RetrogeneDB ID:

retro_hsap_3763

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:94463217..94463759(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000219807
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ARF1
Ensembl ID:ENSG00000143761
Aliases:None
Description:ADP-ribosylation factor 1 [Source:HGNC Symbol;Acc:652]


Retrocopy-Parental alignment summary:






>retro_hsap_3763
ATGGGGAGCATCTTTGTCAACCTCTTCGAAAGCATTTTTGGCAAAAAAGAAATGCACATCCTCATCGTGGTCCTCAGTGC
TGCAGGGAAAACAACAATCCTATATAAGCTGAAGCTGAGTGACATCATGACCACCATCCCTACCATAGGCTTCAATGTGG
AAACCATGGAGTACAGGAACATCAGCTTAACCATGTGGAACATGGGCAGCCAAGAAAACATCTGGCCTCTGTGGCACCAC
TACTTCCAGAATACACAAGGACTGATCTTCGTAGTGGACAGCAATGATAGAAAGTGTGGAAAGGAGGCCTGGGAGGAGCT
CTTTAGGATGCTGGCTGAGGATGAGCTCTGGGTGCAGTCCTCCTGGTGTTTGCCAACAAGCAGGGCCTCCCCAATGCCAG
GAATGCAGCCAAGATCACAGACAAGCTGGGGCTGCATTACCTGTGCCACAGGAACTGGTGCATTTAGGCCACCTATGCCA
TTAGTGGAGACAGGCTCTGTGAAGGACTGGACTGGCTGTCCAATCAACTCTGGAACCAGAAG

ORF - retro_hsap_3763 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.82 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMGNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGG
MG.IF.NLF...FGKKEM.IL.V.L.AAGKTTILYKLKL..I.TTIPTIGFNVET.EY.NIS.T.W..G.
RetrocopyMGSIFVNLFESIFGKKEMHILIVVLSAAGKTTILYKLKLSDIMTTIPTIGFNVETMEYRNISLTMWNMGS
ParentalQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDEL-RDAVLLVFANKQDLPNAMNAAEI
Q..I.PLW.HYFQNTQGLIFVVDSNDR....EA.EEL.RMLAEDEL...AVLLVFANKQ.LPNA.NAA.I
RetrocopyQENIWPLWHHYFQNTQGLIFVVDSNDRKCGKEAWEELFRMLAEDEL<LGAVLLVFANKQGLPNARNAAKI
ParentalTDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK
TDKLGLH.L.HRNW.I.AT.A.SGD.L.EGLDWLSNQL.NQK
RetrocopyTDKLGLHYLCHRNWCI*ATYAISGDRLCEGLDWLSNQLWNQK

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 224 .28 RPM
bodymap2_adrenal 0 .00 RPM 197 .98 RPM
bodymap2_brain 0 .00 RPM 155 .22 RPM
bodymap2_breast 0 .00 RPM 148 .99 RPM
bodymap2_colon 0 .00 RPM 202 .31 RPM
bodymap2_heart 0 .00 RPM 152 .25 RPM
bodymap2_kidney 0 .00 RPM 223 .68 RPM
bodymap2_liver 0 .00 RPM 188 .17 RPM
bodymap2_lung 0 .00 RPM 436 .08 RPM
bodymap2_lymph_node 0 .00 RPM 226 .92 RPM
bodymap2_ovary 0 .00 RPM 175 .38 RPM
bodymap2_prostate 0 .00 RPM 278 .44 RPM
bodymap2_skeletal_muscle 0 .00 RPM 314 .49 RPM
bodymap2_testis 0 .00 RPM 234 .06 RPM
bodymap2_thyroid 0 .00 RPM 198 .10 RPM
bodymap2_white_blood_cells 0 .00 RPM 319 .26 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3763 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3763 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3763 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3763 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3763 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2531
Pongo abelii retro_pabe_3159
Parental genes homology:
Parental genes homology involve 18 parental genes, and 50 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG0000001667110 retrocopies
retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Cavia porcellus ENSCPOG000000211741 retrocopy
retro_cpor_1310,
Ciona savignyi ENSCSAVG000000070111 retrocopy
retro_csav_2,
Felis catus ENSFCAG000000293741 retrocopy
retro_fcat_1829,
Homo sapiens ENSG000001341081 retrocopy
retro_hsap_361,
Homo sapiens ENSG000001342871 retrocopy
retro_hsap_36,
Homo sapiens ENSG00000143761 3 retrocopies
retro_hsap_1008, retro_hsap_1160, retro_hsap_3763 ,
Homo sapiens ENSG000001683742 retrocopies
retro_hsap_1296, retro_hsap_4221,
Gallus gallus ENSGALG000000053931 retrocopy
retro_ggal_7,
Gorilla gorilla ENSGGOG000000112635 retrocopies
retro_ggor_161, retro_ggor_2531, retro_ggor_3071, retro_ggor_801, retro_ggor_906,
Latimeria chalumnae ENSLACG000000190091 retrocopy
retro_lcha_10,
Myotis lucifugus ENSMLUG000000070206 retrocopies
retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Mus musculus ENSMUSG000000480761 retrocopy
retro_mmus_1718,
Oryctolagus cuniculus ENSOCUG000000236452 retrocopies
retro_ocun_1137, retro_ocun_247,
Pan troglodytes ENSPTRG000000020662 retrocopies
retro_ptro_112, retro_ptro_5,
Tupaia belangeri ENSTBEG000000092189 retrocopies
retro_tbel_1943, retro_tbel_2224, retro_tbel_2310, retro_tbel_2358, retro_tbel_2662, retro_tbel_2770, retro_tbel_3103, retro_tbel_4217, retro_tbel_4624,
Tetraodon nigroviridis ENSTNIG000000116851 retrocopy
retro_tnig_19,
Tursiops truncatus ENSTTRG000000141862 retrocopies
retro_ttru_1679, retro_ttru_347,

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 ) 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 .00 RPM
FIN_HG00277 0 .00 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 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 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 .00 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 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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



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