RetrogeneDB ID:

retro_hsap_2106

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:58478565..58479657(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000233426
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:EIF3F
Ensembl ID:ENSG00000175390
Aliases:EIF3F, EIF3S5, eIF3-p47
Description:eukaryotic translation initiation factor 3, subunit F [Source:HGNC Symbol;Acc:3275]


Retrocopy-Parental alignment summary:






>retro_hsap_2106
CTCGACAAGATGGCCACACCGGCGGTACCAGCAAGTGCTCCTCCGGCCACGCCAGCCCCAGTCCCGGCGGCGGTCCCAGC
CTCTGCCCCAGCCTCAGTTCCAGCGCCAACGCCAGCACCGGCTGCGGCTCCGGTTCCCGCTGCGGCTCCAGCCTCATCCT
CAGACCCTGCGGCAGCATCGGCTACAACTGCGGCTCCTGGCCAGACCCCGGCCTCAGCGCAAGCTCCAGCGCAGACCCCA
GCGCCCGCTCTGCCTGGTCCTGCTCTTCCAGGGCCCTTCCCCGGCGGCCGCGTGGTCAGGCTGCACCCAGTCATTTTGGC
CTCCATTGTGGACAGCTACGAGAGACGCAACGAGGGTGCTGCCCGAGTTATCGGGACCCTGTTGGGAACTGTCGACAAAC
ACTCAGTGGAGGTCACCAATTGCTTTTCAGTGCCGCACAATGAGTCAGAAGATGAAGTGGCTGTTGACATGGAATTTGCT
AAGAATATGTATGAACTGCATAAAAAAGTTTCTCCAAATGAGCTCATCCTGGGCTGGTACGCTACAGGCCATGACATCAC
AGAGCACTCTGTGCTGATCCATGAGTACTACAGCCGAGAGGCCCCCAACCCCATCCACCTCACTGTGGACACAAGTCTCC
AGAACGGCCGCATGAGCATCAAAGCCTATGTCAGCACTTTAATGGGTGTCCCTGGGAGGACCATGGGAGTGATGTTCACA
CCTCTGACAGTGAAATACGCATACTATGACACTGAACGCATCGGAGTTGAGCTGATCATGAAGACCTGCTTTAGCCCCAA
CAGAGTGATTGGACTCTTAAGTGACTTGCAGCAAGTAGGAGGGGCATCAGCTCGCATCCAGGATGCCCTGAGTACAGTGT
TGCAATATGCAGAGGATGTACTGTCTGGAAAGGTGTCAGCTGACAATACTGTGGGCCGCTTCCTGATGAGCCTGGTTAAC
CGAGTACCGAAAATAGTTCCCGATGACTTTGAGACCATGCTCAACAGCAACATCAATGACCTTTTGATGGTGACCTACCT
GGCCAACCTCACACAGTCACAGATTGCCCTCAATGAAAAACTTGTAAACCTG

ORF - retro_hsap_2106 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.7 %
Parental protein coverage: 96.77 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLDKMATPAVPVSAPPATPTP----VPAAAPASVPAPTPAPAAAPVPAAAPASSSDPAAAAAATAAPGQTP
LDKMATPAVP.SAPPATP.P....VPA.APASVPAPTPAPAAAPVPAAAPASSSDPAAA.A.TAAPGQTP
RetrocopyLDKMATPAVPASAPPATPAPVPAAVPASAPASVPAPTPAPAAAPVPAAAPASSSDPAAASATTAAPGQTP
ParentalASAQAPAQTPAPALPGPALPGPFPGGRVVRLHPVILASIVDSYERRNEGAARVIGTLLGTVDKHSVEVTN
ASAQAPAQTPAPALPGPALPGPFPGGRVVRLHPVILASIVDSYERRNEGAARVIGTLLGTVDKHSVEVTN
RetrocopyASAQAPAQTPAPALPGPALPGPFPGGRVVRLHPVILASIVDSYERRNEGAARVIGTLLGTVDKHSVEVTN
ParentalCFSVPHNESEDEVAVDMEFAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVD
CFSVPHNESEDEVAVDMEFAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVD
RetrocopyCFSVPHNESEDEVAVDMEFAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVD
ParentalTSLQNGRMSIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGVDLIMKTCFSPNRVIGLSSDLQQVG
TSLQNGRMSIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGV.LIMKTCFSPNRVIGL.SDLQQVG
RetrocopyTSLQNGRMSIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGVELIMKTCFSPNRVIGLLSDLQQVG
ParentalGASARIQDALSTVLQYAEDVLSGKVSADNTVGRFLMSLVNQVPKIVPDDFETMLNSNINDLLMVTYLANL
GASARIQDALSTVLQYAEDVLSGKVSADNTVGRFLMSLVN.VPKIVPDDFETMLNSNINDLLMVTYLANL
RetrocopyGASARIQDALSTVLQYAEDVLSGKVSADNTVGRFLMSLVNRVPKIVPDDFETMLNSNINDLLMVTYLANL
ParentalTQSQIALNEKLVNL
TQSQIALNEKLVNL
RetrocopyTQSQIALNEKLVNL

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 5 .05 RPM 123 .58 RPM
bodymap2_adrenal 0 .61 RPM 167 .34 RPM
bodymap2_brain 2 .27 RPM 61 .18 RPM
bodymap2_breast 1 .28 RPM 98 .97 RPM
bodymap2_colon 5 .63 RPM 168 .38 RPM
bodymap2_heart 0 .15 RPM 74 .14 RPM
bodymap2_kidney 2 .01 RPM 83 .03 RPM
bodymap2_liver 0 .63 RPM 43 .79 RPM
bodymap2_lung 1 .05 RPM 104 .24 RPM
bodymap2_lymph_node 2 .03 RPM 130 .82 RPM
bodymap2_ovary 2 .83 RPM 198 .17 RPM
bodymap2_prostate 3 .48 RPM 207 .30 RPM
bodymap2_skeletal_muscle 1 .93 RPM 135 .19 RPM
bodymap2_testis 3 .47 RPM 138 .80 RPM
bodymap2_thyroid 0 .96 RPM 107 .73 RPM
bodymap2_white_blood_cells 2 .38 RPM 225 .27 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2106 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2106 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2106 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2106 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2106 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000048611 retrocopy
retro_btau_527,
Callithrix jacchus ENSCJAG000000119031 retrocopy
retro_cjac_1416,
Echinops telfairi ENSETEG000000027172 retrocopies
retro_etel_1583, retro_etel_35,
Homo sapiens ENSG000001030352 retrocopies
retro_hsap_1781, retro_hsap_234,
Homo sapiens ENSG00000175390 3 retrocopies
retro_hsap_2106 , retro_hsap_2512, retro_hsap_4321,
Gorilla gorilla ENSGGOG000000117025 retrocopies
retro_ggor_1566, retro_ggor_1567, retro_ggor_1568, retro_ggor_1589, retro_ggor_1590,
Myotis lucifugus ENSMLUG000000008251 retrocopy
retro_mluc_2356,
Otolemur garnettii ENSOGAG000000032203 retrocopies
retro_ogar_3041, retro_ogar_859, retro_ogar_863,
Pan troglodytes ENSPTRG000000033261 retrocopy
retro_ptro_197,

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 = 3.59 RPM Legend:


Library Retrogene expression
CEU_NA11831 1 .73 RPM
CEU_NA11843 1 .31 RPM
CEU_NA11930 3 .23 RPM
CEU_NA12004 2 .96 RPM
CEU_NA12400 1 .96 RPM
CEU_NA12751 2 .19 RPM
CEU_NA12760 3 .59 RPM
CEU_NA12827 2 .88 RPM
CEU_NA12872 1 .66 RPM
CEU_NA12873 2 .42 RPM
FIN_HG00183 2 .47 RPM
FIN_HG00277 1 .85 RPM
FIN_HG00315 1 .88 RPM
FIN_HG00321 1 .24 RPM
FIN_HG00328 0 .80 RPM
FIN_HG00338 2 .38 RPM
FIN_HG00349 2 .99 RPM
FIN_HG00375 2 .15 RPM
FIN_HG00377 2 .19 RPM
FIN_HG00378 2 .04 RPM
GBR_HG00099 1 .34 RPM
GBR_HG00111 1 .78 RPM
GBR_HG00114 1 .60 RPM
GBR_HG00119 1 .72 RPM
GBR_HG00131 1 .98 RPM
GBR_HG00133 1 .25 RPM
GBR_HG00134 1 .97 RPM
GBR_HG00137 2 .01 RPM
GBR_HG00142 2 .86 RPM
GBR_HG00143 1 .47 RPM
TSI_NA20512 2 .29 RPM
TSI_NA20513 2 .03 RPM
TSI_NA20518 2 .89 RPM
TSI_NA20532 1 .90 RPM
TSI_NA20538 2 .12 RPM
TSI_NA20756 2 .10 RPM
TSI_NA20765 1 .16 RPM
TSI_NA20771 2 .13 RPM
TSI_NA20786 2 .67 RPM
TSI_NA20798 2 .56 RPM
YRI_NA18870 3 .38 RPM
YRI_NA18907 1 .39 RPM
YRI_NA18916 1 .12 RPM
YRI_NA19093 1 .09 RPM
YRI_NA19099 1 .36 RPM
YRI_NA19114 2 .04 RPM
YRI_NA19118 1 .97 RPM
YRI_NA19213 1 .46 RPM
YRI_NA19214 0 .66 RPM
YRI_NA19223 0 .52 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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