RetrogeneDB ID:

retro_hsap_277

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:192769731..192770076(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000226814
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ITGB1BP1
Ensembl ID:ENSG00000119185
Aliases:ITGB1BP1, ICAP-1A, ICAP-1B, ICAP-1alpha, ICAP1, ICAP1A, ICAP1B
Description:integrin beta 1 binding protein 1 [Source:HGNC Symbol;Acc:23927]


Retrocopy-Parental alignment summary:






>retro_hsap_277
AGACACCGTAGTAGCAGTTCCCAAAGTGGTGAAATCAGTACTAAGAGCAAGTCTGTAGATTCTAGCCTTGGGGGCCTTTC
ATAGTCCAGCCCTGCGGCCAGCCTCAATACAGATTCCACCAAGAGCTCAGAATAAAGCAACAATAATTCAAATACGTGTG
CAGAATTTCAAATAAAATATGTTGGTGCCATTAAGACACTGAAACTCTCTGAGAGAAGATGTCTTAAAGGGCCACTAGAC
CTGATAAATTATATAGATGTTGCCCAGCAAGATGAAAAGTTGCCTCTTGTTCCTCTGGAGGAAAAATTTATAATGGGAGT
TTCCAAATATAATACAAGTATCAAC

ORF - retro_hsap_277 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.26 %
Parental protein coverage: 84.56 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRHSSSSSQSSEISTKSKSVDSSLGGLSRSSTVASLDTDSTKSSGQSNNNSDTCAEFRIKYVGAIEKLKLS
RH.SSSSQS.EISTKSKSVDSSLGGLS.SS..ASL.TDSTKSS..SNNNS.TCAEF.IKYVGAI..LKLS
RetrocopyRHRSSSSQSGEISTKSKSVDSSLGGLS*SSPAASLNTDSTKSSE*SNNNSNTCAEFQIKYVGAIKTLKLS
ParentalEGKGLEGPLDLINYIDVAQQDGKLPFVPPEEEFIMGVSKYGIKVS
E...L.GPLDLINYIDVAQQD.KLP.VP.EE.FIMGVSKY.....
RetrocopyERRCLKGPLDLINYIDVAQQDEKLPLVPLEEKFIMGVSKYNTSIN

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 81 .96 RPM
bodymap2_adrenal 0 .00 RPM 29 .35 RPM
bodymap2_brain 0 .00 RPM 47 .28 RPM
bodymap2_breast 0 .00 RPM 138 .31 RPM
bodymap2_colon 0 .00 RPM 74 .85 RPM
bodymap2_heart 0 .00 RPM 39 .84 RPM
bodymap2_kidney 0 .00 RPM 63 .51 RPM
bodymap2_liver 0 .00 RPM 12 .44 RPM
bodymap2_lung 0 .00 RPM 22 .54 RPM
bodymap2_lymph_node 0 .00 RPM 35 .82 RPM
bodymap2_ovary 0 .00 RPM 32 .37 RPM
bodymap2_prostate 0 .00 RPM 57 .68 RPM
bodymap2_skeletal_muscle 0 .00 RPM 23 .88 RPM
bodymap2_testis 0 .00 RPM 30 .22 RPM
bodymap2_thyroid 0 .00 RPM 29 .75 RPM
bodymap2_white_blood_cells 0 .00 RPM 44 .22 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_277 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_277 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_277 retrocopy 5' end.

Lab - click to see more details

retro_hsap_277 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_277 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_231
Gorilla gorilla retro_ggor_321
Pongo abelii retro_pabe_391
Macaca mulatta retro_mmul_563
Parental genes homology:
Parental genes homology involve 19 parental genes, and 35 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000130632 retrocopies
retro_btau_1221, retro_btau_1435,
Choloepus hoffmanni ENSCHOG000000136022 retrocopies
retro_chof_1385, retro_chof_432,
Callithrix jacchus ENSCJAG000000062503 retrocopies
retro_cjac_1650, retro_cjac_2776, retro_cjac_393,
Dasypus novemcinctus ENSDNOG000000089303 retrocopies
retro_dnov_1422, retro_dnov_2198, retro_dnov_727,
Homo sapiens ENSG00000119185 1 retrocopy
retro_hsap_277 ,
Gorilla gorilla ENSGGOG000000017541 retrocopy
retro_ggor_321,
Macropus eugenii ENSMEUG000000067611 retrocopy
retro_meug_1434,
Microcebus murinus ENSMICG000000023597 retrocopies
retro_mmur_1251, retro_mmur_1342, retro_mmur_1375, retro_mmur_1523, retro_mmur_1539, retro_mmur_244, retro_mmur_442,
Myotis lucifugus ENSMLUG000000106292 retrocopies
retro_mluc_1218, retro_mluc_1752,
Macaca mulatta ENSMMUG000000180361 retrocopy
retro_mmul_563,
Nomascus leucogenys ENSNLEG000000133221 retrocopy
retro_nleu_1488,
Oryctolagus cuniculus ENSOCUG000000037261 retrocopy
retro_ocun_120,
Otolemur garnettii ENSOGAG000000016794 retrocopies
retro_ogar_1235, retro_ogar_1383, retro_ogar_2353, retro_ogar_981,
Procavia capensis ENSPCAG000000059761 retrocopy
retro_pcap_241,
Pongo abelii ENSPPYG000000126671 retrocopy
retro_pabe_391,
Pan troglodytes ENSPTRG000000116371 retrocopy
retro_ptro_231,
Sorex araneus ENSSARG000000097991 retrocopy
retro_sara_735,
Tarsius syrichta ENSTSYG000000145371 retrocopy
retro_tsyr_225,
Tursiops truncatus ENSTTRG000000008591 retrocopy
retro_ttru_712,

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 ) 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 .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 .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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