RetrogeneDB ID:

retro_hsap_1369

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:14:82383335..82384229(+)
Located in intron of:ENSG00000259035
Retrocopy
information
Ensembl ID:ENSG00000258501
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF3L
Ensembl ID:ENSG00000100129
Aliases:EIF3L, EIF3EIP, EIF3S11, EIF3S6IP, HSPC021, HSPC025, MSTP005
Description:eukaryotic translation initiation factor 3, subunit L [Source:HGNC Symbol;Acc:18138]


Retrocopy-Parental alignment summary:






>retro_hsap_1369
GAGATGCTTGGTTACTTCAGCCTTGTGGGGTTTCTCTGCCTGCAATCCCTGTTAGGAGATTAGTACCAGGCCATCAAGGT
GCTAGAGAACATCGAGCTGAACCAGAAGATCATGTATTCCTGTGTGTTAGAGTGCCAGGTCACCACATACTATTATCTTG
GGTTTGCGTATTTGATGATGCATTGCTACCAGGACGCCATCCAGGTCTTCACCAATATCCTCTTCTACATCCAGAGGACC
AAGAGCATGTTCCAGAGGACCACATGTAAGTATGAGATGATTAACAAGCAGAATGATCAGATGCATGCGCTGCTGGCCAT
TGCCCTCATGATGTACCCCATGCATATCGATGAGAGCATTCACCTCCAGCTGCAGGAGAAATATGGGGACAAGTTGCTGC
GCAAGCAGAAAGGTCACCCACAAGTCTATGAAGAACTTTTCAGTTACTCCTGCCCCAAGTTCCTGTCGCCTGTAGTGCCC
AGCTATGATAACGTGTACCCCAACTACCACAGAGAGCCCTTCCTGCAGCAGCTGGAGGTGTTTTCCGATGAAGCATGGCA
GCAGGCCCAGCTTTCAAGCATCTGCAGCTTCCTCAAGCTCTACACCACCATGCCTGTGGCCAAGCTTGCTGGCTCCCTGG
ACCTTACAGAACAGGAGTTCCGGATCCAGCTTCTGGTCTTCAAACACAAGATGAAGAACCTGGTGTGGACCAGCAGCATC
TCAGCCCTGGATGGTGAATTTTAATCGGTCTCAGTGGTTGACTTCTACATCGATAAGGACATGATCCACATCATAGACAC
CAAGGTCACCAAGCGCTATGGGGATATCTTCATCCATCAGATCCACAAATTTGAGGAGCTTAATCGAATCCTGAAGTAGA
TGGGACAGAGACCC

ORF - retro_hsap_1369 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.57 %
Parental protein coverage: 57.75 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKMLGYFSLVGLLRLHSLLGDYYQAIKVLENIELNKKSMYSRVPECQVTTYYYVGFAYLMMRRYQDAIRVF
.MLGYFSLVG.L.L.SLLGD.YQAIKVLENIELN.K.MYS.V.ECQVTTYYY.GFAYLMM..YQDAI.VF
RetrocopyEMLGYFSLVGFLCLQSLLGD*YQAIKVLENIELNQKIMYSCVLECQVTTYYYLGFAYLMMHCYQDAIQVF
ParentalANILLYIQRTKSMFQRTTYKYEMINKQNEQMHALLAIALTMYPMRIDESIHLQLREKYGDKMLRMQKGDP
.NIL.YIQRTKSMFQRTT.KYEMINKQN.QMHALLAIAL.MYPM.IDESIHLQL.EKYGDK.LR.QKG.P
RetrocopyTNILFYIQRTKSMFQRTTCKYEMINKQNDQMHALLAIALMMYPMHIDESIHLQLQEKYGDKLLRKQKGHP
ParentalQVYEELFSYSCPKFLSPVVPNYDNVHPNYHKEPFLQQLKVFSDEVQQQAQLSTIRSFLKLYTTMPVAKLA
QVYEELFSYSCPKFLSPVVP.YDNV.PNYH.EPFLQQL.VFSDE..QQAQLS.I.SFLKLYTTMPVAKLA
RetrocopyQVYEELFSYSCPKFLSPVVPSYDNVYPNYHREPFLQQLEVFSDEAWQQAQLSSICSFLKLYTTMPVAKLA
ParentalGFLDLTEQEFRIQLLVFKHKMKNLVWTSGISALDGEFQSASEVDFYIDKDMIHIADTKVARRYGDFFIRQ
G.LDLTEQEFRIQLLVFKHKMKNLVWTS.ISALDGEF.S.S.VDFYIDKDMIHI.DTKV..RYGD.FI.Q
RetrocopyGSLDLTEQEFRIQLLVFKHKMKNLVWTSSISALDGEF*SVSVVDFYIDKDMIHIIDTKVTKRYGDIFIHQ
ParentalIHKFEELNRTLKKMGQRP
IHKFEELNR.LK.MGQRP
RetrocopyIHKFEELNRILK*MGQRP

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 295 .88 RPM
bodymap2_adrenal 0 .00 RPM 258 .98 RPM
bodymap2_brain 0 .00 RPM 118 .26 RPM
bodymap2_breast 0 .00 RPM 239 .96 RPM
bodymap2_colon 0 .02 RPM 375 .04 RPM
bodymap2_heart 0 .00 RPM 154 .15 RPM
bodymap2_kidney 0 .00 RPM 164 .55 RPM
bodymap2_liver 0 .00 RPM 99 .41 RPM
bodymap2_lung 0 .02 RPM 263 .98 RPM
bodymap2_lymph_node 0 .00 RPM 329 .88 RPM
bodymap2_ovary 0 .00 RPM 613 .68 RPM
bodymap2_prostate 0 .00 RPM 569 .81 RPM
bodymap2_skeletal_muscle 0 .00 RPM 309 .07 RPM
bodymap2_testis 0 .00 RPM 285 .34 RPM
bodymap2_thyroid 0 .00 RPM 238 .52 RPM
bodymap2_white_blood_cells 0 .02 RPM 539 .23 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1369 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1369 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1369 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1369 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1369 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 4 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000058852 retrocopies
retro_cpor_1288, retro_cpor_410,
Homo sapiens ENSG00000100129 1 retrocopy
retro_hsap_1369 ,
Monodelphis domestica ENSMODG000000190683 retrocopies
retro_mdom_1247, retro_mdom_1585, retro_mdom_432,
Otolemur garnettii ENSOGAG000000294441 retrocopy
retro_ogar_1635,

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 = 0.03 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 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 .02 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 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 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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