RetrogeneDB ID:

retro_hsap_2307

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:112697881..112698613(-)
Located in intron of:ENSG00000153208
Retrocopy
information
Ensembl ID:ENSG00000225496
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:C14orf166
Ensembl ID:ENSG00000087302
Aliases:C14orf166, CGI99, CLE, CLE7, LCRP369, RLLM1
Description:chromosome 14 open reading frame 166 [Source:HGNC Symbol;Acc:23169]


Retrocopy-Parental alignment summary:






>retro_hsap_2307
ATGTTCCAATGAAAGCTGACGGCTCTTGACTACCACAACCCCGCCGGTTTCAACTGCAAAGATGAAACAGAATTTAGAAA
CTTCACTGTTTGGCTTGAAGACCAGAAAATCAGATACTACAAGACTGAAGACAGAGGTAATTTAAGAAACATCCACAGCA
GTGACTGGCCCGAGTTCTTTCAAAAGTATCTCAGAGATGTTAACTGTCGTTTAAAGATTCAAGATCGACAAGAAGCTATT
GACTGGCTTCTTGGTTTAGCTGTTAGATTTGAATATGGAGATAATGCTGAAAAATACAAGGACTTAGTACCTGATAATGC
AAAAACTGCTGACAATGCAACTAAAAATGCAGAACCATTGATAAATTTGGACGTAAATAATCCTGATTTTAAGCCTGGTG
TAATGGCTTTGGCTAACCTGCTTCAGGTTCAATGTCATGATGATTGCCTGGTAATGCTTAAGGCAATTCAAATTTTGGTT
CAGGAGCACCTGACACAGGATGCAGTTGCTAAAGCAAATCAAACAAAAGAGGGCTTGCCTGTTGCTTTAGACAAACATAT
TCTTGGTTTTGACACAGGAGATGCAGTTCTTAATGAAGCTACTCAAATTCTGTGACTGCTGTATACAGAAGAGCTCAGAC
AGCTACAGACAAAAATTAATGAAGCCATAGCAGCTGTTCAGGCAATTATTGCTGATGCAAGGACAGACCACAGGCTGGGA
AAAGTTGGAAGA

ORF - retro_hsap_2307 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.75 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMFRRKLTALDYHNPAGFNCKDETEFRNFIVWLEDQKIRHYKIEDRGNLRNIHSSDWPKFFEKYLRDVNCP
MF..KLTALDYHNPAGFNCKDETEFRNF.VWLEDQKIR.YK.EDRGNLRNIHSSDWP.FF.KYLRDVNC.
RetrocopyMFQ*KLTALDYHNPAGFNCKDETEFRNFTVWLEDQKIRYYKTEDRGNLRNIHSSDWPEFFQKYLRDVNCR
ParentalFKIQDRQEAIDWLLGLAVRLEYGDNAEKYKDLVPDNSKTADNATKNAEPLINLDVNNPDFKAGVMALANL
.KIQDRQEAIDWLLGLAVR.EYGDNAEKYKDLVPDN.KTADNATKNAEPLINLDVNNPDFK.GVMALANL
RetrocopyLKIQDRQEAIDWLLGLAVRFEYGDNAEKYKDLVPDNAKTADNATKNAEPLINLDVNNPDFKPGVMALANL
ParentalLQIQRHDDYLVMLKAIRILVQERLTQDAVAKANQTKEGLPVALDKHILGFDTGDAVLNEAAQILRLLHIE
LQ.Q.HDD.LVMLKAI.ILVQE.LTQDAVAKANQTKEGLPVALDKHILGFDTGDAVLNEA.QIL.LL..E
RetrocopyLQVQCHDDCLVMLKAIQILVQEHLTQDAVAKANQTKEGLPVALDKHILGFDTGDAVLNEATQIL*LLYTE
ParentalELRELQTKINEAIVAVQAIIADPKTDHRLGKVGR
ELR.LQTKINEAI.AVQAIIAD..TDHRLGKVGR
RetrocopyELRQLQTKINEAIAAVQAIIADARTDHRLGKVGR

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 84 .38 RPM
bodymap2_adrenal 0 .14 RPM 82 .68 RPM
bodymap2_brain 0 .12 RPM 36 .21 RPM
bodymap2_breast 0 .00 RPM 92 .67 RPM
bodymap2_colon 0 .00 RPM 98 .96 RPM
bodymap2_heart 0 .07 RPM 81 .76 RPM
bodymap2_kidney 0 .00 RPM 68 .58 RPM
bodymap2_liver 0 .02 RPM 43 .71 RPM
bodymap2_lung 0 .00 RPM 70 .73 RPM
bodymap2_lymph_node 0 .00 RPM 72 .78 RPM
bodymap2_ovary 0 .00 RPM 119 .69 RPM
bodymap2_prostate 0 .00 RPM 85 .44 RPM
bodymap2_skeletal_muscle 0 .00 RPM 77 .13 RPM
bodymap2_testis 0 .00 RPM 150 .24 RPM
bodymap2_thyroid 0 .00 RPM 74 .46 RPM
bodymap2_white_blood_cells 0 .00 RPM 79 .52 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2307 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2307 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2307 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2307 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2307 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1631
Pongo abelii retro_pabe_1980
Parental genes homology:
Parental genes homology involve 29 parental genes, and 70 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000020832 retrocopies
retro_amel_224, retro_amel_302,
Canis familiaris ENSCAFG000000146484 retrocopies
retro_cfam_1025, retro_cfam_2042, retro_cfam_237, retro_cfam_734,
Callithrix jacchus ENSCJAG000000069263 retrocopies
retro_cjac_1262, retro_cjac_1947, retro_cjac_3207,
Cavia porcellus ENSCPOG000000013176 retrocopies
retro_cpor_1041, retro_cpor_1177, retro_cpor_1239, retro_cpor_1247, retro_cpor_517, retro_cpor_541,
Dasypus novemcinctus ENSDNOG000000032483 retrocopies
retro_dnov_458, retro_dnov_572, retro_dnov_609,
Dipodomys ordii ENSDORG000000123351 retrocopy
retro_dord_619,
Equus caballus ENSECAG000000126001 retrocopy
retro_ecab_483,
Erinaceus europaeus ENSEEUG000000155831 retrocopy
retro_eeur_366,
Felis catus ENSFCAG000000026633 retrocopies
retro_fcat_1160, retro_fcat_1415, retro_fcat_948,
Homo sapiens ENSG00000087302 1 retrocopy
retro_hsap_2307 ,
Loxodonta africana ENSLAFG000000031621 retrocopy
retro_lafr_301,
Microcebus murinus ENSMICG000000087201 retrocopy
retro_mmur_857,
Myotis lucifugus ENSMLUG000000086436 retrocopies
retro_mluc_1228, retro_mluc_1518, retro_mluc_1834, retro_mluc_2610, retro_mluc_456, retro_mluc_676,
Macaca mulatta ENSMMUG000000182002 retrocopies
retro_mmul_1045, retro_mmul_2025,
Monodelphis domestica ENSMODG000000132111 retrocopy
retro_mdom_1296,
Mustela putorius furoENSMPUG000000052536 retrocopies
retro_mputfur_1333, retro_mputfur_1421, retro_mputfur_203, retro_mputfur_328, retro_mputfur_655, retro_mputfur_797,
Mus musculus ENSMUSG000000218072 retrocopies
retro_mmus_140, retro_mmus_3203,
Nomascus leucogenys ENSNLEG000000124061 retrocopy
retro_nleu_2749,
Oryctolagus cuniculus ENSOCUG000000146811 retrocopy
retro_ocun_221,
Otolemur garnettii ENSOGAG000000132325 retrocopies
retro_ogar_1060, retro_ogar_1856, retro_ogar_2351, retro_ogar_2976, retro_ogar_3192,
Ochotona princeps ENSOPRG000000163522 retrocopies
retro_opri_257, retro_opri_884,
Pongo abelii ENSPPYG000000058141 retrocopy
retro_pabe_1980,
Pan troglodytes ENSPTRG000000063441 retrocopy
retro_ptro_1631,
Pteropus vampyrus ENSPVAG000000133921 retrocopy
retro_pvam_1088,
Sus scrofa ENSSSCG000000050291 retrocopy
retro_sscr_1093,
Tupaia belangeri ENSTBEG000000138985 retrocopies
retro_tbel_2579, retro_tbel_4337, retro_tbel_683, retro_tbel_880, retro_tbel_881,
Tarsius syrichta ENSTSYG000000045286 retrocopies
retro_tsyr_1183, retro_tsyr_1289, retro_tsyr_1353, retro_tsyr_157, retro_tsyr_541, retro_tsyr_939,
Tursiops truncatus ENSTTRG000000057211 retrocopy
retro_ttru_83,
Vicugna pacos ENSVPAG000000114431 retrocopy
retro_vpac_142,

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 = 0.15 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 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 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .15 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .10 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .03 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 .02 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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





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