RetrogeneDB ID:

retro_hsap_2128

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:98822632..98824129(+)
Located in intron of:ENSG00000168658
Retrocopy
information
Ensembl ID:ENSG00000231635
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ATP5B
Ensembl ID:ENSG00000110955
Aliases:ATP5B, ATPMB, ATPSB, HEL-S-271
Description:ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide [Source:HGNC Symbol;Acc:830]


Retrocopy-Parental alignment summary:






>retro_hsap_2128
ATGTCTGCTGCCTCAGCCTCCAGGGCCTTGCAGGAACTCAGCCCGTCAGTGTTGCTACTCCAAGCTCAGGTCTTGCCATG
GGCCACTCTGGCAGCAATCCAATCTACCAGGAAATATGGGCACAAACATCACCTTTGCTGAAGACAGGCACCACCACTGG
GTGTATTGTGGTGGTCATTGATGCAGTAGTGGATATCCAGTTTGATGAGGGACTACCATCTATTTTAAATGCCCAGCAAG
TACAAGGCAGGGAGACCAGGCTGGTTTTTGTGGTGACCCAGCATTTGGGTGAGAGCACAGTAAGGATTATGCTATGAATG
GTACAGAAGGCTTGTTTAGAGGCCAGAAAGTCCTGGATTCTGGTGCACCAATCGAAAGTCCTGTTGGTCCTGAGACTTTG
AGCAGAATCATGAACATCATTGGAGAGCCTATTGATGAAAGCGGTCCCATCAAAATGAAACAGTTTGCTCCCATTTATGT
TGAGGCTCCTGAGTTCATGGAAATTAGCGTTGAGCAAGAAATTCTGGTGGCTAGTATCAAAGTTGTGGATTTCCTCACTC
CCTAGCCAAGAGTGGCAAAATTGGGCTTTTTAGTGGTGTTGGAGTTGACAAGATTGTACCCATCATGGAGTTAATCAATA
ATGTTGCCAAAGCCCATGGTGCTTAATCTGGGTTTGCTGGTGTTTTTGAGAGGACCTGTAAGGGCAATGACTTATATTAT
GAAATGACTGAGTCTGGTGTTGTCAACTTAAAAAATGTTACCTCCAAGGTAATGCTGATGTAAGGTCAGATGAATGAACC
ACATGCTACTCATGCCCAGGTAGCTCTGACTGGACTGACTGTGGCTGAATACTTCAGAGACCAAGAAGTTCAAGATGTAC
TCCTGTTTATTGATAATATCTTTCACTTCACCCATGCTGGCTCAAGGGTGTCTGCCTTATTGGGCAGAATCCCTTCTGCT
GTGGGCTATCAGCCTACCCTGGCCACTGACATGGTGGGTATGATGTGGGGAAAGAATTGCCACTACCAAGAGGAGATCTA
TCACCTCTGTACAGGCTATGTACCTGCTGATGACTCGACTGCCTCTGCTACTTCCTTTGCTCATTTGGATGCCACCACTG
TGCTGCCCCATGCTGTCACTGAGCTGGGCATCTATCTACATGTGGATCCTCTGGACTCCATCTCTCACATCATGGATCCC
AACATTGTTGGCAATGAGCATAATGATGTTGCCCGTGGGGTGCAAAAGATTCTGCATGGCTACAAATCCCTCCATACGTT
ATTGTCATAATCCATATTGGGTATGGATTAACTTTCTGAGGAAGACAAGTTGACTGTGTCTTGAATGTGGATAATACAAC
GTTTCTTGTCTCAGCCATTCCAGGCTGCTGAGGTCATCACAGGTCATATGGGGAAGTCAGTACTCCTGAAGGAGACCATT
AAAGGATTTCAGCAGATTTTGATAGGTGAACATGACCATCTCTCAGAACGGGCCTTC

ORF - retro_hsap_2128 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.49 %
Parental protein coverage: 94.52 %
Number of stop codons detected: 5
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalVAAAPASGALRRLTPSASLPPAQLLLRAAPTAVHPVRDYA-AQTSPSPKAGAATGRIVAVIGAVVDVQFD
..AA.AS.AL..L.PS..L..AQ.L..A...A....R.Y..AQTSP..K.G..TG.IV.VI.AVVD.QFD
RetrocopyMSAASASRALQELSPSVLLLQAQVLPWATLAAIQSTRKYG<AQTSPLLKTGTTTGCIVVVIDAVVDIQFD
ParentalEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTI-AMDGTEGLVRGQKVLDSGAPIKIPVGPETLGRIM
EGLP.ILNA..VQGRETRLV..V.QHLGESTVR...AM.GTEGL.RGQKVLDSGAPI..PVGPETL.RIM
RetrocopyEGLPSILNAQQVQGRETRLVFVVTQHLGESTVRIM<AMNGTEGLFRGQKVLDSGAPIESPVGPETLSRIM
ParentalNVIGEPIDERGPIKTKQFAPIHAEAPEFMEMSVEQEILVTGIKVVDLLAP-YAKGGKIGLFGGAGVGKTV
N.IGEPIDE.GPIK.KQFAPI..EAPEFME.SVEQEILV..IKVVD.L.P..AK.GKIGLF.G.GV.K.V
RetrocopyNIIGEPIDESGPIKMKQFAPIYVEAPEFMEISVEQEILVASIKVVDFLTP<LAKSGKIGLFSGVGVDKIV
ParentalLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVAL
.IMELINNVAKAHG..S.FAGV.ERT..GNDLY.EM.ESGV.NLK..TSKV.L..GQMNEP....A.VAL
RetrocopyPIMELINNVAKAHGA*SGFAGVFERTCKGNDLYYEMTESGVVNLKNVTSKVMLM*GQMNEPHATHAQVAL
ParentalTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTKKGSI
TGLTVAEYFRDQE.QDVLLFIDNIF.FT.AGS.VSALLGRIPSAVGYQPTLATDM..M...........I
RetrocopyTGLTVAEYFRDQEVQDVLLFIDNIFHFTHAGSRVSALLGRIPSAVGYQPTLATDMVGMMWGKNCHYQEEI
ParentalTSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIVGSEHYDVARGV
......YVPADD.T..A.AT.FAHLDATTVL..A..ELGIY..VDPLDS.S.IMDPNIVG.EH.DVARGV
RetrocopyYHLCTGYVPADDST--ASATSFAHLDATTVLPHAVTELGIYLHVDPLDSISHIMDPNIVGNEHNDVARGV
ParentalQKILQDYKSLQDIIA--ILGMDELSEEDKLTVSRARKIQRFLSQPFQVAEVFTGHMGKLVPLKETIKGFQ
QKIL..YKSL.......ILGMD.LSEEDKLTVS....IQRFLSQPFQ.AEV.TGHMGK.V.LKETIKGFQ
RetrocopyQKILHGYKSLHTLLS*SILGMD*LSEEDKLTVS*MWIIQRFLSQPFQAAEVITGHMGKSVLLKETIKGFQ
ParentalQILAGEYDHLPEQAF
QIL.GE.DHL.E.AF
RetrocopyQILIGEHDHLSERAF

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 282 .74 RPM
bodymap2_adrenal 0 .00 RPM 302 .89 RPM
bodymap2_brain 0 .00 RPM 491 .42 RPM
bodymap2_breast 0 .02 RPM 427 .40 RPM
bodymap2_colon 0 .00 RPM 386 .49 RPM
bodymap2_heart 0 .00 RPM 1719 .87 RPM
bodymap2_kidney 0 .00 RPM 919 .08 RPM
bodymap2_liver 0 .00 RPM 369 .62 RPM
bodymap2_lung 0 .00 RPM 298 .52 RPM
bodymap2_lymph_node 0 .00 RPM 268 .64 RPM
bodymap2_ovary 0 .00 RPM 260 .12 RPM
bodymap2_prostate 0 .00 RPM 427 .51 RPM
bodymap2_skeletal_muscle 0 .00 RPM 571 .44 RPM
bodymap2_testis 0 .00 RPM 330 .36 RPM
bodymap2_thyroid 0 .00 RPM 517 .46 RPM
bodymap2_white_blood_cells 0 .00 RPM 396 .14 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2128 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2128 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2128 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2128 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2128 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1557
Gorilla gorilla retro_ggor_1648
Pongo abelii retro_pabe_1921
Parental genes homology:
Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000167521 retrocopy
retro_acar_181,
Bos taurus ENSBTAG000000133151 retrocopy
retro_btau_1264,
Choloepus hoffmanni ENSCHOG000000053501 retrocopy
retro_chof_1544,
Callithrix jacchus ENSCJAG000000335712 retrocopies
retro_cjac_1488, retro_cjac_928,
Dasypus novemcinctus ENSDNOG000000112891 retrocopy
retro_dnov_361,
Echinops telfairi ENSETEG000000102081 retrocopy
retro_etel_2162,
Homo sapiens ENSG00000110955 1 retrocopy
retro_hsap_2128 ,
Gorilla gorilla ENSGGOG000000115961 retrocopy
retro_ggor_1648,
Macropus eugenii ENSMEUG000000028756 retrocopies
retro_meug_1416, retro_meug_1608, retro_meug_411, retro_meug_430, retro_meug_685, retro_meug_908,
Microcebus murinus ENSMICG000000010841 retrocopy
retro_mmur_495,
Macaca mulatta ENSMMUG000000010271 retrocopy
retro_mmul_103,
Pongo abelii ENSPPYG000000046682 retrocopies
retro_pabe_1921, retro_pabe_2032,
Pan troglodytes ENSPTRG000000051071 retrocopy
retro_ptro_1557,
Sus scrofa ENSSSCG000000004051 retrocopy
retro_sscr_453,
Tursiops truncatus ENSTTRG000000021441 retrocopy
retro_ttru_371,
Vicugna pacos ENSVPAG000000040252 retrocopies
retro_vpac_405, retro_vpac_562,

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 = 0.07 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 .07 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 .07 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 .03 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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