RetrogeneDB ID:

retro_hsap_2913

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:13978965..13979589(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000224569
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:C9orf78
Ensembl ID:ENSG00000136819
Aliases:C9orf78, HCA59, HSPC220, bA409K20.3
Description:chromosome 9 open reading frame 78 [Source:HGNC Symbol;Acc:24932]


Retrocopy-Parental alignment summary:






>retro_hsap_2913
GATCCCTTTCAGATGAAGATAGGTGATGTGGATATGAAGAAACTGAAGGAAAAGAGCAAAGATAAAATCAGTAAAGAGGA
AGACTTTCACTTGGGGACATCATTTTCTGCAGAAACCAACTGAAGGGATGAGGATGCAGACATGATGAAGTACACTGAGA
CAGAGCTAAAGAAGAGGAAAGGGATTGTGGAACATGAGGAACAGAAAGTCAAGCCAAGGAATGCAGAGGATTGTCTTTAT
GAACTTCCAGAAAACATCCACATTTCCTCAGCAAAGAAGACCAAGAAGATGTTTTCCAACCAGATGCTGAGTGGCATTCC
TGAGTTGGACCTTGGCATCAATGCTAGAATAAAAAATATCATTTCTTCAGAGGATGCCAAGGTCCATCTGCTGGCAGAGT
AGCAGAATAAGAAAAAAGACAGTAAGCTATCCTTCATGCCTACCAACATGTCTGTGAATTACGTGCAGCAGAACAGATTT
TATCATGAGGAGCTCAACGTTCCCATACAGAGAAACACAGAAGAACCCAAAACCAGACTCTTGAGGGTAGGCGACACGGA
GAAGCTAGGTGACACAGAGAAGGCAGAGGCTGAGAGGTCCCCTCCTAACCACAAGCATCCTGAT

ORF - retro_hsap_2913 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.03 %
Parental protein coverage: 72.32 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalDPFQMKTGGMVDMKKLKERGKDKISEEEDLHLGTSFSAETNRRDEDADMMKYIETELKKRKGIVEHEEQK
DPFQMK.G..VDMKKLKE..KDKIS.EED.HLGTSFSAETN.RDEDADMMKY.ETELKKRKGIVEHEEQK
RetrocopyDPFQMKIGD-VDMKKLKEKSKDKISKEEDFHLGTSFSAETN*RDEDADMMKYTETELKKRKGIVEHEEQK
ParentalVKPKNAEDCLYELPENIRVSSAKKTEEMLSNQMLSGIPEVDLGIDAKIKNIISTEDAKARLLAEQQNKKK
VKP.NAEDCLYELPENI..SSAKKT..M.SNQMLSGIPE.DLGI.A.IKNIIS.EDAK..LLAE.QNKKK
RetrocopyVKPRNAEDCLYELPENIHISSAKKTKKMFSNQMLSGIPELDLGINARIKNIISSEDAKVHLLAE*QNKKK
ParentalDSETSFVPTNMAVNYVQHNRFYHEELNAPIRRNKEEPKARPLRVGDTEKPEPERSPPNRKRPANEKATD
DS..SF.PTNM.VNYVQ.NRFYHEELN.PI.RN.EEPK.R.LRVGDTEK............P.N.K..D
RetrocopyDSKLSFMPTNMSVNYVQQNRFYHEELNVPIQRNTEEPKTRLLRVGDTEKLGDTEKAEAERSPPNHKHPD

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 46 .77 RPM
bodymap2_adrenal 0 .00 RPM 92 .83 RPM
bodymap2_brain 0 .00 RPM 64 .67 RPM
bodymap2_breast 0 .00 RPM 41 .17 RPM
bodymap2_colon 0 .00 RPM 63 .50 RPM
bodymap2_heart 0 .00 RPM 26 .09 RPM
bodymap2_kidney 0 .14 RPM 57 .35 RPM
bodymap2_liver 0 .00 RPM 33 .99 RPM
bodymap2_lung 0 .00 RPM 49 .05 RPM
bodymap2_lymph_node 0 .00 RPM 60 .83 RPM
bodymap2_ovary 0 .00 RPM 48 .75 RPM
bodymap2_prostate 0 .00 RPM 61 .69 RPM
bodymap2_skeletal_muscle 0 .00 RPM 53 .55 RPM
bodymap2_testis 0 .00 RPM 75 .24 RPM
bodymap2_thyroid 0 .00 RPM 73 .14 RPM
bodymap2_white_blood_cells 0 .00 RPM 95 .39 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2913 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2913 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2913 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2913 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2913 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1969
Pongo abelii retro_pabe_2426
Macaca mulatta retro_mmul_1870
Callithrix jacchus retro_cjac_2299
Parental genes homology:
Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000199791 retrocopy
retro_cfam_116,
Choloepus hoffmanni ENSCHOG000000138953 retrocopies
retro_chof_1103, retro_chof_1747, retro_chof_978,
Callithrix jacchus ENSCJAG000000203183 retrocopies
retro_cjac_1757, retro_cjac_2299, retro_cjac_2778,
Dasypus novemcinctus ENSDNOG000000192141 retrocopy
retro_dnov_1540,
Homo sapiens ENSG00000136819 3 retrocopies
retro_hsap_2872, retro_hsap_2913 , retro_hsap_320,
Gorilla gorilla ENSGGOG000000133581 retrocopy
retro_ggor_1990,
Macropus eugenii ENSMEUG000000105243 retrocopies
retro_meug_1046, retro_meug_1241, retro_meug_508,
Macaca mulatta ENSMMUG000000037952 retrocopies
retro_mmul_1460, retro_mmul_1870,
Monodelphis domestica ENSMODG000000068321 retrocopy
retro_mdom_518,
Nomascus leucogenys ENSNLEG000000176583 retrocopies
retro_nleu_1763, retro_nleu_614, retro_nleu_823,
Otolemur garnettii ENSOGAG000000097701 retrocopy
retro_ogar_1015,
Pongo abelii ENSPPYG000000196851 retrocopy
retro_pabe_2426,
Pan troglodytes ENSPTRG000000214653 retrocopies
retro_ptro_1943, retro_ptro_1969, retro_ptro_258,
Sarcophilus harrisii ENSSHAG000000123131 retrocopy
retro_shar_746,

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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