RetrogeneDB ID:

retro_hsap_4780

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:8824705..8825049(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000231619
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ANAPC15
Ensembl ID:ENSG00000110200
Aliases:ANAPC15, APC15, C11orf51
Description:anaphase promoting complex subunit 15 [Source:HGNC Symbol;Acc:24531]


Retrocopy-Parental alignment summary:






>retro_hsap_4780
TCACTCTTCCTTTGTGGGACTGAGACACTGTGGTTTAATCTGGATCGACCTTGTATGGGAGAGACAGAGCTGCAGCAGCA
GGAACAGCAGCATCAGACCTGGCTCGAAAGCATCACAGAGAAAGACAACAATCTGGTTCCTATTGGCAAGCCAGCCTCAG
AGCACTATGATGATGAGGAAGAGGAGGATGATGAAGACAATGAGGATAGTGAAGAGGACTTAGAGGATGATGAGGACATG
CAGGACATGGACAAGATGAATGACTACAATGGGTCACCTGATGACGGAGAGGTCAATGAGGTGGACATGAAGGAAACGAA
CAGGATGTGGACCAGTGAATGATC

ORF - retro_hsap_4780 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.07 %
Parental protein coverage: 95.04 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSLFPRVTETLWFNLDRPCVEETELQQQEQQHQAWLQSIAEKDNNLVPIGKPASEHYDDEEEEDDEDDEDS
SLF...TETLWFNLDRPC..ETELQQQEQQHQ.WL.SI.EKDNNLVPIGKPASEHYDDEEEEDDED.EDS
RetrocopySLFLCGTETLWFNLDRPCMGETELQQQEQQHQTWLESITEKDNNLVPIGKPASEHYDDEEEEDDEDNEDS
ParentalEEDSEDDEDMQDMDEMNDYNESPDDGEVNEVDM-EGNEQDQDQWMI
EED.EDDEDMQDMD.MNDYN.SPDDGEVNEVDM.EGNEQD.DQ.MI
RetrocopyEEDLEDDEDMQDMDKMNDYNGSPDDGEVNEVDM<EGNEQDVDQ*MI

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 2 .58 RPM
bodymap2_adrenal 0 .00 RPM 8 .09 RPM
bodymap2_brain 0 .00 RPM 6 .00 RPM
bodymap2_breast 0 .00 RPM 6 .07 RPM
bodymap2_colon 0 .00 RPM 4 .37 RPM
bodymap2_heart 0 .00 RPM 4 .12 RPM
bodymap2_kidney 0 .00 RPM 4 .71 RPM
bodymap2_liver 0 .00 RPM 1 .82 RPM
bodymap2_lung 0 .00 RPM 2 .60 RPM
bodymap2_lymph_node 0 .00 RPM 1 .75 RPM
bodymap2_ovary 0 .00 RPM 3 .10 RPM
bodymap2_prostate 0 .00 RPM 5 .85 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .84 RPM
bodymap2_testis 0 .00 RPM 11 .33 RPM
bodymap2_thyroid 0 .00 RPM 9 .11 RPM
bodymap2_white_blood_cells 0 .00 RPM 5 .55 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4780 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4780 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4780 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4780 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4780 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2977
Pongo abelii retro_pabe_3720
Macaca mulatta retro_mmul_2551
Parental genes homology:
Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000108431 retrocopy
retro_amel_298,
Bos taurus ENSBTAG000000029992 retrocopies
retro_btau_252, retro_btau_269,
Canis familiaris ENSCAFG000000057811 retrocopy
retro_cfam_1752,
Equus caballus ENSECAG000000210411 retrocopy
retro_ecab_470,
Felis catus ENSFCAG000000053211 retrocopy
retro_fcat_1350,
Homo sapiens ENSG00000110200 1 retrocopy
retro_hsap_4780 ,
Myotis lucifugus ENSMLUG000000141201 retrocopy
retro_mluc_238,
Macaca mulatta ENSMMUG000000162701 retrocopy
retro_mmul_2551,
Mustela putorius furoENSMPUG000000102601 retrocopy
retro_mputfur_596,
Nomascus leucogenys ENSNLEG000000172341 retrocopy
retro_nleu_1100,
Pongo abelii ENSPPYG000000036462 retrocopies
retro_pabe_2388, retro_pabe_3720,
Pteropus vampyrus ENSPVAG000000157971 retrocopy
retro_pvam_404,
Sorex araneus ENSSARG000000041712 retrocopies
retro_sara_444, retro_sara_686,
Tarsius syrichta ENSTSYG000000141791 retrocopy
retro_tsyr_35,
Tursiops truncatus ENSTTRG000000107731 retrocopy
retro_ttru_277,

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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