RetrogeneDB ID:

retro_hsap_904

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:82822229..82822520(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000254965
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:C1D
Ensembl ID:ENSG00000197223
Aliases:None
Description:C1D nuclear receptor corepressor [Source:HGNC Symbol;Acc:29911]


Retrocopy-Parental alignment summary:






>retro_hsap_904
CAGACTGGATTTGAAGGCTGTGAGTCAGTCATTAAGGCACATGAAGAAATTAATGAAGACCATCCAGTGGAAATTCATGA
ATATTTGTCAATGCTTGAGAATTACACTGGTGCTGTGGATAATATGCTAAAGACCATGATGTCTGTTTCTTGAAATGAGT
TGTTGCAGAAGTTGGACCCACTTAAACAAGTGAAAGTGGATTTAGTTTCTATGTACACATTAAATTTAAAGTTTTGAGTT
TATTTGGCAACTCAAGGAGTTAATACTAAGAAACAGCTAGTAAAGCAGGAA

ORF - retro_hsap_904 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.2 %
Parental protein coverage: 53.89 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalEEGEEQSWSAIMAGEEINEDYPVEIHEYLSAFENSIGAVDEMLKTMMSVSRNELLQKLDPLEQAKVDLVS
..G.E...S.I.A.EEINED.PVEIHEYLS..EN..GAVD.MLKTMMSVS.NELLQKLDPL.Q.KVDLVS
RetrocopyQTGFEGCESVIKAHEEINEDHPVEIHEYLSMLENYTGAVDNMLKTMMSVS*NELLQKLDPLKQVKVDLVS
ParentalAYTLNSMFWVYLATQGVNPKEHPVKQE
.YTLN..F.VYLATQGVN.K...VKQE
RetrocopyMYTLNLKF*VYLATQGVNTKKQLVKQE

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 .40 RPM 9 .34 RPM
bodymap2_adrenal 0 .35 RPM 18 .61 RPM
bodymap2_brain 0 .00 RPM 17 .32 RPM
bodymap2_breast 0 .58 RPM 17 .59 RPM
bodymap2_colon 0 .00 RPM 13 .26 RPM
bodymap2_heart 0 .00 RPM 12 .68 RPM
bodymap2_kidney 0 .00 RPM 21 .88 RPM
bodymap2_liver 0 .04 RPM 11 .64 RPM
bodymap2_lung 0 .00 RPM 17 .04 RPM
bodymap2_lymph_node 0 .00 RPM 15 .46 RPM
bodymap2_ovary 0 .00 RPM 16 .15 RPM
bodymap2_prostate 0 .03 RPM 17 .48 RPM
bodymap2_skeletal_muscle 0 .00 RPM 9 .88 RPM
bodymap2_testis 0 .02 RPM 19 .42 RPM
bodymap2_thyroid 0 .00 RPM 18 .76 RPM
bodymap2_white_blood_cells 0 .37 RPM 20 .38 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_904 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_904 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_904 retrocopy 5' end.

Lab - click to see more details

retro_hsap_904 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_904 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_624
Gorilla gorilla retro_ggor_731
Macaca mulatta retro_mmul_1109
Callithrix jacchus retro_cjac_856
Parental genes homology:
Parental genes homology involve 25 parental genes, and 57 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000048591 retrocopy
retro_amel_561,
Bos taurus ENSBTAG000000045671 retrocopy
retro_btau_1532,
Canis familiaris ENSCAFG000000300991 retrocopy
retro_cfam_1469,
Choloepus hoffmanni ENSCHOG000000067193 retrocopies
retro_chof_1368, retro_chof_2011, retro_chof_710,
Callithrix jacchus ENSCJAG000000065892 retrocopies
retro_cjac_2930, retro_cjac_856,
Cavia porcellus ENSCPOG000000067391 retrocopy
retro_cpor_1251,
Echinops telfairi ENSETEG000000148575 retrocopies
retro_etel_152, retro_etel_1820, retro_etel_2119, retro_etel_2163, retro_etel_524,
Felis catus ENSFCAG000000289331 retrocopy
retro_fcat_1091,
Homo sapiens ENSG00000197223 5 retrocopies
retro_hsap_659, retro_hsap_699, retro_hsap_700, retro_hsap_701, retro_hsap_904 ,
Gorilla gorilla ENSGGOG000000259823 retrocopies
retro_ggor_573, retro_ggor_596, retro_ggor_731,
Loxodonta africana ENSLAFG000000020831 retrocopy
retro_lafr_1016,
Myotis lucifugus ENSMLUG000000107914 retrocopies
retro_mluc_1048, retro_mluc_2082, retro_mluc_235, retro_mluc_391,
Macaca mulatta ENSMMUG000000172093 retrocopies
retro_mmul_1109, retro_mmul_334, retro_mmul_336,
Monodelphis domestica ENSMODG000000035613 retrocopies
retro_mdom_1237, retro_mdom_1677, retro_mdom_941,
Nomascus leucogenys ENSNLEG000000099734 retrocopies
retro_nleu_2506, retro_nleu_2507, retro_nleu_2948, retro_nleu_379,
Oryctolagus cuniculus ENSOCUG000000097711 retrocopy
retro_ocun_142,
Ochotona princeps ENSOPRG000000095863 retrocopies
retro_opri_1141, retro_opri_193, retro_opri_718,
Pongo abelii ENSPPYG000000123541 retrocopy
retro_pabe_202,
Pan troglodytes ENSPTRG000000235583 retrocopies
retro_ptro_443, retro_ptro_479, retro_ptro_624,
Rattus norvegicus ENSRNOG000000059821 retrocopy
retro_rnor_2402,
Sorex araneus ENSSARG000000039131 retrocopy
retro_sara_566,
Sarcophilus harrisii ENSSHAG000000083521 retrocopy
retro_shar_603,
Sus scrofa ENSSSCG000000083542 retrocopies
retro_sscr_660, retro_sscr_812,
Tupaia belangeri ENSTBEG000000097974 retrocopies
retro_tbel_1112, retro_tbel_2362, retro_tbel_864, retro_tbel_898,
Tursiops truncatus ENSTTRG000000139822 retrocopies
retro_ttru_1192, retro_ttru_423,

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 = 0.4 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .11 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .20 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .10 RPM
CEU_NA12760 0 .13 RPM
CEU_NA12827 0 .14 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .14 RPM
FIN_HG00277 0 .15 RPM
FIN_HG00315 0 .08 RPM
FIN_HG00321 0 .09 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .15 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .15 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .21 RPM
GBR_HG00114 0 .18 RPM
GBR_HG00119 0 .10 RPM
GBR_HG00131 0 .17 RPM
GBR_HG00133 0 .10 RPM
GBR_HG00134 0 .11 RPM
GBR_HG00137 0 .30 RPM
GBR_HG00142 0 .19 RPM
GBR_HG00143 0 .16 RPM
TSI_NA20512 0 .06 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .14 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .09 RPM
TSI_NA20765 0 .21 RPM
TSI_NA20771 0 .11 RPM
TSI_NA20786 0 .18 RPM
TSI_NA20798 0 .12 RPM
YRI_NA18870 0 .07 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .06 RPM
YRI_NA19093 0 .13 RPM
YRI_NA19099 0 .35 RPM
YRI_NA19114 0 .08 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .10 RPM
YRI_NA19214 0 .15 RPM
YRI_NA19223 0 .40 RPM

Indel association:

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



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