RetrogeneDB ID:

retro_hsap_3341

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:78295950..78296566(-)
Located in intron of:ENSG00000132837
Retrocopy
information
Ensembl ID:ENSG00000214890
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:IMPACT
Ensembl ID:ENSG00000154059
Aliases:IMPACT, RWDD5
Description:impact RWD domain protein [Source:HGNC Symbol;Acc:20387]


Retrocopy-Parental alignment summary:






>retro_hsap_3341
CAGAATATTGGTGAAAGTATTCTTTACCTGTGAGTGGAGAAAATAAGAGATGTTCCAATACAAAAACCTCAGATGACAGA
ACCAGGCCCAGAGGCAAAGAAAGAAACTGAAGAGGAAGATGTTGAATGTGAAGATGATCTCATTTTTGCATGTCAGCCAG
AAAGTTCGGTGACAGCACTGGATTTTGATATCAGTGAAAATCAAAGAGAAATAGAATTATCTCTGATTGATCATGGCATT
TCTGTTACAGACCGAATAAGTACTTTTCAGGCAGACTTTGATCCAGTAGTTTGTCCCAAACAGGTGAAAATGGTTCTTTC
CAACTTGTATGAGAATAAGAAAATAGCTAGTACCACCCACAGCATCTATGCCTACAGAGTATATTGTGAGAATAAACAGA
CCTTCTTACAGGATTGTGAGGATGATGGGGAAAGAGCAGCTGGTGGGCATCTTCTTCATCTCATGGAGATTTTAAATGTG
AGGAATATCATGGTGGTGGTATCACGCTGGTATGGAGGGATTCTGTAGGACCAGATCACTTTAAACATAACTGTGCCAGA
AACATACTAGTGGAGAAGAACAACACACATTCACCTGAAAATCATCTAAGGCTTTG

ORF - retro_hsap_3341 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.28 %
Parental protein coverage: 65.94 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalQNIGESILYLWVEKIRDVLIQKSQMTEPGPDVKKKTEEEDVECEDDLILACQPESSLKALDFDISETRTE
QNIGESILYL.VEKIRDV.IQK.QMTEPGP..KK.TEEEDVECEDDLI.ACQPESS..ALDFDISE...E
RetrocopyQNIGESILYL*VEKIRDVPIQKPQMTEPGPEAKKETEEEDVECEDDLIFACQPESSVTALDFDISENQRE
ParentalVEVEELPPIDHGIPITDRRSTFQAHLAPVVCPKQVKMVLSKLYENKKIASATHNIYAYRIYCEDKQTFLQ
....EL..IDHGI..TDR.STFQA...PVVCPKQVKMVLS.LYENKKIAS.TH.IYAYR.YCE.KQTFLQ
RetrocopyI---ELSLIDHGISVTDRISTFQADFDPVVCPKQVKMVLSNLYENKKIASTTHSIYAYRVYCENKQTFLQ
ParentalDCEDDGETAAGGRLLHLMEILNVKNVMVVVSRWYGGIL-LGPDRFKHINNCARNILVEKNYTNSPE-ESS
DCEDDGE.AAGG.LLHLMEILNV.N.MVVVSRWYGGIL..GPD.FKH..NCARNILVEKN.T.SPE..SS
RetrocopyDCEDDGERAAGGHLLHLMEILNVRNIMVVVSRWYGGIL<VGPDHFKH--NCARNILVEKNNTHSPE<KSS
ParentalKAL
KAL
RetrocopyKAL

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 .02 RPM 41 .25 RPM
bodymap2_adrenal 0 .00 RPM 47 .61 RPM
bodymap2_brain 0 .00 RPM 40 .95 RPM
bodymap2_breast 0 .00 RPM 48 .54 RPM
bodymap2_colon 0 .00 RPM 24 .44 RPM
bodymap2_heart 0 .00 RPM 28 .93 RPM
bodymap2_kidney 0 .04 RPM 39 .05 RPM
bodymap2_liver 0 .04 RPM 24 .63 RPM
bodymap2_lung 0 .00 RPM 18 .16 RPM
bodymap2_lymph_node 0 .00 RPM 18 .07 RPM
bodymap2_ovary 0 .00 RPM 55 .17 RPM
bodymap2_prostate 0 .05 RPM 49 .03 RPM
bodymap2_skeletal_muscle 0 .00 RPM 14 .48 RPM
bodymap2_testis 0 .00 RPM 103 .52 RPM
bodymap2_thyroid 0 .06 RPM 67 .77 RPM
bodymap2_white_blood_cells 0 .00 RPM 30 .56 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3341 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3341 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3341 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3341 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3341 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2141
Pongo abelii retro_pabe_2753
Parental genes homology:
Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000130681 retrocopy
retro_chof_2523,
Erinaceus europaeus ENSEEUG000000039621 retrocopy
retro_eeur_409,
Homo sapiens ENSG00000154059 1 retrocopy
retro_hsap_3341 ,
Macaca mulatta ENSMMUG000000046641 retrocopy
retro_mmul_1041,
Nomascus leucogenys ENSNLEG000000065821 retrocopy
retro_nleu_1166,
Pongo abelii ENSPPYG000000090711 retrocopy
retro_pabe_2753,
Pan troglodytes ENSPTRG000000099271 retrocopy
retro_ptro_2141,
Sorex araneus ENSSARG000000028361 retrocopy
retro_sara_719,

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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