RetrogeneDB ID:

retro_hsap_3459

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:38555098..38556253(+)
Located in intron of:ENSG00000183826
Retrocopy
information
Ensembl ID:ENSG00000217227
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TFG
Ensembl ID:ENSG00000114354
Aliases:TFG, HMSNP, SPG57, TF6, TRKT3
Description:TRK-fused gene [Source:HGNC Symbol;Acc:11758]


Retrocopy-Parental alignment summary:






>retro_hsap_3459
ATGAACAGACAGTTGGACCTAAGTGGGAAGGTAATCATGAAAGCTCAACTTGGGGAGGATATTCCAAAAATTCCTATTCA
TAATGAAGATATTAATATTACTTATGATGAATTAGTGCTAATGATGCAACGAGTTTTCAGGGGAAAACTTCTGCGTAATG
TTGAAGTAACAATAAAGTATAAAGATGCAGATGACGATCTTATAACAATTTTTGATAGTTCTGATCTTTCCTTTGCAATT
CAGTGTAGTAGGACACTGAAATTGACATTATTTGTTAATGGCCAACGAAGACCCCTTGAATCAAGTCAGGTGAAATATCT
CTGTCGAGAACTGACAGAACTTTGAAATAAAGTGAATCACTTATTGGATAGCTTGGAACCACCTGGAAAACCAGGACCTT
CCACTAATATTCCTGAAAATGTTACTGTGAATGGTAGGGAAGAAAAGCCTGCTTCTTCGGATTCTTCTGGAAAACAGTCT
ACTCAGGTTATGGCAGCAAGTATGTCAGCTTTTGACCCTTTTAAAAAACCAAGATGAAATAAAAAATAATGTTACGTCGG
CATTTGGCTTAACAGATGATCAGGTTTCAGGGCAACCCAGTGCTCCTGCAGAAGACTGTTCAGGAACATCTGACAGCATT
GCCGCCTCCTCCTCAGTAGCAGCTCACCCACCAGGAGTTCAGCCACAGCAACCACCATATACAGAAGCTAAGATACAAGC
AGGTCAGACTGAAAGTCAGCTGTATCAATAGTACCAGCAACAGGCTAGCTATGGTGCACCGTGTCTGCGGGCTCTACCTC
AGCAGCCTCAACAGTATGGTATTCAGTATTCAAAAAGCCAGAGTCAGCAGACTGGACTCCAAACAACCTCAGCAGTTCCA
AGGATATGGCCAGCAACCAACTACCCAGGCACCAGCTCCTGCCTTTTTGGTCAGCCTCAACAACTGCCTGCTCAGCTGCC
ACACAGTACCAGGCAAGCAATTATCCTGCACAAATTTATACTACCCAAACTTTTCAGCCTACTAATTATACTGTGGCCCC
TGCCTCTCAACCTAGAATGGCTCCAAGCCAACCTGGGGCCTATAGACCAAGATCAAGTTTTACTTCACTTCCTGTAAGTA
GCATGACCCCTCCTCCAACTGGGCCTAATCCTTAT

ORF - retro_hsap_3459 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.55 %
Parental protein coverage: 95.25 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMNGQLDLSGKLIIKAQLGEDIRRIPIHNED--ITYDELVLMMQRVFRGKLLSNDEVTIKYKDEDGDLITI
MN.QLDLSGK.I.KAQLGEDI..IPIHNED..ITYDELVLMMQRVFRGKLL.N.EVTIKYKD.D.DLITI
RetrocopyMNRQLDLSGKVIMKAQLGEDIPKIPIHNEDINITYDELVLMMQRVFRGKLLRNVEVTIKYKDADDDLITI
ParentalFDSSDLSFAIQCSRILKLTLFVNGQPRPLESSQVKYLRRELIELRNKVNRLLDSLEPPGEPGPSTNIPEN
FDSSDLSFAIQCSR.LKLTLFVNGQ.RPLESSQVKYL.REL.EL.NKVN.LLDSLEPPG.PGPSTNIPEN
RetrocopyFDSSDLSFAIQCSRTLKLTLFVNGQRRPLESSQVKYLCRELTEL*NKVNHLLDSLEPPGKPGPSTNIPEN
ParentalDTVDGREEKSA-SDSSGKQSTQVMAASMSAFDP-LKNQDEINKNVMSAFGLTDDQVSGPPSAPAEDRSGT
.TV.GREEK.A.SDSSGKQSTQVMAASMSAFDP.LKNQDEI..NV.SAFGLTDDQVSG.PSAPAED.SGT
RetrocopyVTVNGREEKPASSDSSGKQSTQVMAASMSAFDP>LKNQDEIKNNVTSAFGLTDDQVSGQPSAPAEDCSGT
ParentalPDSIASSSS-AAHPPGVQPQQPPYTGAQTQAGQIEGQMYQQYQQQAGYGAQQPQAPPQQPQQYGIQYSAS
.DSIA.SSS.AAHPPGVQPQQPPYT.A..QAGQ.E.Q.YQ.YQQQA.YGA....A.PQQPQQYGIQYS.S
RetrocopySDSIAASSSVAAHPPGVQPQQPPYTEAKIQAGQTESQLYQ*YQQQASYGAPCLRALPQQPQQYGIQYSKS
ParentalYSQQTGPQ-QPQQFQGYGQQPTSQAPAPAF-SGQPQQLPAQPPQ-QYQASNYPAQTYTAQTSQPTNYTVA
.SQQTG.Q.QPQQFQGYGQQPT.QAPAPAF..GQPQQLPAQ.P..QYQASNYPAQ.YT.QT.QPTNYTVA
RetrocopyQSQQTGLQ>QPQQFQGYGQQPTTQAPAPAF<FGQPQQLPAQLPH<QYQASNYPAQIYTTQTFQPTNYTVA
ParentalPASQPGMAPSQPGAYQPRPGFTSLPGSTMTPPPSGPNPY
PASQP.MAPSQPGAY.PR..FTSLP.S.MTPPP.GPNPY
RetrocopyPASQPRMAPSQPGAYRPRSSFTSLPVSSMTPPPTGPNPY

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 57 .17 RPM
bodymap2_adrenal 0 .04 RPM 61 .65 RPM
bodymap2_brain 0 .02 RPM 56 .80 RPM
bodymap2_breast 0 .00 RPM 73 .44 RPM
bodymap2_colon 0 .00 RPM 74 .56 RPM
bodymap2_heart 0 .02 RPM 63 .93 RPM
bodymap2_kidney 0 .06 RPM 102 .53 RPM
bodymap2_liver 0 .00 RPM 85 .23 RPM
bodymap2_lung 0 .00 RPM 75 .30 RPM
bodymap2_lymph_node 0 .00 RPM 69 .39 RPM
bodymap2_ovary 0 .02 RPM 86 .01 RPM
bodymap2_prostate 0 .00 RPM 72 .97 RPM
bodymap2_skeletal_muscle 0 .00 RPM 74 .21 RPM
bodymap2_testis 0 .04 RPM 95 .45 RPM
bodymap2_thyroid 0 .02 RPM 79 .43 RPM
bodymap2_white_blood_cells 0 .00 RPM 47 .23 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3459 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3459 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3459 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3459 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3459 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2345
Pongo abelii retro_pabe_2860
Macaca mulatta retro_mmul_1760
Parental genes homology:
Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000139281 retrocopy
retro_chof_406,
Homo sapiens ENSG00000114354 1 retrocopy
retro_hsap_3459 ,
Macaca mulatta ENSMMUG000000028631 retrocopy
retro_mmul_1760,
Nomascus leucogenys ENSNLEG000000028491 retrocopy
retro_nleu_2712,
Ochotona princeps ENSOPRG000000007813 retrocopies
retro_opri_34, retro_opri_849, retro_opri_958,
Pongo abelii ENSPPYG000000135971 retrocopy
retro_pabe_2860,
Pan troglodytes ENSPTRG000000151651 retrocopy
retro_ptro_2345,
Pteropus vampyrus ENSPVAG000000173311 retrocopy
retro_pvam_1122,
Ictidomys tridecemlineatus ENSSTOG000000257791 retrocopy
retro_itri_457,

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 = 0.06 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 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .03 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 .06 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 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 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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