RetrogeneDB ID:

retro_hsap_3646

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:112937907..112939082(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000225580
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PA2G4
Ensembl ID:ENSG00000170515
Aliases:PA2G4, EBP1, HG4-1, p38-2G4
Description:proliferation-associated 2G4, 38kDa [Source:HGNC Symbol;Acc:8550]


Retrocopy-Parental alignment summary:






>retro_hsap_3646
ATGTAGGGTGAGGACGAGCAGCAGAAGCAAACTATCGCTGAAGACCTGGTTGTGACCAAGTATAAGATGGGGGGCGACAT
TGCCCACCGGGTACTTAGGTCCTTGGTGGAAGCATCTAGCTCAGGTGTATTGGTACTGAGCCTGTGTGAGAAAAGTGATG
CCGTGATTATGGAAGAAACAGGGAAAATCTTCAAGAAAGAAAAGGAAATGAAGAAAGGCATTGCTTTTCCCACCAGTATT
TCAGTAAATAACTGTGTATGTCACTTCTCCCCTTTGGAGAGTGGCCAGGATTATATTCTCAAGGAAGGTGACTTGGTAAA
AATTGACCTTGGGGTCTATGTGGATGGCTTCATCGCTAATGTAGCTCATACTTTTGTGGTTGATGTGGCTCAGGGGACCC
AAGTAACAGGGAGGAAAGCAGATGTTATTAAGGCAGCTCACCTTTGTGCTGAAGCTGCCCTACGCCTGGTCAAACCTGGA
AATCAGAACACACAAGTGACAGAAGCCTGGAACAAAGTTGCCCAGTAATTTAACTACAAGCCAATAGAAGGTATGCTGTC
ACACCAGTTGAAGCAGCATGTCATCGATGGAGAAAAAACCGTTATCCAGAATCCCACAGACCAGCAGAAGAAGGACCACG
AAAAAGATGAATTTGAGGTATATGAAGTATACGCTGTGGATGTTCTCATCAGCTCAGGAGAGGGCAAGGCCAAGGATGCA
GGACAGAGAACCCCTATTTACAAATGAGACACTCCTGAAGAGTATGGACTGAAAATGAAAACTTCACGTGCCTTCTTCAG
TGGATGGAAAGGCGTTTTGATGTCATGCTGTTTACTTTAAGAGCATTTGAAGATGAGAAGAAGGCTCGGATAGGTGTGGT
GGAGTGTGCCAAACATGAACTGCTGCAACCATTTAATGTTCTCCATGAGAAGGAGAGTGAATTTTTTGCCCAGTTTAAAT
TTACAGTTCTGCTCATGCCCAGTGGCCCCATGCGGATAACCAGTAGTCCCCTCAAGCCTGACCTCTACAAGTCTGAGATG
GAGGTCCAGGATGCAGAGCTAAAGGCCCTGCTCGAGTTCTGCAAGTCGAAAAACCCAGAAAAAAAAAAGAAGGCCTCCAA
GACTGCAGAAAATGCCACCAGTGGGGAAATATTAGAAGAAAATGAAGCTGGGGAC

ORF - retro_hsap_3646 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.34 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSGEDEQQEQTIAEDLVVTKYKMGGDIANRVLRSLVEASSSGVSVLSLCEKGDAMIMEETGKIFKKEKEM
M.GEDEQQ.QTIAEDLVVTKYKMGGDIA.RVLRSLVEASSSGV.VLSLCEK.DA.IMEETGKIFKKEKEM
RetrocopyM*GEDEQQKQTIAEDLVVTKYKMGGDIAHRVLRSLVEASSSGVLVLSLCEKSDAVIMEETGKIFKKEKEM
ParentalKKGIAFPTSISVNNCVCHFSPLKSDQDYILKEGDLVKIDLGVHVDGFIANVAHTFVVDVAQGTQVTGRKA
KKGIAFPTSISVNNCVCHFSPL.S.QDYILKEGDLVKIDLGV.VDGFIANVAHTFVVDVAQGTQVTGRKA
RetrocopyKKGIAFPTSISVNNCVCHFSPLESGQDYILKEGDLVKIDLGVYVDGFIANVAHTFVVDVAQGTQVTGRKA
ParentalDVIKAAHLCAEAALRLVKPGNQNTQVTEAWNKVAHSFNCTPIEGMLSHQLKQHVIDGEKTIIQNPTDQQK
DVIKAAHLCAEAALRLVKPGNQNTQVTEAWNKVA..FN..PIEGMLSHQLKQHVIDGEKT.IQNPTDQQK
RetrocopyDVIKAAHLCAEAALRLVKPGNQNTQVTEAWNKVAQ*FNYKPIEGMLSHQLKQHVIDGEKTVIQNPTDQQK
ParentalKDHEKAEFEVHEVYAVDVLVSSGEGKAKDAGQRTTIYKRDPSKQYGLKMKTSRAFFSE-VERRFDAMPFT
KDHEK.EFEV.EVYAVDVL.SSGEGKAKDAGQRT.IYK.D....YGLKMKTSRAFFS...ERRFD.M.FT
RetrocopyKDHEKDEFEVYEVYAVDVLISSGEGKAKDAGQRTPIYK*DTPEEYGLKMKTSRAFFSG<MERRFDVMLFT
ParentalLRAFEDEKKARMGVVECAKHELLQPFNVLYEKEGEFVAQFKFTVLLMPNGPMRITSGPFEPDLYKSEMEV
LRAFEDEKKAR.GVVECAKHELLQPFNVL.EKE.EF.AQFKFTVLLMP.GPMRITS.P..PDLYKSEMEV
RetrocopyLRAFEDEKKARIGVVECAKHELLQPFNVLHEKESEFFAQFKFTVLLMPSGPMRITSSPLKPDLYKSEMEV
ParentalQDAELKALLQSSASRKTQKKKKKKASKTAENATSGETLEENEAGD
QDAELKALL....S.........KASKTAENATSGE.LEENEAGD
RetrocopyQDAELKALLEFCKSK--NPXXXXKASKTAENATSGEILEENEAGD

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 .02 RPM 102 .89 RPM
bodymap2_adrenal 0 .02 RPM 101 .45 RPM
bodymap2_brain 0 .00 RPM 71 .63 RPM
bodymap2_breast 0 .02 RPM 69 .57 RPM
bodymap2_colon 0 .02 RPM 128 .02 RPM
bodymap2_heart 0 .00 RPM 41 .59 RPM
bodymap2_kidney 0 .00 RPM 64 .89 RPM
bodymap2_liver 0 .00 RPM 50 .34 RPM
bodymap2_lung 0 .09 RPM 93 .58 RPM
bodymap2_lymph_node 0 .00 RPM 72 .80 RPM
bodymap2_ovary 0 .02 RPM 115 .14 RPM
bodymap2_prostate 0 .07 RPM 106 .95 RPM
bodymap2_skeletal_muscle 0 .02 RPM 129 .57 RPM
bodymap2_testis 0 .00 RPM 110 .08 RPM
bodymap2_thyroid 0 .04 RPM 95 .53 RPM
bodymap2_white_blood_cells 0 .00 RPM 78 .59 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3646 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3646 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3646 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3646 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3646 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_2993
Parental genes homology:
Parental genes homology involve 13 parental genes, and 38 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000071812 retrocopies
retro_chof_1089, retro_chof_1847,
Callithrix jacchus ENSCJAG000000118112 retrocopies
retro_cjac_4214, retro_cjac_4215,
Homo sapiens ENSG00000170515 6 retrocopies
retro_hsap_1930, retro_hsap_2413, retro_hsap_2868, retro_hsap_3646 , retro_hsap_4191, retro_hsap_4895,
Macaca mulatta ENSMMUG000000021642 retrocopies
retro_mmul_1168, retro_mmul_2631,
Mus musculus ENSMUSG000000253641 retrocopy
retro_mmus_2803,
Nomascus leucogenys ENSNLEG000000175446 retrocopies
retro_nleu_1212, retro_nleu_1260, retro_nleu_163, retro_nleu_3024, retro_nleu_506, retro_nleu_612,
Oryctolagus cuniculus ENSOCUG000000173421 retrocopy
retro_ocun_1733,
Pongo abelii ENSPPYG000000258517 retrocopies
retro_pabe_1595, retro_pabe_1778, retro_pabe_2375, retro_pabe_2869, retro_pabe_2993, retro_pabe_3430, retro_pabe_3807,
Pan troglodytes ENSPTRG000000050766 retrocopies
retro_ptro_1289, retro_ptro_1389, retro_ptro_1940, retro_ptro_2471, retro_ptro_2846, retro_ptro_3263,
Sus scrofa ENSSSCG000000003771 retrocopy
retro_sscr_338,
Sus scrofa ENSSSCG000000226662 retrocopies
retro_sscr_1143, retro_sscr_337,
Tarsius syrichta ENSTSYG000000067771 retrocopy
retro_tsyr_746,
Vicugna pacos ENSVPAG000000095231 retrocopy
retro_vpac_2,

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 = 0.34 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .06 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .18 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .11 RPM
CEU_NA12873 0 .10 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .08 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .12 RPM
FIN_HG00338 0 .09 RPM
FIN_HG00349 0 .34 RPM
FIN_HG00375 0 .07 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .15 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .07 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .09 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .13 RPM
TSI_NA20512 0 .06 RPM
TSI_NA20513 0 .12 RPM
TSI_NA20518 0 .19 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .08 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .24 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .11 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .08 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .02 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).





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