RetrogeneDB ID:

retro_hsap_1145

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:95680095..95680614(-)
Located in intron of:ENSG00000028203
Retrocopy
information
Ensembl ID:ENSG00000257666
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CBX3
Ensembl ID:ENSG00000122565
Aliases:CBX3, HECH, HP1-GAMMA, HP1Hs-gamma
Description:chromobox homolog 3 [Source:HGNC Symbol;Acc:1553]


Retrocopy-Parental alignment summary:






>retro_hsap_1145
ATGGCCTCCAACAAAACCACATTGCAAAACATGGGAAAGAAACAGAATGGAAAAGTAAAAAAGTTGAAGAGGCAGAGCCT
GAAGAATTTGTGGTGGAAAATGTACTAGATAGACACGCAGGGAATGGGAAAGTGGAATATTTCCTGAAGGAATTTACAGA
TGCTGACAATACTTTGGAACCTGAAGAAAATTTAGATTGTCCAGAGTTAATTGAAGCATTTCTTAATTCTCAAAAAGCTG
GTGAAGAAAAAGATGGTACAAAAAGAAAACCTTTATCTGGCAGTGAATCTGATGACAGCAAATCAAAGAAGAGATGCTGT
TGACAAACCAAGAGGAATTGCCAGAGGTCTTGATCCTGAAAGAATAATTGGTGCCACAGATGGCAGTGAAGAATTGATGT
TGCTCATGAAATGGAAGGATTCAGATGAGGCAGACTTGGTGCTGGCACAAAAGGCAAATATGAAGTATCCTCAAATTGAA
ATTGCTTTTTATGAAGAAAGACTAACTTGGTATTCTTGT

ORF - retro_hsap_1145 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.92 %
Parental protein coverage: 96.72 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMASNKTTLQKMGKKQNGK-SKKVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDC
MASNKTTLQ.MGKKQNGK.SKKVEEAEPEEFVVE.VLDR...NGKVEYFLK...FTDADNT.EPEENLDC
RetrocopyMASNKTTLQNMGKKQNGK<SKKVEEAEPEEFVVENVLDRHAGNGKVEYFLK--EFTDADNTLEPEENLDC
ParentalPELIEAFLNSQKAGKEKDGTKRKSLSDSESDDSKSKKK-RDAADKPRGFARGLDPERIIGATDSSGELMF
PELIEAFLNSQKAG.EKDGTKRK.LS.SESDD..SK.K.RDA.DKPRG.ARGLDPERIIGATD.S.ELM.
RetrocopyPELIEAFLNSQKAGEEKDGTKRKPLSGSESDD--SKSK>RDAVDKPRGIARGLDPERIIGATDGSEELML
ParentalLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLTWHSC
LMKWKDSDEADLVLA..ANMK.PQI.IAFYEERLTW.SC
RetrocopyLMKWKDSDEADLVLAQKANMKYPQIEIAFYEERLTWYSC

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 .10 RPM 80 .86 RPM
bodymap2_adrenal 0 .02 RPM 120 .32 RPM
bodymap2_brain 0 .02 RPM 96 .53 RPM
bodymap2_breast 0 .04 RPM 90 .72 RPM
bodymap2_colon 0 .08 RPM 114 .62 RPM
bodymap2_heart 0 .04 RPM 57 .25 RPM
bodymap2_kidney 0 .00 RPM 134 .05 RPM
bodymap2_liver 0 .00 RPM 48 .92 RPM
bodymap2_lung 0 .00 RPM 102 .48 RPM
bodymap2_lymph_node 0 .00 RPM 120 .81 RPM
bodymap2_ovary 0 .04 RPM 121 .93 RPM
bodymap2_prostate 0 .09 RPM 106 .43 RPM
bodymap2_skeletal_muscle 0 .00 RPM 50 .11 RPM
bodymap2_testis 0 .00 RPM 233 .46 RPM
bodymap2_thyroid 0 .00 RPM 103 .27 RPM
bodymap2_white_blood_cells 0 .00 RPM 138 .39 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1145 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1145 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1145 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1145 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1145 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_780
Pongo abelii retro_pabe_951
Callithrix jacchus retro_cjac_3322
Parental genes homology:
Parental genes homology involve 11 parental genes, and 67 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG0000001384322 retrocopies
retro_chof_1128, retro_chof_1147, retro_chof_1156, retro_chof_1178, retro_chof_1210, retro_chof_1223, retro_chof_132, retro_chof_1569, retro_chof_1672, retro_chof_1779, retro_chof_1863, retro_chof_1962, retro_chof_222, retro_chof_2269, retro_chof_2347, retro_chof_2379, retro_chof_2435, retro_chof_2695, retro_chof_411, retro_chof_676, retro_chof_87, retro_chof_936,
Cavia porcellus ENSCPOG000000151681 retrocopy
retro_cpor_66,
Felis catus ENSFCAG000000152246 retrocopies
retro_fcat_1005, retro_fcat_1103, retro_fcat_1485, retro_fcat_1519, retro_fcat_336, retro_fcat_473,
Homo sapiens ENSG000000949161 retrocopy
retro_hsap_2811,
Homo sapiens ENSG000001084683 retrocopies
retro_hsap_4654, retro_hsap_4790, retro_hsap_4840,
Homo sapiens ENSG00000122565 9 retrocopies
retro_hsap_1071, retro_hsap_1145 , retro_hsap_1902, retro_hsap_2332, retro_hsap_2771, retro_hsap_3368, retro_hsap_3650, retro_hsap_766, retro_hsap_910,
Nomascus leucogenys ENSNLEG000000149319 retrocopies
retro_nleu_141, retro_nleu_1685, retro_nleu_2462, retro_nleu_373, retro_nleu_397, retro_nleu_511, retro_nleu_676, retro_nleu_944, retro_nleu_964,
Ochotona princeps ENSOPRG000000117139 retrocopies
retro_opri_103, retro_opri_159, retro_opri_209, retro_opri_300, retro_opri_429, retro_opri_569, retro_opri_598, retro_opri_728, retro_opri_733,
Sorex araneus ENSSARG000000080112 retrocopies
retro_sara_496, retro_sara_709,
Sarcophilus harrisii ENSSHAG000000179131 retrocopy
retro_shar_153,
Sus scrofa ENSSSCG000000167114 retrocopies
retro_sscr_1031, retro_sscr_204, retro_sscr_420, retro_sscr_755,

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 = 0.14 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .10 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 .03 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .06 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .14 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 .06 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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





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