RetrogeneDB ID:

retro_hsap_2516

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:21:21131675..21132279(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000215353
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:C1QBP
Ensembl ID:ENSG00000108561
Aliases:C1QBP, GC1QBP, HABP1, SF2p32, gC1Q-R, gC1qR, p32
Description:complement component 1, q subcomponent binding protein [Source:HGNC Symbol;Acc:1243]


Retrocopy-Parental alignment summary:






>retro_hsap_2516
AAGGAGACTGTTGATATCCTGAATGGTGAAATTGAGGAGGAGAGGAAAATCCAGAAGCATAAAACCCTCCCTAAGATGTC
TGGAGGATGGGAGCGGCAGTTAAATGGGACAGAAGCTAAATTAGTGGGAAAAGCTGCCGGGGAAAGATCGCTGTCACTTT
CAACATTAACAACAGCATCCCACCGACACTTGATGGCAAGGAGGAACCCTCGAAAGGGCAGCAAGTTGGAGAACAGGAGC
CTGAATTGACATCACCTCCCAATTTCGTGGTCCAAGTTTTGAAGAGTGGTGGCAAGAAGGCCCTTGTGCTGGACTGTCAC
TACCCAGAGGATGAGGGTGGGCCAGAAGAGGAGGTTGAGAGTGACCTTTTCTCTATCAGGGAAGTAACTTTCAGTCCAAT
GGGGAGTCTCAATGAAAGGACACTAATTTTATACTCAACACAGATTTCCGGGACTCGGCCTTATATGACCACCTAGTGGA
TTTCCTTGTGAATGGAGGGGTGGCCAACCCTTTTGCCCATAAGCTAATGGAGCTCAGCACAGCCCTGGAGGAGCAGGAGT
ACATGACTTTTCTTGAAGACCTCAGAAGTTCTGTCAAGAGCCAG

ORF - retro_hsap_2516 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.12 %
Parental protein coverage: 71.99 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalKAFVDFLSDEIKEERKIQKHKTLPKMSGGWELELNGTEAKLVRKVAGE-KITVTFNINNSIPPTFDGEEE
K..VD.L..EI.EERKIQKHKTLPKMSGGWE..LNGTEAKLV.K.AGE.KI.VTFNINNSIPPT.DG.EE
RetrocopyKETVDILNGEIEEERKIQKHKTLPKMSGGWERQLNGTEAKLVGKAAGE<KIAVTFNINNSIPPTLDGKEE
ParentalPSQGQKVEEQEPELTSTPNFVVEVIKNDDGKKALVLDCHYPEDEVGQEDEAESDIFSIREVSF-QSTGES
PS.GQ.V.EQEPELTS.PNFVV.V.K...GKKALVLDCHYPEDE.G.E.E.ESD.FSIREV.F.QS.GES
RetrocopyPSKGQQVGEQEPELTSPPNFVVQVLKSG-GKKALVLDCHYPEDEGGPEEEVESDLFSIREVTF<QSNGES
ParentalEWKDTNYTLNTDSLDWALYDHLMDFLADRGVDNTFADELVELSTALEHQEYITFLEDLKSFVKSQ
..KDTN..LNTD..D.ALYDHL.DFL...GV.N.FA..L.ELSTALE.QEY.TFLEDL.S.VKSQ
RetrocopyQ*KDTNFILNTDFRDSALYDHLVDFLVNGGVANPFAHKLMELSTALEEQEYMTFLEDLRSSVKSQ

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 40 .37 RPM
bodymap2_adrenal 0 .00 RPM 87 .06 RPM
bodymap2_brain 0 .00 RPM 69 .31 RPM
bodymap2_breast 0 .00 RPM 44 .24 RPM
bodymap2_colon 0 .00 RPM 54 .22 RPM
bodymap2_heart 0 .00 RPM 54 .92 RPM
bodymap2_kidney 0 .00 RPM 73 .66 RPM
bodymap2_liver 0 .00 RPM 62 .63 RPM
bodymap2_lung 0 .00 RPM 39 .03 RPM
bodymap2_lymph_node 0 .00 RPM 52 .50 RPM
bodymap2_ovary 0 .00 RPM 57 .97 RPM
bodymap2_prostate 0 .00 RPM 57 .69 RPM
bodymap2_skeletal_muscle 0 .00 RPM 53 .93 RPM
bodymap2_testis 0 .00 RPM 86 .10 RPM
bodymap2_thyroid 0 .00 RPM 52 .11 RPM
bodymap2_white_blood_cells 0 .00 RPM 59 .32 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2516 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2516 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2516 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2516 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2516 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1569
Parental genes homology:
Parental genes homology involve 15 parental genes, and 55 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000060432 retrocopies
retro_amel_1734, retro_amel_356,
Callithrix jacchus ENSCJAG000000113526 retrocopies
retro_cjac_2041, retro_cjac_2408, retro_cjac_4033, retro_cjac_604, retro_cjac_680, retro_cjac_946,
Dasypus novemcinctus ENSDNOG000000088873 retrocopies
retro_dnov_1151, retro_dnov_1946, retro_dnov_702,
Felis catus ENSFCAG000000264743 retrocopies
retro_fcat_1135, retro_fcat_1763, retro_fcat_892,
Homo sapiens ENSG00000108561 2 retrocopies
retro_hsap_1475, retro_hsap_2516 ,
Gorilla gorilla ENSGGOG000000027455 retrocopies
retro_ggor_1133, retro_ggor_1569, retro_ggor_3007, retro_ggor_3008, retro_ggor_717,
Macropus eugenii ENSMEUG0000001488213 retrocopies
retro_meug_1068, retro_meug_1347, retro_meug_1363, retro_meug_1446, retro_meug_1901, retro_meug_1940, retro_meug_1970, retro_meug_2069, retro_meug_2128, retro_meug_434, retro_meug_580, retro_meug_988, retro_meug_989,
Macaca mulatta ENSMMUG000000065921 retrocopy
retro_mmul_1554,
Nomascus leucogenys ENSNLEG000000090812 retrocopies
retro_nleu_2379, retro_nleu_3038,
Otolemur garnettii ENSOGAG000000016105 retrocopies
retro_ogar_1376, retro_ogar_2502, retro_ogar_2518, retro_ogar_2879, retro_ogar_768,
Ochotona princeps ENSOPRG000000131501 retrocopy
retro_opri_408,
Pongo abelii ENSPPYG000000078706 retrocopies
retro_pabe_1222, retro_pabe_1385, retro_pabe_1413, retro_pabe_1866, retro_pabe_1868, retro_pabe_670,
Pan troglodytes ENSPTRG000000086313 retrocopies
retro_ptro_1140, retro_ptro_1461, retro_ptro_998,
Pteropus vampyrus ENSPVAG000000024661 retrocopy
retro_pvam_384,
Sarcophilus harrisii ENSSHAG000000024412 retrocopies
retro_shar_620, retro_shar_813,

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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