KVQKLKDSEAELQWRRELMKKNLEAQHKELEEKRRQF
ParentalEDEKANWEAQQRILEQQNSSRTLEKNKKKGKIF
EDEKANWEAQQ.ILE.QNSSRTLEKNKKKGKIF
RetrocopyEDEKANWEAQQHILE-QNSSRTLEKNKKKGKIF

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 .08 RPM 203 .87 RPM
bodymap2_adrenal 0 .33 RPM 253 .27 RPM
bodymap2_brain 0 .09 RPM 639 .14 RPM
bodymap2_breast 0 .12 RPM 197 .71 RPM
bodymap2_colon 0 .00 RPM 315 .37 RPM
bodymap2_heart 0 .17 RPM 160 .41 RPM
bodymap2_kidney 0 .02 RPM 155 .37 RPM
bodymap2_liver 0 .00 RPM 45 .94 RPM
bodymap2_lung 0 .00 RPM 245 .48 RPM
bodymap2_lymph_node 0 .00 RPM 253 .67 RPM
bodymap2_ovary 0 .17 RPM 340 .87 RPM
bodymap2_prostate 0 .00 RPM 273 .09 RPM
bodymap2_skeletal_muscle 0 .02 RPM 84 .26 RPM
bodymap2_testis 0 .02 RPM 298 .73 RPM
bodymap2_thyroid 0 .02 RPM 187 .16 RPM
bodymap2_white_blood_cells 0 .00 RPM 302 .96 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3810 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3810 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3810 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3810 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3810 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2585
Parental genes homology:
Parental genes homology involve 13 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000122762 retrocopies
retro_cjac_1259, retro_cjac_3809,
Echinops telfairi ENSETEG000000156243 retrocopies
retro_etel_1263, retro_etel_282, retro_etel_517,
Homo sapiens ENSG00000122545 2 retrocopies
retro_hsap_3810 , retro_hsap_4202,
Homo sapiens ENSG000001865221 retrocopy
retro_hsap_4060,
Gorilla gorilla ENSGGOG000000011751 retrocopy
retro_ggor_2816,
Monodelphis domestica ENSMODG000000211671 retrocopy
retro_mdom_1672,
Nomascus leucogenys ENSNLEG000000016731 retrocopy
retro_nleu_2152,
Otolemur garnettii ENSOGAG000000060151 retrocopy
retro_ogar_1193,
Pongo abelii ENSPPYG000000176391 retrocopy
retro_pabe_3438,
Pan troglodytes ENSPTRG000000190802 retrocopies
retro_ptro_2585, retro_ptro_2853,
Rattus norvegicus ENSRNOG000000065459 retrocopies
retro_rnor_1424, retro_rnor_1425, retro_rnor_1426, retro_rnor_1427, retro_rnor_1428, retro_rnor_1431, retro_rnor_1445, retro_rnor_1446, retro_rnor_821,
Sarcophilus harrisii ENSSHAG000000037881 retrocopy
retro_shar_258,
Ictidomys tridecemlineatus ENSSTOG000000213783 retrocopies
retro_itri_1332, retro_itri_1736, retro_itri_1771,

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 = 0.2 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .09 RPM
CEU_NA11930 0 .13 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .13 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .08 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .09 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .08 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .12 RPM
GBR_HG00111 0 .06 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .10 RPM
GBR_HG00134 0 .11 RPM
GBR_HG00137 0 .08 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .10 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .10 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .20 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .08 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .05 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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



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