RetrogeneDB ID:

retro_hsap_3834

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:27531303..27532382(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000235574
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CCDC86
Ensembl ID:ENSG00000110104
Aliases:None
Description:coiled-coil domain containing 86 [Source:HGNC Symbol;Acc:28359]


Retrocopy-Parental alignment summary:






>retro_hsap_3834
ATGGATACACCGCCAAGGCGAAGCCGACAGCTGGAAGGCCTAGGGCCTGAATCCCTCCAGAGCCTCACCTCAGTTTCACG
TAGGAGATGGGTCCTTGTGGAGTTCGAGTTGGACACAGAAGAAACGAGGGAGCCCGGGTCTCCTCCGAGTGTGCAACAAG
CTGGCCTGGGGCCCCCCGAAAGGACGCTGGAGAGAAGCCCAGGATCACCCAGTCTTTGCAGCAGGGTGCAGGCTTGGAGT
CCCCCCAAGGGCGGCTAGAATCAGGTCCAGGGTCCCCCCAGTGTCAGCAAGGCCTACACCTGGAGTCGCCTCAAAGACAG
CTGGAGTCCAGTCCTCAATCCCCACGATGTCAGCCGAAGCCAAGTGAGGAGGCACCCAAGTGTGCTCAGGGCCAGGGAGT
ACCTGGCCTCGGAGTTGGCCCAAAGTAAGGAGGAGCTGATCCCAGGGGGCCCCCCAGCATCAGCTACTGCCGGGCCCAGG
ATCACCAGAGCCTTAACCCCAGTCAGGAAGCTCCGGGTCCGGAGCCCTCTCAGCCACTACTGCAGCTAACACTCGAGGCA
CCTGGCTTCCCCCAGGGTCAGCACGAGCAGAGCAAACCACCTCCAGCTGGGGAGATGGTGACAGACGGCTTCGGGGCAAA
GAAGCCAAAGGGTTCTTCATCCCAGGCCCCAGCGTCCAAGAAGCTGAAGGAGGAGGAGCTTCCTGTAATCCCGAAGGGGA
AGCCCAAGTCGGGGCAAGTGTGGAAGGACCGCTCCAAGAAAAGATTCTCTCAGATGCTTTAGGACAAGCCCCTGCGTATA
TCGTGGCAGCGGAAGATGAAGCAGGAGAGGAAGCTGGCCAAGGACTTTGCCCGTCACCTGGAGGAGGAGTAGGAGAGGCG
CCGCCAGGAGAAGAAACAGCGTCGGGCGGAGAACCTGAAATGCCGCCTGGAGAACGAGCGGAAGGTGGAGATCGTCCAAG
TGATCCGAAACCCTGCCAAGCTCAAGCGGGCAAAGCAGCAGCAGCTGCGCTCCATTGAGAAGCGGGACACCCTAGCCCTG
CTGCAGAAGCAGCCGCCCTAGCGGCCGGCAGCCAAGATC

ORF - retro_hsap_3834 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80. %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMDTPLRRSRRLGGLRPESPESLTSVSRTRRALVEFESNPEETREPGSPPSVQRAGLG-SPERPPKTSPG-
MDTP.RRSR.L.GL.PES..SLTSVSR.R..LVEFE...EETREPGSPPSVQ.AGLG..P.......P..
RetrocopyMDTPPRRSRQLEGLGPESLQSLTSVSRRRWVLVEFELDTEETREPGSPPSVQQAGLG<APRKDAGEKPRI
ParentalSPRLQQGAGLESPQGQPEPGAASPQRQQDLHLESPQRQPEYSPESPRCQPKPSEEAPKCSQDQGV-LASE
...LQQGAGLESPQG..E.G..SPQ.QQ.LHLESPQRQ.E.SP.SPRCQPKPSEEAPKC.Q.QGV.LASE
RetrocopyTQSLQQGAGLESPQGRLESGPGSPQCQQGLHLESPQRQLESSPQSPRCQPKPSEEAPKCAQGQGV>LASE
ParentalLAQNKEELTPG-APQHQLPPVPGSPEP-YPGQQAPGPEPSQPLLELTPRAPGSPRGQHEPSKPPPAGETV
LAQ.KEEL.PG.APQHQL.P.PGSPEP..P.Q.APGPEPSQPLL.LT..APG.P.GQHE.SKPPPAGE.V
RetrocopyLAQSKEELIPG>APQHQLLPGPGSPEP>NPSQEAPGPEPSQPLLQLTLEAPGFPQGQHEQSKPPPAGEMV
ParentalTGGFGAKKRKGSSSQAPASKKLNKEELPVIPKGKPKSGRVWKDRSKKRFSQMLQDKPLRTSWQRKMKERQ
T.GFGAKK.KGSSSQAPASKKL..EELPVIPKGKPKSG.VWKDRSKKRFSQML.DKPLR.SWQRKMK..Q
RetrocopyTDGFGAKKPKGSSSQAPASKKLKEEELPVIPKGKPKSGQVWKDRSKKRFSQML*DKPLRISWQRKMK--Q
ParentalERKLAKDFARHLEEEKERRRQEKKQRRAENLKRRLENERKAEVVQVIRNPAKLKRAKKKQLRSIEKRDTL
ERKLAKDFARHLEEE.ERRRQEKKQRRAENLK.RLENERK.E.VQVIRNPAKLKRAK..QLRSIEKRDTL
RetrocopyERKLAKDFARHLEEE*ERRRQEKKQRRAENLKCRLENERKVEIVQVIRNPAKLKRAKQQQLRSIEKRDTL
ParentalALLQKQPPQQPAAKI
ALLQKQPP..PAAKI
RetrocopyALLQKQPP*RPAAKI

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 17 .13 RPM
bodymap2_adrenal 0 .00 RPM 15 .56 RPM
bodymap2_brain 0 .00 RPM 7 .17 RPM
bodymap2_breast 0 .00 RPM 9 .14 RPM
bodymap2_colon 0 .08 RPM 7 .83 RPM
bodymap2_heart 0 .00 RPM 3 .69 RPM
bodymap2_kidney 0 .00 RPM 7 .61 RPM
bodymap2_liver 0 .04 RPM 5 .30 RPM
bodymap2_lung 0 .00 RPM 6 .01 RPM
bodymap2_lymph_node 0 .00 RPM 7 .77 RPM
bodymap2_ovary 0 .04 RPM 15 .88 RPM
bodymap2_prostate 0 .00 RPM 7 .22 RPM
bodymap2_skeletal_muscle 0 .20 RPM 11 .17 RPM
bodymap2_testis 0 .06 RPM 34 .39 RPM
bodymap2_thyroid 0 .04 RPM 16 .36 RPM
bodymap2_white_blood_cells 0 .00 RPM 5 .20 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3834 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3834 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3834 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3834 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3834 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2610
Gorilla gorilla retro_ggor_2582
Macaca mulatta retro_mmul_1622
Parental genes homology:
Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000110104 2 retrocopies
retro_hsap_3276, retro_hsap_3834 ,
Gorilla gorilla ENSGGOG000000136701 retrocopy
retro_ggor_2582,
Macaca mulatta ENSMMUG000000000191 retrocopy
retro_mmul_1622,
Nomascus leucogenys ENSNLEG000000135821 retrocopy
retro_nleu_2131,
Pongo abelii ENSPPYG000000032051 retrocopy
retro_pabe_2818,
Pan troglodytes ENSPTRG000000037212 retrocopies
retro_ptro_2216, retro_ptro_2610,

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 = 0.07 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 .03 RPM
FIN_HG00277 0 .07 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 .02 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 .05 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 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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



Copyright © RetrogeneDB 2014-2017