RetrogeneDB ID:

retro_hsap_4253

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:38452781..38453968(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000225254
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ARMC8
Ensembl ID:ENSG00000114098
Aliases:ARMC8, GID5, HSPC056, VID28
Description:armadillo repeat containing 8 [Source:HGNC Symbol;Acc:24999]


Retrocopy-Parental alignment summary:






>retro_hsap_4253
GTATTAAAGACATTGCCTTATTTGGTTCAAACATGCAGTAAGAAGAGATTACTAGAGGAGAGAGTTAAAGGAGCTGAGAC
ACTTGCCTATCTGATTGAACCAGATATTGAGCTACAGAGAATCGCTAGTGTAACTGATCACCTCATCGCCATGTTTGCTG
ACTATTTCAAGTATCCCAACTCATTGAGTGCCATCACTGATAGTAAAAGGCTTGATCATGATTTAAAACATGCTCATGAA
CTCTGCCAGGCTGCATTCAATCTCTACGACTCTCTTAGAGCAAATGATGAAGACATTCAGAAGAAAAGCCCTGAGACTGA
AAATATGATGGACTGAATTGTGACTGGCTTGTCTGAGTCTAGTGTCAAGGTGCGGTTACCTGCTCTCAGATGTTTGCACC
ATTTATCCAGATCTGTGCAGCAGCTTCAAAACAGTTTCTAGGATCACACTCTGTGAAAACCTTTAATGAAGGTTTTACAA
AATGCACCAGATGAAATCCTAGTAGCAGCATCTTCCATGGTATATAATCTTCTTGAATTTTCTCCAAGGAAAGAGTCAAT
TTTAAAATCAGGAGTTGTAAAGCTACTTTGTGGATTAACCCAGAGTGAAAATCCTGCTTTATGAGTGAGCAGAATTTGGG
ATTTAATGAATATGGCATTTCAGGCTGAACAAAAAATAAAAGCAGACATGTTACAAAGCTTGAGTGCTGAACAGCTATTC
TGGTTATTATCAGATTCAGATTTGAATGTCCTGATGAAGACACTGGGACTTCTTAGAAATATCCTCTTGACCTGGCTTCA
TATAATAAAATAATGAGTACTCATGGAAAGTAAATTATGCAAGCTGTCATCCTTATTCTGGAAGGGGAACATAACTTTAA
GGTCAAAGAGTAGATACTGTGCATCTTAGCCAATATAAAAGATGAGACAACAGCAAAAGAATGTATTATGACCAATGATG
ATATCCTTCAGAAAATCAAATATTACATGGACCATTCACATGTCAAACTGCAGCTTCCAGCTATGTTTTGTATATCAAAC
CTCATATGGAATGAAGAAGAAGGTTCACAAGAATGCCAGGATAAATTATGAGACATGGGCATCATAGATATTCTACATAA
ACCGAGTCAGCCACCAGATTCAGACCTTTGTGACAAGGCAAAGATGGCACTGCAGCAGTACCTGGCA

ORF - retro_hsap_4253 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.66 %
Parental protein coverage: 59.88 %
Number of stop codons detected: 7
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalVLKTLPCLVRMCSKERLLEERVEGAETLAYLIEPDVELQRIASITDHLIAMLADYFKYPSSVSAITDIKR
VLKTLP.LV..CSK.RLLEERV.GAETLAYLIEPD.ELQRIAS.TDHLIAM.ADYFKYP.S.SAITD.KR
RetrocopyVLKTLPYLVQTCSKKRLLEERVKGAETLAYLIEPDIELQRIASVTDHLIAMFADYFKYPNSLSAITDSKR
ParentalLDHDLKHAHELRQAAFKLYASLGANDEDIRKKIIETENMMDRIVTGLSESSVKVRLAAVRCLHSLSRSVQ
LDHDLKHAHEL.QAAF.LY.SL.ANDEDI.KK..ETENMMD.IVTGLSESSVKVRL.A.RCLH.LSRSVQ
RetrocopyLDHDLKHAHELCQAAFNLYDSLRANDEDIQKKSPETENMMD*IVTGLSESSVKVRLPALRCLHHLSRSVQ
ParentalQLRTSFQDHAVWKPLMKVLQNAPDEILVVASSMLCNLLLEFSPSKEPILESGAVELLCGLTQSENPALRV
QL..SF.DH...KPLMKVLQNAPDEILV.ASSM..N.LLEFSP.KE.IL.SG.V.LLCGLTQSENPAL.V
RetrocopyQLQNSF*DHTL*KPLMKVLQNAPDEILVAASSMVYN-LLEFSPRKESILKSGVVKLLCGLTQSENPAL*V
ParentalNGIWALMNMAFQAEQKIKADILRSLSTEQLFRLLSDSDLNVLMKTLGLLRNLLSTRPHI-DKIMSTHGKQ
..IW.LMNMAFQAEQKIKAD.L.SLS.EQLF.LLSDSDLNVLMKTLGLLRN.L.T..HI..KIMSTHGK.
RetrocopySRIWDLMNMAFQAEQKIKADMLQSLSAEQLFWLLSDSDLNVLMKTLGLLRNILLTWLHI<NKIMSTHGK*
ParentalIMQAVTLILEGEHNIEVKEQTLCILANIADGTTAKDLIMTNDDILQKIKYYMGHSHVKLQLAAMFCISNL
IMQAV.LILEGEHN..VKE..LCILANI.D.TTAK..IMTNDDILQKIKYYM.HSHVKLQL.AMFCISNL
RetrocopyIMQAVILILEGEHNFKVKE*ILCILANIKDETTAKECIMTNDDILQKIKYYMDHSHVKLQLPAMFCISNL
ParentalIWNEEEGSQERQDKLRDMGIVDILHKLSQSPDSNLCDKAKMALQQYLA
IWNEEEGSQE.QDKL.DMGI.DILHK.SQ.PDS.LCDKAKMALQQYLA
RetrocopyIWNEEEGSQECQDKL*DMGIIDILHKPSQPPDSDLCDKAKMALQQYLA

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 .51 RPM
bodymap2_adrenal 0 .00 RPM 50 .44 RPM
bodymap2_brain 0 .00 RPM 58 .32 RPM
bodymap2_breast 0 .00 RPM 43 .58 RPM
bodymap2_colon 0 .00 RPM 42 .38 RPM
bodymap2_heart 0 .00 RPM 33 .38 RPM
bodymap2_kidney 0 .00 RPM 52 .11 RPM
bodymap2_liver 0 .00 RPM 16 .67 RPM
bodymap2_lung 0 .00 RPM 37 .64 RPM
bodymap2_lymph_node 0 .00 RPM 37 .50 RPM
bodymap2_ovary 0 .00 RPM 58 .35 RPM
bodymap2_prostate 0 .00 RPM 57 .90 RPM
bodymap2_skeletal_muscle 0 .00 RPM 58 .53 RPM
bodymap2_testis 0 .19 RPM 47 .08 RPM
bodymap2_thyroid 0 .00 RPM 60 .52 RPM
bodymap2_white_blood_cells 0 .00 RPM 79 .26 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4253 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4253 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4253 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4253 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4253 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2851
Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000114098 1 retrocopy
retro_hsap_4253 ,
Gorilla gorilla ENSGGOG000000235351 retrocopy
retro_ggor_2851,
Macaca mulatta ENSMMUG000000212851 retrocopy
retro_mmul_1142,
Pongo abelii ENSPPYG000000141402 retrocopies
retro_pabe_3384, retro_pabe_3385,

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 = 0.04 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .04 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 .02 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 .03 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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