RetrogeneDB ID:

retro_hsap_3790

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:134813343..134814441(+)
Located in intron of:ENSG00000146856
Retrocopy
information
Ensembl ID:ENSG00000223500
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RNF14
Ensembl ID:ENSG00000013561
Aliases:RNF14, ARA54, HFB30, TRIAD2
Description:ring finger protein 14 [Source:HGNC Symbol;Acc:10058]


Retrocopy-Parental alignment summary:






>retro_hsap_3790
CTATCTGCTCTATGGGAAGAACACCCTGGCAGCGTGATCCCGTTTGCCTGGATGCAATTTCTTAAGGAAGAGACCCTAGT
ATACCTGAATATTGTCTCTCCTTTTGAGCTCAAGATTGATTCTCAGAAAAAAAGTGCAGAGAAGGACAGCTCAAGCCTCT
CCCAACACAGAGCTAGATTTTGGAGGAACTTCTGGATCTGATACAGACCAAGAGGAAACTGTGGATGAGACAGCTGTGTG
CAGGATGTGGAATCATTGTTAAATATGATCCAGGAAATCTTGGACTTTGATCAAGCTCAGCAGATAAAATGCTTTAATAG
TAATTTGTTCCTGTGCAATATCTGTTTCTGTAAGAAGCTGGGTAGTGAATGCATGTACTTCTTGGAGTGCAGGCATGTGT
ACTGCAAAGACTGTCTGAAGGACTACTTTGAAATCCAGATCAGAGATGGCCAGGTTCAATGCCTCAACTGCCCAGAACCA
AAGTGCCCTTCAGTGGCCACTACTGGTCAGGTCAAAGAGCTAGTGGAAGCAGAGTTATTTGCCTATTATGACTGCCTTCT
CCTCCAGTCCACCTTGGACCTGATGGCAGATGTGGTGTACTGCCCCCACGCATGCTGCCAGCTGCCTGTGATGCAGGAGC
CTGGCTACATCATGGGTATCTGCTCCAGCTGCAATTTTGCCTTCTGTACCTTGTGCAGGTTGACCTACCATGGGGTCTCT
CCATGTAAGGTGACTGCAGAGAAATTAATAGACTTACTAAATGAATACCTGCAAGCAGATAAGGCCAATAAAAGACTTTT
GGAACAAAGGTATGATAAGAGGGTGATTCAGAAGGCACTGGAAGAGATGGAAAGTAAGGAGTGGCTAGAGAAAAACTTCA
AGAACTGACCATGTTGTGGAACTCCCATAGAGAAATTAGATGGATATAACAAGATGACATGTACTGGCTGTATGCAATAT
TTCTGTTGGATTTGCATGAGTTCTCTCTCTAGAGCAAACCCTTACAAACATTTCACTGATCCTGCTTCAACATGTCTTAA
ACAGCTGTTTTATGCTGTGGATGTTGATGAAGATATTTGGGAAGATGAGATTGAAGAC

ORF - retro_hsap_3790 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.6 %
Parental protein coverage: 77. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLDNLWEEHRGSVVLFAWMQFLKEETLAYLNIVSPFELKIGSQKK-VQRRTAQASPNTELDFGGAAGSDVD
L..LWEEH.GSV..FAWMQFLKEETL.YLNIVSPFELKI.SQKK.VQRRTAQASPNTELDFGG..GSD.D
RetrocopyLSALWEEHPGSVIPFAWMQFLKEETLVYLNIVSPFELKIDSQKK>VQRRTAQASPNTELDFGGTSGSDTD
Parental-QEEIVD-ERAVQDVESLSNLIQEILDFDQAQQIKCFNSKLFLCSICFCEKLGSECMYFLECRHVYCKAC
..E........VQDVESL.N.IQEILDFDQAQQIKCFNS.LFLC.ICFC.KLGSECMYFLECRHVYCK.C
RetrocopyQEETVDE<DSCVQDVESLLNMIQEILDFDQAQQIKCFNSNLFLCNICFCKKLGSECMYFLECRHVYCKDC
ParentalLKDYFEIQIRDGQVQCLNCPEPKCPSVATPGQVKELVEAELFARYDRLLLQSSLDLMADVVYCPRPCCQL
LKDYFEIQIRDGQVQCLNCPEPKCPSVAT.GQVKELVEAELFA.YD.LLLQS.LDLMADVVYCP..CCQL
RetrocopyLKDYFEIQIRDGQVQCLNCPEPKCPSVATTGQVKELVEAELFAYYDCLLLQSTLDLMADVVYCPHACCQL
ParentalPVMQEPGCTMGICSSCNFAFCTLCRLTYHGVSPCKVTAEKLMDLRNEYLQADEANKRLLDQRYGKRVIQK
PVMQEPG..MGICSSCNFAFCTLCRLTYHGVSPCKVTAEKL.DL.NEYLQAD.ANKRLL.QRY.KRVIQK
RetrocopyPVMQEPGYIMGICSSCNFAFCTLCRLTYHGVSPCKVTAEKLIDLLNEYLQADKANKRLLEQRYDKRVIQK
ParentalALEEMESKEWLEKNSKSCPCCGTPIEKLDGCNKMTCTGCMQYFCWICMGSLSRANPYKHFNDPGSPCFNR
ALEEMESKEWLEKN.K..PCCGTPIEKLDG.NKMTCTGCMQYFCWICM.SLSRANPYKHF.DP.S.C...
RetrocopyALEEMESKEWLEKNFKN*PCCGTPIEKLDGYNKMTCTGCMQYFCWICMSSLSRANPYKHFTDPASTCLKQ
ParentalLFYAVDVDDDIWEDEVED
LFYAVDVD.DIWEDE.ED
RetrocopyLFYAVDVDEDIWEDEIED

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 34 .87 RPM
bodymap2_adrenal 0 .08 RPM 33 .53 RPM
bodymap2_brain 0 .12 RPM 63 .55 RPM
bodymap2_breast 0 .00 RPM 89 .16 RPM
bodymap2_colon 0 .00 RPM 43 .82 RPM
bodymap2_heart 0 .00 RPM 94 .50 RPM
bodymap2_kidney 0 .19 RPM 91 .01 RPM
bodymap2_liver 0 .00 RPM 41 .30 RPM
bodymap2_lung 0 .00 RPM 28 .73 RPM
bodymap2_lymph_node 0 .27 RPM 34 .83 RPM
bodymap2_ovary 0 .08 RPM 49 .52 RPM
bodymap2_prostate 0 .10 RPM 58 .91 RPM
bodymap2_skeletal_muscle 0 .00 RPM 23 .26 RPM
bodymap2_testis 0 .08 RPM 85 .91 RPM
bodymap2_thyroid 0 .00 RPM 72 .58 RPM
bodymap2_white_blood_cells 0 .00 RPM 40 .48 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3790 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3790 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3790 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3790 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3790 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2571
Pongo abelii retro_pabe_3095
Macaca mulatta retro_mmul_1647
Parental genes homology:
Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000078031 retrocopy
retro_dnov_332,
Dasypus novemcinctus ENSDNOG000000244231 retrocopy
retro_dnov_1704,
Homo sapiens ENSG00000013561 2 retrocopies
retro_hsap_3790 , retro_hsap_3881,
Gorilla gorilla ENSGGOG000000085421 retrocopy
retro_ggor_2612,
Macaca mulatta ENSMMUG000000097682 retrocopies
retro_mmul_1647, retro_mmul_934,
Pongo abelii ENSPPYG000000158942 retrocopies
retro_pabe_3095, retro_pabe_3115,
Pan troglodytes ENSPTRG000000173562 retrocopies
retro_ptro_2571, retro_ptro_2643,

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 = 0.08 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .07 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .06 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 .02 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 .00 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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