RetrogeneDB ID:

retro_hsap_3507

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:111751567..111752984(+)
Located in intron of:ENSG00000009413
Retrocopy
information
Ensembl ID:ENSG00000218676
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:BRD7
Ensembl ID:ENSG00000166164
Aliases:BRD7, BP75, CELTIX1, NAG4
Description:bromodomain containing 7 [Source:HGNC Symbol;Acc:14310]


Retrocopy-Parental alignment summary:






>retro_hsap_3507
ATGAAAGAAAAGATCAAGAACAATGACTACCAGTCCATAGAAAAACTAAAGGATATTTTCAAACTAATGTGTACTAATGC
CATGATTTACAATAAACCAGAGACCATTTATTATAAAGCTGCAAAGAAGCGGTTGCACTCGGGGATGAAAATTCTTAGAC
ATGAAAGAATTCAGAGCCTGAAGCAGAGCATAGACTTCATGGCTGACTTGCAGAAAACTCAAAAGCAGGAAGACAGAACA
GACACCTCGCAGAGTGGGGAGGACAGAGGCTGCTGGCCGAGAAGAGAGAGGACTCTGGAGATGCCAAAGCACACGCCTTC
AAGAGTCCCAGCAAAGAAAATAAAAAGAAAGACAAAGACATGCTTGAAGATAAGTTTAAAAGCAATAATTTAGAGAGAGC
GCAGGAGCAGCTTGACCGCATCGTGAAGGAATCTGGAGGAAAGCTGACCAGGCGGCTTGTGAACAGTCAGTGCAAATTGG
AAAGAAGAAAACCAGACGGAACAACAATGTTGGGACTTCTCCATCCTGTGGATCTCATTGTAGGAGAGCCAGGCTACTGC
CCTGTGAGACTGGGAATGACAACTGGAAGACTTCAGTCTGGTGTGAATACTTTGCAGGGGTTCAAAGAGGACAAAAGAAC
AAAGTCACTCCAGTGTTATATTTGAATTATGGGCCCTACAGTTCTTATGCACCGCATTATGACTCCACATATGCAAATAT
CAACAAGAATGATTCTGATTTAATCTATTCAACCTATGGGGAAGACACAGATCTTCCAAGCGATCTCAGCAGCCATGAGT
TTTTGGCCACGTGCCAAGATTATCCATCTGTGATGGCAGATAGTTTACTGGATGTTTTAACAAAAGGAGGGCATTCCAGG
ACCCTACAAGAGATTTAGATGTCACTGCCTGAAGATGGAAGGCCATACTAGGACACCTGACACAGCAAAAGAAATGGAGA
TTACAGAAGTAGAGCCACCAGGATGTCTGGACTCCAATACTTCAAGACAGGCTCATAGCGCTGAAAGCAGTAACAAACTT
TGGCGTTCCGGTTAAAGTTTTTGATTCTGAGGAAGCTGAAATATTCCAGAAGAAACTTGATGAGACCACCAGATTGCTCA
GGGAGCTAGCTCCAGGAAGCCCAGAATGAATGTTTCAACACCAGACCCCCTCCCAACATGATCTGTCTCTTGGGTCCCTC
ATACAGAGAAATGCATCTCACTGAACAAGTGACCAATAATCTTAAAGAACTTGCACAGCAAGTAACTACAGGTGATATCA
TAAGCACATACGGAGTTTGAAAAGCAATGGGGATTTCCATTCCTTCCCCCGTCATGGAAAACAACTCTGTGGATTTGACA
GAAGATACTGAAGAACCTAAAAAGACGAATGTTGCTGAATGTGGACCTGGTGGAAGT

ORF - retro_hsap_3507 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.84 %
Parental protein coverage: 72.35 %
Number of stop codons detected: 3
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKILSQERIQSLKQSIDFMADL
MKEKIKNNDYQSIE.LKD.FKLMCTNAMIYNKPETIYYKAAKK.LHSGMKIL..ERIQSLKQSIDFMADL
RetrocopyMKEKIKNNDYQSIEKLKDIFKLMCTNAMIYNKPETIYYKAAKKRLHSGMKILRHERIQSLKQSIDFMADL
ParentalQKTRKQKDGTDTSQSGEDGGCWQR-EREDSGDAEAHAFKSPSKENKKKDKDMLEDKFKSNNLEREQEQLD
QKT.KQ.D.TDTSQSGED.GCW.R..REDSGDA.AHAFKSPSKENKKKDKDMLEDKFKSNNLER.QEQLD
RetrocopyQKTQKQEDRTDTSQSGEDRGCWPR<KREDSGDAKAHAFKSPSKENKKKDKDMLEDKFKSNNLERAQEQLD
ParentalRIVKESGGKLTRRLVNSQCEFERRKPDGTTTLGLLHPVDPIVGEPGYCPVRLGMTTGRLQSGVNTLQGFK
RIVKESGGKLTRRLVNSQC..ERRKPDGTT.LGLLHPVD.IVGEPGYCPVRLGMTTGRLQSGVNTLQGFK
RetrocopyRIVKESGGKLTRRLVNSQCKLERRKPDGTTMLGLLHPVDLIVGEPGYCPVRLGMTTGRLQSGVNTLQGFK
ParentalEDKR-NKVTPVLYLNYGPYSSYAPHYDSTFANISKDDSDLIYSTYGEDSDLPSDFSIHEFLATCQDYPYV
EDKR.NKVTPVLYLNYGPYSSYAPHYDST.ANI.K.DSDLIYSTYGED.DLPSD.S.HEFLATCQDYP.V
RetrocopyEDKR<NKVTPVLYLNYGPYSSYAPHYDSTYANINKNDSDLIYSTYGEDTDLPSDLSSHEFLATCQDYPSV
ParentalMADSLLDVLTKGGHSRTLQEMEMSLPED-EGHTRTLDTAKEMEITEVEPPGRLDSST-QDRLIALKAVTN
MADSLLDVLTKGGHSRTLQE..MSLPED.EGHTRT.DTAKEMEITEVEPPG.LDS.T.QDRLIALKAVTN
RetrocopyMADSLLDVLTKGGHSRTLQEI*MSLPED>EGHTRTPDTAKEMEITEVEPPGCLDSNT>QDRLIALKAVTN
ParentalFGVPVEVFDSEEAEIFQKKLDETTRLLRELQEAQNERLSTRPPPNMICL-LG-PSYREMHLAEQVTNNLK
FGVPV.VFDSEEAEIFQKKLDETTRLLREL.....E.......P....L.LG.PSYREMHL.EQVTNNLK
RetrocopyFGVPVKVFDSEEAEIFQKKLDETTRLLRELAPGSPE*MFQHQTPSQHDLSLG>PSYREMHLTEQVTNNLK
ParentalELAQQVTPGDIVSTYGVRKAMGISIPSPVMENNFVDLTEDTEEPKKTDVAECGPGGS
ELAQQVT.GDI.STYGV.KAMGISIPSPVMENN.VDLTEDTEEPKKT.VAECGPGGS
RetrocopyELAQQVTTGDIISTYGV*KAMGISIPSPVMENNSVDLTEDTEEPKKTNVAECGPGGS

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 .26 RPM 39 .62 RPM
bodymap2_adrenal 0 .04 RPM 48 .80 RPM
bodymap2_brain 0 .00 RPM 44 .00 RPM
bodymap2_breast 0 .23 RPM 41 .63 RPM
bodymap2_colon 0 .08 RPM 66 .26 RPM
bodymap2_heart 0 .13 RPM 28 .47 RPM
bodymap2_kidney 0 .00 RPM 54 .64 RPM
bodymap2_liver 0 .00 RPM 18 .74 RPM
bodymap2_lung 0 .00 RPM 40 .68 RPM
bodymap2_lymph_node 0 .00 RPM 46 .78 RPM
bodymap2_ovary 0 .06 RPM 62 .88 RPM
bodymap2_prostate 0 .05 RPM 66 .61 RPM
bodymap2_skeletal_muscle 0 .00 RPM 40 .92 RPM
bodymap2_testis 0 .15 RPM 130 .92 RPM
bodymap2_thyroid 0 .04 RPM 62 .35 RPM
bodymap2_white_blood_cells 0 .00 RPM 72 .37 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3507 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3507 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3507 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3507 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3507 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2379
Gorilla gorilla retro_ggor_2372
Parental genes homology:
Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000093551 retrocopy
retro_chof_2431,
Callithrix jacchus ENSCJAG000000018321 retrocopy
retro_cjac_2372,
Homo sapiens ENSG00000166164 2 retrocopies
retro_hsap_2723, retro_hsap_3507 ,
Gorilla gorilla ENSGGOG000000148242 retrocopies
retro_ggor_1895, retro_ggor_2372,
Monodelphis domestica ENSMODG000000130571 retrocopy
retro_mdom_152,
Otolemur garnettii ENSOGAG000000112892 retrocopies
retro_ogar_326, retro_ogar_438,
Pan troglodytes ENSPTRG000000081033 retrocopies
retro_ptro_1840, retro_ptro_2379, retro_ptro_2384,

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 = 0.22 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .20 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .12 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .22 RPM
FIN_HG00183 0 .08 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .14 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .17 RPM
GBR_HG00111 0 .06 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .11 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .07 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .06 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .06 RPM

Indel association:

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



Copyright © RetrogeneDB 2014-2017