RetrogeneDB ID:

retro_hsap_3953

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:51772098..51772555(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000253340
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PDCD10
Ensembl ID:ENSG00000114209
Aliases:PDCD10, CCM3, TFAR15
Description:programmed cell death 10 [Source:HGNC Symbol;Acc:8761]


Retrocopy-Parental alignment summary:






>retro_hsap_3953
GTAAATCTGTCTGCAGCTCAGATACTGAGAGTGGCTTTCATTAAGGCCAATAAAGGAAACCCTGGTCTCACACAATACAT
TGTTTTGGCAACTTTAGAGAAAAAAAATATAAACATTAAGATCACAGGATTTCTTCTTATGGCAGCTGTTAATGTATAAT
AGTAGATAATTGAATGACTAGAGCCAGAATTCCAGGATGTAAATGAAAGTCACAAGCACTTACACAAATTCTCAGTAAGT
TTCCAGTGAGCTCAATGACAGAGTGAGGATTCTGTAGACAATTAAGGATATAAAGAGTGAAATAAAAGAGCTCGATATAG
TGAATAATGTCTTCAAGAAATATCAATACCAGAACTACGGGGCACTTGAACACCAAAAGAAAGTATTTTTAAAGTATTCT
AAAAGTTTCAATGGTATTCTGAAAACTTATTTCAAAGATGACAAAGCAACAAATGTT

ORF - retro_hsap_3953 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.88 %
Parental protein coverage: 73.11 %
Number of stop codons detected: 5
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVNLSAAQTLRAAFIKAEKENPGLTQDIIMKILEKKSVEVNFTESLLRMAADDVEEYMIERPEPEFQDLNE
VNLSAAQ.LR.AFIKA.K.NPGLTQ.I....LE........T..LL.MAA..V....IE..EPEFQD.NE
RetrocopyVNLSAAQILRVAFIKANKGNPGLTQYIVLATLEXXXINIKITGFLL-MAAVNV***IIE*LEPEFQDVNE
Parental-KARALKQILSKIP-DEINDRVRFLQTIKDIASAIKELLDTVNNVFKKYQYQNRRALEHQKKEFVKYSKS
.K..AL.QILSK.P..E.NDRVR.L.TIKDI.S.IKEL.D.VNNVFKKYQYQN..ALEHQKK.F.KYSKS
Retrocopy<KSQALTQILSKFP<SELNDRVRIL*TIKDIKSEIKEL-DIVNNVFKKYQYQNYGALEHQKKVFLKYSKS
ParentalFSDTLKTYFKDGKAINV
F...LKTYFKD.KA.NV
RetrocopyFNGILKTYFKDDKATNV

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 27 .17 RPM
bodymap2_adrenal 0 .00 RPM 28 .76 RPM
bodymap2_brain 0 .00 RPM 34 .48 RPM
bodymap2_breast 0 .00 RPM 32 .12 RPM
bodymap2_colon 0 .00 RPM 32 .23 RPM
bodymap2_heart 0 .00 RPM 22 .97 RPM
bodymap2_kidney 0 .00 RPM 40 .49 RPM
bodymap2_liver 0 .00 RPM 14 .34 RPM
bodymap2_lung 0 .00 RPM 35 .85 RPM
bodymap2_lymph_node 0 .00 RPM 31 .50 RPM
bodymap2_ovary 0 .00 RPM 28 .11 RPM
bodymap2_prostate 0 .00 RPM 31 .96 RPM
bodymap2_skeletal_muscle 0 .00 RPM 6 .20 RPM
bodymap2_testis 0 .00 RPM 58 .14 RPM
bodymap2_thyroid 0 .08 RPM 40 .11 RPM
bodymap2_white_blood_cells 0 .00 RPM 58 .20 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3953 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3953 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3953 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3953 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3953 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2683
Gorilla gorilla retro_ggor_2656
Pongo abelii retro_pabe_3257
Macaca mulatta retro_mmul_2288
Parental genes homology:
Parental genes homology involve 24 parental genes, and 38 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000021811 retrocopy
retro_amel_420,
Bos taurus ENSBTAG000000317092 retrocopies
retro_btau_1623, retro_btau_713,
Canis familiaris ENSCAFG000000145692 retrocopies
retro_cfam_1988, retro_cfam_687,
Callithrix jacchus ENSCJAG000000027632 retrocopies
retro_cjac_1442, retro_cjac_4178,
Dasypus novemcinctus ENSDNOG000000158541 retrocopy
retro_dnov_351,
Homo sapiens ENSG00000114209 1 retrocopy
retro_hsap_3953 ,
Gorilla gorilla ENSGGOG000000086211 retrocopy
retro_ggor_2656,
Loxodonta africana ENSLAFG000000068231 retrocopy
retro_lafr_409,
Microcebus murinus ENSMICG000000070041 retrocopy
retro_mmur_1008,
Myotis lucifugus ENSMLUG000000169781 retrocopy
retro_mluc_1331,
Macaca mulatta ENSMMUG000000059382 retrocopies
retro_mmul_1090, retro_mmul_2288,
Mustela putorius furoENSMPUG000000170751 retrocopy
retro_mputfur_298,
Mus musculus ENSMUSG000000278351 retrocopy
retro_mmus_2113,
Nomascus leucogenys ENSNLEG000000048741 retrocopy
retro_nleu_532,
Otolemur garnettii ENSOGAG000000138871 retrocopy
retro_ogar_540,
Oreochromis niloticus ENSONIG000000055531 retrocopy
retro_onil_40,
Procavia capensis ENSPCAG000000103851 retrocopy
retro_pcap_283,
Pongo abelii ENSPPYG000000297501 retrocopy
retro_pabe_3257,
Pan troglodytes ENSPTRG000000155981 retrocopy
retro_ptro_2683,
Sarcophilus harrisii ENSSHAG000000054431 retrocopy
retro_shar_414,
Ictidomys tridecemlineatus ENSSTOG000000284423 retrocopies
retro_itri_1208, retro_itri_1377, retro_itri_322,
Tupaia belangeri ENSTBEG000000002409 retrocopies
retro_tbel_1498, retro_tbel_1690, retro_tbel_2223, retro_tbel_2903, retro_tbel_3430, retro_tbel_3898, retro_tbel_3900, retro_tbel_4532, retro_tbel_95,
Tarsius syrichta ENSTSYG000000007081 retrocopy
retro_tsyr_1786,
Tursiops truncatus ENSTTRG000000163151 retrocopy
retro_ttru_635,

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).



Copyright © RetrogeneDB 2014-2017