RetrogeneDB ID:

retro_hsap_357

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:26845847..26846741(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000224129
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DPPA2
Ensembl ID:ENSG00000163530
Aliases:DPPA2, CT100, ECAT15-2, PESCRG1
Description:developmental pluripotency associated 2 [Source:HGNC Symbol;Acc:19197]


Retrocopy-Parental alignment summary:






>retro_hsap_357
ATGTCAGACTCAAATTTGGATAGCAGCAAGAAGAATTTCTTTGAGGGGGAAGTAGCTGATGAGGAAAGTGTGATTTTGAC
ATTGCTGCCAGTTAAAGATGACCCAAATATGGAACAAACAGAACCAAGTGTTTCTTCAACTTCTGATGTCAAACTGGAGA
AACCTATGAAATACAATCAAGGTCATCTACTTCAAACAAATTAACAATTTACAGCTCCACAAAAAGCTAGATGCAAAATA
CCAGCTCTTCCCTTGCCGACCATTTTGCCTCCCATTAATAAGGTGTGTTGGGACACTTTGCGGGACTGGTGCCAACAACT
CAGTTTGAGTACTAATGGCAAGAAAATCGAAGTTTATCTGAGGGTCCATAGGCCTGCTTACCCTGAACAACAGCAAGATA
TGCCTGAAATGTCACAAGAGACCAGATTACAGCGGTGTTCAAGGAAACACAAGGCAGTGACCAAGAGAGCAAGGCTTCAG
AAAACTTATGAGATGAATGAGAGAGCAGAAGAGACGAATACAGTCGAAGTGATAACTTCAGCGCAGGGAGCCATGTTGGC
ATCAAGGGCAAGAATTGCTGCAAGAGCTGTTGAGCCTGAGGCTGTGAATTCAAGTTCCATTCCTGTTTCTCTTGAGGCCT
TTTTGATGCAAGCCGCTGGTGTCAGGTGGTGTGTGGTCCATGGCAGACTTCTCTCGGCAGACACAAAGGGTTGAGTACGC
CTGCAGTTTCATGCAGGTCAGGCTTGAGTGCCTACCACTCACAGGAGGATGATTTCTCTCTTCTTGTTACCTGCCTGCAT
TTTCCCATCCCCAGGCACAGAAGATAATATGTTATGCCCCAACTGTGCTAAGAAGAATAAGAAGATGATGAAAAGATTAA
TGACAATAGAGAAG

ORF - retro_hsap_357 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.6 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSDANLDSSKKNFLEGEVDDEESVILTLVPVKDDANMEQMEPSVSSTSDVKLEKPKKYNPGHLLQTNEQF
MSD.NLDSSKKNF.EGEV.DEESVILTL.PVKDD.NMEQ.EPSVSSTSDVKLEKP.KYN.GHLLQTN.QF
RetrocopyMSDSNLDSSKKNFFEGEVADEESVILTLLPVKDDPNMEQTEPSVSSTSDVKLEKPMKYNQGHLLQTN*QF
ParentalTAPQKARCKIPALPLPTILPPINKVCRDTLRDWCQQLGLSTNGKKIEVYLRLHRHAYPEQRQDMPEMSQE
TAPQKARCKIPALPLPTILPPINKVC.DTLRDWCQQL.LSTNGKKIEVYLR.HR.AYPEQ.QDMPEMSQE
RetrocopyTAPQKARCKIPALPLPTILPPINKVCWDTLRDWCQQLSLSTNGKKIEVYLRVHRPAYPEQQQDMPEMSQE
ParentalTRLQRCSRKRKAVTKRARLQRSYEMNERAEETNTVEVITSAPGAMLASWARIAARAVQPKALNSCSIPVS
TRLQRCSRK.KAVTKRARLQ..YEMNERAEETNTVEVITSA.GAMLAS.ARIAARAV.P.A.NS.SIPVS
RetrocopyTRLQRCSRKHKAVTKRARLQKTYEMNERAEETNTVEVITSAQGAMLASRARIAARAVEPEAVNSSSIPVS
ParentalVEAFLMQASGVRWCVVHGRLLSADTKGWVRLQFHAGQAWVPTTHRRMISLFLLPACIFPSPGIEDNMLCP
.EAFLMQA.GVRWCVVHGRLLSADTKG.VRLQFHAGQA.VPTTHRRMISLFLLPACIFPSPG.EDNMLCP
RetrocopyLEAFLMQAAGVRWCVVHGRLLSADTKG*VRLQFHAGQA*VPTTHRRMISLFLLPACIFPSPGTEDNMLCP
ParentalDCAKRNKKMMKRLMTVEK
.CAK.NKKMMKRLMT.EK
RetrocopyNCAKKNKKMMKRLMTIEK

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 0 .00 RPM
bodymap2_adrenal 0 .00 RPM 0 .00 RPM
bodymap2_brain 0 .00 RPM 0 .00 RPM
bodymap2_breast 0 .00 RPM 0 .00 RPM
bodymap2_colon 0 .00 RPM 0 .00 RPM
bodymap2_heart 0 .00 RPM 0 .00 RPM
bodymap2_kidney 0 .00 RPM 0 .06 RPM
bodymap2_liver 0 .00 RPM 0 .00 RPM
bodymap2_lung 0 .00 RPM 0 .00 RPM
bodymap2_lymph_node 0 .00 RPM 0 .00 RPM
bodymap2_ovary 0 .00 RPM 0 .00 RPM
bodymap2_prostate 0 .00 RPM 0 .00 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .00 RPM 11 .31 RPM
bodymap2_thyroid 0 .00 RPM 0 .00 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_357 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_357 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_357 retrocopy 5' end.

Lab - click to see more details

retro_hsap_357 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_357 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_281
Pongo abelii retro_pabe_346
Macaca mulatta retro_mmul_475
Parental genes homology:
Parental genes homology involve 21 parental genes, and 64 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000204602 retrocopies
retro_btau_435, retro_btau_529,
Callithrix jacchus ENSCJAG000000201684 retrocopies
retro_cjac_1378, retro_cjac_1991, retro_cjac_3832, retro_cjac_944,
Dasypus novemcinctus ENSDNOG000000107456 retrocopies
retro_dnov_1248, retro_dnov_1626, retro_dnov_1714, retro_dnov_2462, retro_dnov_2583, retro_dnov_2656,
Erinaceus europaeus ENSEEUG000000089444 retrocopies
retro_eeur_205, retro_eeur_415, retro_eeur_426, retro_eeur_616,
Echinops telfairi ENSETEG000000079854 retrocopies
retro_etel_2051, retro_etel_2058, retro_etel_506, retro_etel_918,
Homo sapiens ENSG000001215701 retrocopy
retro_hsap_893,
Homo sapiens ENSG00000163530 3 retrocopies
retro_hsap_1642, retro_hsap_2903, retro_hsap_357 ,
Microcebus murinus ENSMICG000000137446 retrocopies
retro_mmur_1171, retro_mmur_156, retro_mmur_1634, retro_mmur_213, retro_mmur_598, retro_mmur_955,
Myotis lucifugus ENSMLUG000000074441 retrocopy
retro_mluc_1706,
Macaca mulatta ENSMMUG000000221123 retrocopies
retro_mmul_1550, retro_mmul_342, retro_mmul_475,
Monodelphis domestica ENSMODG000000180833 retrocopies
retro_mdom_1057, retro_mdom_1478, retro_mdom_999,
Mus musculus ENSMUSG000000724197 retrocopies
retro_mmus_1303, retro_mmus_1832, retro_mmus_1847, retro_mmus_2391, retro_mmus_2935, retro_mmus_3699, retro_mmus_394,
Nomascus leucogenys ENSNLEG000000040202 retrocopies
retro_nleu_1329, retro_nleu_633,
Oryctolagus cuniculus ENSOCUG000000031751 retrocopy
retro_ocun_61,
Otolemur garnettii ENSOGAG000000312287 retrocopies
retro_ogar_1678, retro_ogar_1722, retro_ogar_1953, retro_ogar_2404, retro_ogar_2567, retro_ogar_2900, retro_ogar_586,
Ochotona princeps ENSOPRG000000050591 retrocopy
retro_opri_433,
Pongo abelii ENSPPYG000000135663 retrocopies
retro_pabe_1360, retro_pabe_2401, retro_pabe_346,
Pan troglodytes ENSPTRG000000151993 retrocopies
retro_ptro_1113, retro_ptro_1962, retro_ptro_281,
Sarcophilus harrisii ENSSHAG000000173981 retrocopy
retro_shar_542,
Tupaia belangeri ENSTBEG000000062121 retrocopy
retro_tbel_3864,
Tursiops truncatus ENSTTRG000000095001 retrocopy
retro_ttru_1524,

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 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 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 .02 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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