RetrogeneDB ID:

retro_hsap_4305

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:116613022..116613866(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000232905
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PDCD2
Ensembl ID:ENSG00000071994
Aliases:PDCD2, RP8, ZMYND7
Description:programmed cell death 2 [Source:HGNC Symbol;Acc:8762]


Retrocopy-Parental alignment summary:






>retro_hsap_4305
GGGACCCGGACCCTGGCCTGCGCGCTGTGCGGCTGCCAGCTCTCCTTCCTGCTACAGGTGTACGCGCTGCTGCCCCGCCG
CGCCGACGCCTTCCACCCCGGAATCTTCCTCTTCTGCTGCTGAGAGCCGCCGTGCTGTGCCGGCCTGCGAGTTTTTACCA
ATCAGCTACCCAGGAAAAATGATTTTTCCTCATATAGGCCACCTTCTGAGAATCCTCTCCCAGAAACAGGACAATCAGTG
TGTCTCTAACTTGAGTCTGGTGCTCATCTCTGCAGAGTTTGTGGTTGTTTAGGACCCAAAACGTGCTCCAGATGCCACAA
AGCGTATTACTGCAGCAAGGAGCATCAAGACCCTAGACCGGAGATTGGCACATAAGCAGGCTTGTACAGAACCAGATCAT
TTGGACCATATAATTCCAGACCACGACTTCCTTTTTCCAGAATTTGCAGTTGTAGTAGAAACAGAAGATGAAGATTACAC
CTGAGGTTGTGGAAAAGGAAGATTACTCAGAGATTATAGGGAGCATGGGTGAGGCACTTGAAGAAGAACTGGATTCCATG
GCAAAACATGAATCCAGGGAAGATAAAATTTTTCAGAAGTTCAAAACTCAGATAGCCCTTGAACCAGAACAGATTCTCAG
ATATGGCAGAGGTATTGCCCCCACCTGGATTCTAGTGAAAATATTCCTCAAGAAAAGGATATTCCAGAGAATATCCTTTG
TGATGCCAAGAAAATGTTTGAATTCCAGGTTATGCCTCAGCTCCTAAACTACCTGAAGGCTGACAGACTGAGCGAGAGCA
TTGACTGGGGCATCCTGGCTGTCTTCACCTGGGCTGAGAGCTGC

ORF - retro_hsap_4305 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.15 %
Parental protein coverage: 81.4 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalGPQALACELCGRPLSFLLQVYAPLPGRPDAFHRCIFLFCCREQPCCAGLRVFRNQLPRKNDFYSYEPPSE
G...LAC.LCG..LSFLLQVYA.LP.R.DAFH..IFLFCC.E.PCCAGLRVF.NQLPRKNDF.SY.PPSE
RetrocopyGTRTLACALCGCQLSFLLQVYALLPRRADAFHPGIFLFCC*EPPCCAGLRVFTNQLPRKNDFSSYRPPSE
ParentalNPPPETGESVCLQLKSGAHLCRVCGCLGPKTCSRCHKAYYCSKEHQ-TLDWRLGHKQACAQPDHLDHIIP
NP.PETG.SVCL.L.SGAHLCRVCGCLGPKTCSRCHKAYYCSKEHQ.TLD.RL.HKQAC..PDHLDHIIP
RetrocopyNPLPETGQSVCL*LESGAHLCRVCGCLGPKTCSRCHKAYYCSKEHQ>TLDRRLAHKQACTEPDHLDHIIP
ParentalDHNFLFPEFEIVIETEDE-IMPEVVEKEDYSEIIGSMGEALEEELDSMAKHESREDKIFQKFKTQIALEP
DH.FLFPEF..V.ETEDE.I.PEVVEKEDYSEIIGSMGEALEEELDSMAKHESREDKIFQKFKTQIALEP
RetrocopyDHDFLFPEFAVVVETEDE>ITPEVVEKEDYSEIIGSMGEALEEELDSMAKHESREDKIFQKFKTQIALEP
ParentalEQILRYGRGIAPIWI-SGENIPQEKDIPD-CPCGAKRILEFQVMPQLLNYLKADRLGKSIDWGILAVFTC
EQILRYGRGIAP.WI.S.ENIPQEKDIP....C.AK...EFQVMPQLLNYLKADRL..SIDWGILAVFT.
RetrocopyEQILRYGRGIAPTWI<SSENIPQEKDIPENILCDAKKMFEFQVMPQLLNYLKADRLSESIDWGILAVFTW
ParentalAESC
AESC
RetrocopyAESC

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 32 .40 RPM
bodymap2_adrenal 0 .00 RPM 61 .27 RPM
bodymap2_brain 0 .00 RPM 25 .08 RPM
bodymap2_breast 0 .00 RPM 38 .37 RPM
bodymap2_colon 0 .00 RPM 39 .85 RPM
bodymap2_heart 0 .00 RPM 23 .57 RPM
bodymap2_kidney 0 .00 RPM 50 .60 RPM
bodymap2_liver 0 .00 RPM 27 .48 RPM
bodymap2_lung 0 .00 RPM 24 .67 RPM
bodymap2_lymph_node 0 .00 RPM 51 .53 RPM
bodymap2_ovary 0 .00 RPM 58 .39 RPM
bodymap2_prostate 0 .00 RPM 40 .77 RPM
bodymap2_skeletal_muscle 0 .00 RPM 26 .95 RPM
bodymap2_testis 0 .00 RPM 50 .64 RPM
bodymap2_thyroid 0 .00 RPM 56 .59 RPM
bodymap2_white_blood_cells 0 .00 RPM 57 .49 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4305 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4305 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4305 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4305 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4305 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2876
Pongo abelii retro_pabe_3505
Parental genes homology:
Parental genes homology involve 15 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000170752 retrocopies
retro_amel_1329, retro_amel_1404,
Callithrix jacchus ENSCJAG000000206341 retrocopy
retro_cjac_3946,
Equus caballus ENSECAG000000168191 retrocopy
retro_ecab_533,
Felis catus ENSFCAG000000070372 retrocopies
retro_fcat_305, retro_fcat_749,
Homo sapiens ENSG00000071994 1 retrocopy
retro_hsap_4305 ,
Gorilla gorilla ENSGGOG000000282292 retrocopies
retro_ggor_2876, retro_ggor_899,
Microcebus murinus ENSMICG000000074741 retrocopy
retro_mmur_108,
Macaca mulatta ENSMMUG000000199161 retrocopy
retro_mmul_1137,
Mustela putorius furoENSMPUG000000072272 retrocopies
retro_mputfur_621, retro_mputfur_707,
Nomascus leucogenys ENSNLEG000000002952 retrocopies
retro_nleu_1458, retro_nleu_2633,
Otolemur garnettii ENSOGAG000000140022 retrocopies
retro_ogar_2090, retro_ogar_2288,
Pongo abelii ENSPPYG000000171932 retrocopies
retro_pabe_3505, retro_pabe_958,
Pan troglodytes ENSPTRG000000188282 retrocopies
retro_ptro_2915, retro_ptro_788,
Pteropus vampyrus ENSPVAG000000108221 retrocopy
retro_pvam_1150,
Sus scrofa ENSSSCG000000253122 retrocopies
retro_sscr_303, retro_sscr_450,

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 = 0.04 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 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 .02 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 .03 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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