RetrogeneDB ID:

retro_hsap_4712

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:74421304..74421619(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000229661
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:BUD31
Ensembl ID:ENSG00000106245
Aliases:BUD31, Cwc14, EDG-2, EDG2, G10, YCR063W, fSAP17
Description:BUD31 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:29629]


Retrocopy-Parental alignment summary:






>retro_hsap_4712
GGAAAGTGGAAAGTGGAATCTCTGTTGCCCATCTTCAGGATCTACCACCAGAAAATATACCATATCGTTGACTTTGTTTA
TAAGTGGAAAGTCATAACCAGAGCACTCTATGAATATTGTATTAAAGAAGGCTATGCAGGAAAAAACCTAATCACAATAT
GGAAAAAGCAAGGCTATGAGAACTTGTGCTGGCTGCTGTGCCTTCAGACATGGAACACCAATTTTGGGACAAACTGCAAT
TGCTGTGTTCCTAAAACAAAGATAGAAGTGGGCTGCATCATTGAGTGCATGCACTGTGGCTGCCAGGGCTGCTCT

ORF - retro_hsap_4712 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.33 %
Parental protein coverage: 91.3 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGKRKVESLWPIFRIHHQKTRYIFDLFYKRKAISRELYEYCIKEGYADKNLIAKWKKQGYENLCCLRCIQT
GK.KVESL.PIFRI.HQK...I.D..YK.K.I.R.LYEYCIKEGYA.KNLI..WKKQGYENLC.L.C.QT
RetrocopyGKWKVESLLPIFRIYHQKIYHIVDFVYKWKVITRALYEYCIKEGYAGKNLITIWKKQGYENLCWLLCLQT
ParentalRDTNFGTNCICRVPKSKLEVGRIIECTHCGCRGCS
..TNFGTNC.C.VPK.K.EVG.IIEC.HCGC.GCS
RetrocopyWNTNFGTNCNCCVPKTKIEVGCIIECMHCGCQGCS

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 23 .63 RPM
bodymap2_adrenal 0 .00 RPM 28 .15 RPM
bodymap2_brain 0 .00 RPM 29 .70 RPM
bodymap2_breast 0 .02 RPM 21 .46 RPM
bodymap2_colon 0 .00 RPM 31 .40 RPM
bodymap2_heart 0 .00 RPM 7 .24 RPM
bodymap2_kidney 0 .00 RPM 26 .51 RPM
bodymap2_liver 0 .00 RPM 11 .19 RPM
bodymap2_lung 0 .00 RPM 27 .73 RPM
bodymap2_lymph_node 0 .00 RPM 19 .57 RPM
bodymap2_ovary 0 .00 RPM 25 .25 RPM
bodymap2_prostate 0 .00 RPM 24 .92 RPM
bodymap2_skeletal_muscle 0 .00 RPM 5 .35 RPM
bodymap2_testis 0 .04 RPM 57 .29 RPM
bodymap2_thyroid 0 .00 RPM 32 .33 RPM
bodymap2_white_blood_cells 0 .00 RPM 27 .50 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4712 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4712 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4712 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4712 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4712 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2928
Pongo abelii retro_pabe_3660
Parental genes homology:
Parental genes homology involve 18 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000062692 retrocopies
retro_amel_1325, retro_amel_997,
Bos taurus ENSBTAG000000204391 retrocopy
retro_btau_1066,
Choloepus hoffmanni ENSCHOG000000040551 retrocopy
retro_chof_1013,
Dipodomys ordii ENSDORG000000007391 retrocopy
retro_dord_58,
Equus caballus ENSECAG000000241512 retrocopies
retro_ecab_254, retro_ecab_672,
Ficedula albicollis ENSFALG000000138041 retrocopy
retro_falb_27,
Homo sapiens ENSG00000106245 1 retrocopy
retro_hsap_4712 ,
Gorilla gorilla ENSGGOG000000151191 retrocopy
retro_ggor_2928,
Loxodonta africana ENSLAFG000000122011 retrocopy
retro_lafr_24,
Macropus eugenii ENSMEUG000000069201 retrocopy
retro_meug_446,
Microcebus murinus ENSMICG000000174262 retrocopies
retro_mmur_470, retro_mmur_622,
Nomascus leucogenys ENSNLEG000000110201 retrocopy
retro_nleu_2053,
Pongo abelii ENSPPYG000000173762 retrocopies
retro_pabe_3313, retro_pabe_3660,
Pan troglodytes ENSPTRG000000194511 retrocopy
retro_ptro_2735,
Pteropus vampyrus ENSPVAG000000075271 retrocopy
retro_pvam_474,
Rattus norvegicus ENSRNOG000000009891 retrocopy
retro_rnor_1852,
Tupaia belangeri ENSTBEG000000106402 retrocopies
retro_tbel_2683, retro_tbel_4119,
Tursiops truncatus ENSTTRG000000030051 retrocopy
retro_ttru_815,

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 = 0.06 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 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 .06 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 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 .02 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 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 .03 RPM
YRI_NA18916 0 .02 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 .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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