RetrogeneDB ID:

retro_hsap_4189

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:90356385..90356865(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000237747
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF3J
Ensembl ID:ENSG00000104131
Aliases:EIF3J, EIF3S1, eIF3-alpha, eIF3-p35
Description:eukaryotic translation initiation factor 3, subunit J [Source:HGNC Symbol;Acc:3270]


Retrocopy-Parental alignment summary:






>retro_hsap_4189
AAAAAGGGGTTAGAAGAACCTGAAGAACTCCAGCTGCTAACACCAGAGGAACAATTAGCAGATAAACCGCAGCTGGAGAA
ATCACAGGAAGAGTCAGACATGGAATTAGCAAAGGCAACTTTTGGTGTTAAGACTACTGTATATGGATCGGATGCTGTAA
ACCCATCTTCAAGGGATGACCTTACAGAGTTTGGAAAGTTACTAAAAGATAAAATTACACAAAATAAAAAGTCACTATAT
TATGCCAGTTTTTTGGAAGTCTTAGTTGGAGATGTGTGTATGTCATTGGAAACTGATGACTTGAAAAAGGTTCTCAATAC
ATTGTGCTTTGAAGTGAAAAACAGAAGCAAGCAAAGCCAAGCCAAAAAGAAGAACAAAGGTATGGTTCCTGGAGGGAGAT
TAAAAGCCACCATGACAAATGATCTGGTAAATTATGGTGGTGATGATGCAGGGTATGCACAAGACTATGAAAATGTCATG

ORF - retro_hsap_4189 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.78 %
Parental protein coverage: 63.18 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKKRLEEPEEPKVLTPEEQLADKLRLKKLQEESDLELAKETFGVNNAVYGIDAMNPSSRDDFTEFGKLLKD
KK.LEEPEE...LTPEEQLADK..L.K.QEESD.ELAK.TFGV...VYG.DA.NPSSRDD.TEFGKLLKD
RetrocopyKKGLEEPEELQLLTPEEQLADKPQLEKSQEESDMELAKATFGVKTTVYGSDAVNPSSRDDLTEFGKLLKD
ParentalKITQYEKSLYYASFLEVLVRDVCISLEIDDLKKITNSLTVLCSEKQKQEKQSKAKKKKKGVVPGGGLKAT
KITQ..KSLYYASFLEVLV.DVC.SLE.DDLKK..N.L...C.E.....KQS.AKKK.KG.VPGG.LKAT
RetrocopyKITQNKKSLYYASFLEVLVGDVCMSLETDDLKKVLNTL---CFEVKNRSKQSQAKKKNKGMVPGGRLKAT
ParentalMKDDLADYGGYDGGYVQDYEDFM
M..DL..YGG.D.GY.QDYE..M
RetrocopyMTNDLVNYGGDDAGYAQDYENVM

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 64 .36 RPM
bodymap2_adrenal 0 .00 RPM 52 .38 RPM
bodymap2_brain 0 .00 RPM 75 .06 RPM
bodymap2_breast 0 .00 RPM 68 .52 RPM
bodymap2_colon 0 .00 RPM 95 .06 RPM
bodymap2_heart 0 .00 RPM 61 .25 RPM
bodymap2_kidney 0 .00 RPM 92 .86 RPM
bodymap2_liver 0 .00 RPM 73 .17 RPM
bodymap2_lung 0 .00 RPM 65 .21 RPM
bodymap2_lymph_node 0 .00 RPM 59 .97 RPM
bodymap2_ovary 0 .02 RPM 73 .97 RPM
bodymap2_prostate 0 .00 RPM 77 .11 RPM
bodymap2_skeletal_muscle 0 .00 RPM 122 .15 RPM
bodymap2_testis 0 .00 RPM 95 .08 RPM
bodymap2_thyroid 0 .00 RPM 91 .18 RPM
bodymap2_white_blood_cells 0 .00 RPM 62 .88 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4189 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4189 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4189 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4189 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4189 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_41
Pongo abelii retro_pabe_3429
Parental genes homology:
Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000024121 retrocopy
retro_cjac_589,
Equus caballus ENSECAG000000087161 retrocopy
retro_ecab_635,
Homo sapiens ENSG00000104131 1 retrocopy
retro_hsap_4189 ,
Gorilla gorilla ENSGGOG000000005482 retrocopies
retro_ggor_1687, retro_ggor_41,
Macropus eugenii ENSMEUG000000103721 retrocopy
retro_meug_256,
Microcebus murinus ENSMICG000000050061 retrocopy
retro_mmur_100,
Monodelphis domestica ENSMODG000000176961 retrocopy
retro_mdom_141,
Mus musculus ENSMUSG000000272361 retrocopy
retro_mmus_18,
Nomascus leucogenys ENSNLEG000000055681 retrocopy
retro_nleu_2848,
Otolemur garnettii ENSOGAG000000046941 retrocopy
retro_ogar_1227,

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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