RetrogeneDB ID:

retro_hsap_3205

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:82120702..82121003(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000248105
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PPDPF
Ensembl ID:ENSG00000125534
Aliases:PPDPF, C20orf149, dJ697K14.9, exdpf
Description:pancreatic progenitor cell differentiation and proliferation factor homolog (zebrafish) [Source:HGNC Symbol;Acc:16142]


Retrocopy-Parental alignment summary:






>retro_hsap_3205
GCAGCCATCTCTTCCAGTGGCTCATTCCTACTCATGCATGACTATTACAAATGCTCCTAGGCTCCACTTCCACCAACGGC
TTCTGTGGAAGTGTTTAGTATTTGGGGATGCCATCCCCCTACCATCACCAGAGTCTCCCCACGGCTGGTCCTAATCACTG
GTGAGCAAGCTTCTTTTTGAGAAATGTATACTCCCATTCATGGCCACAGTATTGGAGTCCTCAGAGCACTCAGGATCTCC
TCAGGTTTCCAGCTGCATGTCCACCCATGACCTGTCTGGGGAAGCCTTGAGAAAGAGGCCT

ORF - retro_hsap_3205 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 55.34 %
Parental protein coverage: 87.72 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalAAIPSSGSLVATHDYYR-RRLGSTSSNSSCSSTECPGEAIP-HPPGLPKADPGHWWASFF-FGKSTLPFM
AAI.SSGS....HDYY....LGSTS.N..C.S....G...P.H...LP.A.P.HW.ASFF.F.K..LPFM
RetrocopyAAISSSGSFLLMHDYYK<MLLGSTSTNGFCGSV*YLGMPSPYHHQSLPTAGPNHW*ASFF<FEKCILPFM
ParentalATVLESAEHSEPPQASSSMTACGLARDAPRKQP
ATVLES.EHS..PQ.SS.M....L...A.RK.P
RetrocopyATVLESSEHSGSPQVSSCMSTHDLSGEALRKRP

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 33 .28 RPM
bodymap2_adrenal 0 .00 RPM 18 .93 RPM
bodymap2_brain 0 .00 RPM 6 .54 RPM
bodymap2_breast 0 .00 RPM 33 .15 RPM
bodymap2_colon 0 .00 RPM 47 .95 RPM
bodymap2_heart 0 .00 RPM 26 .47 RPM
bodymap2_kidney 0 .00 RPM 37 .89 RPM
bodymap2_liver 0 .00 RPM 10 .35 RPM
bodymap2_lung 0 .00 RPM 62 .20 RPM
bodymap2_lymph_node 0 .00 RPM 19 .92 RPM
bodymap2_ovary 0 .00 RPM 21 .86 RPM
bodymap2_prostate 0 .00 RPM 89 .63 RPM
bodymap2_skeletal_muscle 0 .00 RPM 41 .78 RPM
bodymap2_testis 0 .00 RPM 32 .58 RPM
bodymap2_thyroid 0 .00 RPM 25 .84 RPM
bodymap2_white_blood_cells 0 .00 RPM 27 .25 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3205 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3205 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3205 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3205 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3205 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2243
Macaca mulatta retro_mmul_2020
Parental genes homology:
Parental genes homology involve 16 parental genes, and 56 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000318007 retrocopies
retro_btau_1339, retro_btau_1538, retro_btau_1606, retro_btau_1817, retro_btau_1857, retro_btau_385, retro_btau_54,
Equus caballus ENSECAG000000094131 retrocopy
retro_ecab_477,
Felis catus ENSFCAG0000002438614 retrocopies
retro_fcat_1018, retro_fcat_1061, retro_fcat_128, retro_fcat_1293, retro_fcat_1581, retro_fcat_1669, retro_fcat_1685, retro_fcat_194, retro_fcat_308, retro_fcat_325, retro_fcat_355, retro_fcat_440, retro_fcat_711, retro_fcat_789,
Homo sapiens ENSG00000125534 1 retrocopy
retro_hsap_3205 ,
Latimeria chalumnae ENSLACG000000028351 retrocopy
retro_lcha_69,
Loxodonta africana ENSLAFG000000264962 retrocopies
retro_lafr_1082, retro_lafr_251,
Macaca mulatta ENSMMUG000000060642 retrocopies
retro_mmul_2020, retro_mmul_41,
Monodelphis domestica ENSMODG000000168712 retrocopies
retro_mdom_1325, retro_mdom_222,
Mustela putorius furoENSMPUG0000000830112 retrocopies
retro_mputfur_1039, retro_mputfur_1097, retro_mputfur_1247, retro_mputfur_1282, retro_mputfur_1312, retro_mputfur_1327, retro_mputfur_1355, retro_mputfur_347, retro_mputfur_526, retro_mputfur_665, retro_mputfur_788, retro_mputfur_928,
Mus musculus ENSMUSG000000163443 retrocopies
retro_mmus_1224, retro_mmus_658, retro_mmus_815,
Nomascus leucogenys ENSNLEG000000100683 retrocopies
retro_nleu_1154, retro_nleu_1270, retro_nleu_1339,
Otolemur garnettii ENSOGAG000000088102 retrocopies
retro_ogar_1797, retro_ogar_1912,
Pan troglodytes ENSPTRG000000137391 retrocopy
retro_ptro_2243,
Rattus norvegicus ENSRNOG000000127221 retrocopy
retro_rnor_752,
Sarcophilus harrisii ENSSHAG000000183383 retrocopies
retro_shar_637, retro_shar_640, retro_shar_733,
Ictidomys tridecemlineatus ENSSTOG000000078081 retrocopy
retro_itri_1363,

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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