RetrogeneDB ID:

retro_hsap_335

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:242121152..242122355(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000196289
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:BECN1
Ensembl ID:ENSG00000126581
Aliases:BECN1, ATG6, VPS30, beclin1
Description:beclin 1, autophagy related [Source:HGNC Symbol;Acc:1034]


Retrocopy-Parental alignment summary:






>retro_hsap_335
GCCCCGGCGCCCACCTCTGGGCAGGCTGAGCCCGGAGACACCCGGGAGCCCGGCGTCACCACCAGGGAGGTGACAGACGC
TGAGGAGCAACAGGACGGTGCCTCTAGCAGATCCCCTCCAGGCGATGGCAGTGTGTCCAAGGGCCATGCCAACATCTTCA
CCCTGCTGGGGGAGCTTGGCGCCATGCACATGCTCAGTAGCATCCAGAAGGCAGCTGGTGACATTTTTGACATAGTCTCT
GGCCAAGCAGTTGTGGACCATCCCCTGTGTGAAGAATGCACCGACAGTCTTTTAGAGCAGCTGGACATCCAGCTCGCTCT
CACAGAAGCTGACAGTCAGAACTACCAACGCTGCCTGGAGACCGGGGAGCTGGCGACCAGCGAGGACGAGGCGGCGGCGC
TGCGGGCGGAGCTGCGGGACCTGGAGCTGGAGGAGGCCAGGCTGGTGCAGGAGCTGGAGGATGTGGACAGGAACAATGCA
AGAGCAGCGGCGGATCTCCAGGCAGCCCAGGCAGAGGCTGCGGAGCTGGACCAGCAGGAGAGGCAGCACTACAGGGACTA
CAGTGCCTTGAAGCGGCAGCAGCTGGAACTGCTTGATCAGCTGGGGAACGTGGAGAACCAGCTGCAGTATGCCAGGGTCC
AGAGGGACCGGCTGAAGGAAATCAACTGTTTCACCGCCACGTTTGAGATCTGGGTGGAGGGCCCCTTGGGCGTCATCAAT
AACTTCAGGTTGGGCCGCCTCCCCACTGTCCGTGTGGGCTGGAATGAGATTAACACTGCCTGGGGACAGGCGGCCTTGCT
GCTCCTTACCCTGGCCAATACAATTGGACTGCAGTTTCAGAGGTATCGACTCATCCCCTGCGGAAACCATTCGTATCTGA
AGTCTTTAACAGATGACCGCACTGAGCTGCCGTTGTTCTGTTATGGGGGGCAGGATGTTTTCCTCAATAACAAGTATGAC
CGCGCGATGGTGGCCTTCCTGGACTGCATGCAGCAGTTCAAGGAAGAGGCTGAGAAGGGTGAGCTGGGCCTCTCTCTGCC
CTACGGGATCCAGGTGGAGACAGGCCTGATGGAGGACGTTGGCGGCCGAGGGGAATGCTATTCCATCAGAACCCATCTGA
ACACGCAGGAGCTGTGGACAAAGGCACTCAAGTTCATGCTTATAAATTTCAAGTGGAGTCTCATCTGGGTTGCCTCAAGG
TAT

ORF - retro_hsap_335 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.78 %
Parental protein coverage: 89.78 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAPLLTTAQAKPGETQEEETNSGEEPFIETPRQDGVSRRFIPPARMMSTESANSFTLIGEASDGGTMENLS
AP..T..QA.PG.T.E......E....E...QDG.S.R..P.....S...AN.FTL.GE....G.M..LS
RetrocopyAPAPTSGQAEPGDTREPGVTTREVTDAEE-QQDGASSRSPPGDGSVSKGHANIFTLLGEL---GAMHMLS
ParentalRRLKVTGDLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKRCLEILE-QMNEDDSEQLQM
...K..GD.FDI.SGQ..VDHPLCEECTD.LL.QLD.QL..TE...QNY.RCLE..E....ED....L..
RetrocopySIQKAAGDIFDIVSGQAVVDHPLCEECTDSLLEQLDIQLALTEADSQNYQRCLETGELATSEDEAAALRA
ParentalELKELALEEERLIQELEDVEKNRKIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQLELDDELKSVEN
EL..L.LEE.RL.QELEDV..N....A..L...QAEA..LDQ.E.Q..R.YS..KRQQLEL.D.L..VEN
RetrocopyELRDLELEEARLVQELEDVDRNNARAAADLQAAQAEAAELDQQERQHYRDYSALKRQQLELLDQLGNVEN
ParentalQMRYAQTQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEWNEINAAWGQTVLLLHALANKMG
Q..YA..Q.D.LK..N.F.ATF.IW..G..G.INNFRLGRLP.V.V.WNEIN.AWGQ..LLL..LAN..G
RetrocopyQLQYARVQRDRLKEINCFTATFEIWVEGPLGVINNFRLGRLPTVRVGWNEINTAWGQAALLLLTLANTIG
ParentalLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDHAMVAFLDCVQQFKEEVEKGETRFCL
L.FQRYRL.P.GNHSYL.SLTD...ELPL.C.GG...F..NK.D.AMVAFLDC.QQFKEE.EKGE....L
RetrocopyLQFQRYRLIPCGNHSYLKSLTDDRTELPLFCYGGQDVFLNNKYDRAMVAFLDCMQQFKEEAEKGELGLSL
ParentalPYRMDVEKGKIEDTGGSGGSYSIKTQFNSEEQWTKALKFMLTNLKWGLAWVSSQF
PY...VE.G..ED.GG.G..YSI.T..N..E.WTKALKFML.N.KW.L.WV.S..
RetrocopyPYGIQVETGLMEDVGGRGECYSIRTHLNTQELWTKALKFMLINFKWSLIWVASRY

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 49 .56 RPM
bodymap2_adrenal 0 .00 RPM 54 .96 RPM
bodymap2_brain 0 .00 RPM 39 .24 RPM
bodymap2_breast 0 .00 RPM 35 .84 RPM
bodymap2_colon 0 .00 RPM 40 .06 RPM
bodymap2_heart 0 .00 RPM 33 .49 RPM
bodymap2_kidney 0 .00 RPM 37 .82 RPM
bodymap2_liver 0 .00 RPM 17 .96 RPM
bodymap2_lung 0 .00 RPM 27 .04 RPM
bodymap2_lymph_node 0 .00 RPM 35 .82 RPM
bodymap2_ovary 0 .00 RPM 37 .74 RPM
bodymap2_prostate 0 .00 RPM 42 .87 RPM
bodymap2_skeletal_muscle 0 .00 RPM 51 .98 RPM
bodymap2_testis 0 .11 RPM 32 .77 RPM
bodymap2_thyroid 0 .00 RPM 48 .10 RPM
bodymap2_white_blood_cells 0 .00 RPM 58 .49 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_335 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_335 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_335 retrocopy 5' end.

Lab - click to see more details

retro_hsap_335 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_335 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 17 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000068671 retrocopy
retro_amel_16,
Bos taurus ENSBTAG000000199141 retrocopy
retro_btau_226,
Dipodomys ordii ENSDORG000000009561 retrocopy
retro_dord_675,
Felis catus ENSFCAG000000131361 retrocopy
retro_fcat_62,
Homo sapiens ENSG00000126581 1 retrocopy
retro_hsap_335 ,
Macropus eugenii ENSMEUG000000117001 retrocopy
retro_meug_600,
Macaca mulatta ENSMMUG000000299711 retrocopy
retro_mmul_81,
Monodelphis domestica ENSMODG000000150641 retrocopy
retro_mdom_1778,
Mus musculus ENSMUSG000000350861 retrocopy
retro_mmus_390,
Nomascus leucogenys ENSNLEG000000118401 retrocopy
retro_nleu_1776,
Oryctolagus cuniculus ENSOCUG000000159643 retrocopies
retro_ocun_1021, retro_ocun_1732, retro_ocun_218,
Procavia capensis ENSPCAG000000140491 retrocopy
retro_pcap_345,
Pan troglodytes ENSPTRG000000228191 retrocopy
retro_ptro_268,
Sorex araneus ENSSARG000000003671 retrocopy
retro_sara_136,
Sus scrofa ENSSSCG000000173861 retrocopy
retro_sscr_75,
Ictidomys tridecemlineatus ENSSTOG000000126121 retrocopy
retro_itri_25,
Tursiops truncatus ENSTTRG000000117161 retrocopy
retro_ttru_595,

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 .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 .04 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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