RetrogeneDB ID:

retro_hsap_476

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:174336243..174336827(-)
Located in intron of:ENSG00000152061
Retrocopy
information
Ensembl ID:ENSG00000237317
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:FYTTD1
Ensembl ID:ENSG00000122068
Aliases:None
Description:forty-two-three domain containing 1 [Source:HGNC Symbol;Acc:25407]


Retrocopy-Parental alignment summary:






>retro_hsap_476
CCACGTCTAAGTGACAAGAATACAGAACACTATTTTCCAGTGTTAAAAAGAAAGGCAAGCCTTCTGAAACAAAATGAAGT
GCATAGGAAACCAGTTGCAGTTCTCAAGAGACCTAACCAGCTAAACAGAAAAAATAACATTATGTCCAGTTTTACCAGGA
GAGGAAATAAATTAAGCCATCAGAAAGACACTTCACAGGTAACTTTTCTTTTCGGAAGAGGCCTGAAGAAGGTTCAGGCC
CAGTTGAACACGGAACAACTGCTAGATGTAGTAGCAAAGAGAACTAGTCAATGCCAGACATCTATCACAAACGCAGGAAT
CTGACTGTATCTATTGATAACCCTGGAGCAGTACAATGCCCAGCAACTGAGAAACCATGATTAATTCATACTGCTATACC
TTCATTCTTTAAAACACGGCAGCAAGAGAATGTAAAGAAAGTTCCAACGGGTGTTCCCCTACAATTTGACATAAATAGTG
TTGGAAAACAGACAGAGATGGCTTTGAATGAGCACTTTGGGATCCTGAGAAAACAAACAGCCACTCTCACATATAACAAA
GGAGGAAGTCACTTTTTAACTGTG

ORF - retro_hsap_476 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.65 %
Parental protein coverage: 85.9 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPPLSDKNIEQYFPVLKRKANLLRQNEGQRKPVAVLKRPSQLSRKNNIPANFTRSGNKLNHQKDTRQATFL
P.LSDKN.E.YFPVLKRKA.LL.QNE..RKPVAVLKRP.QL.RKNNI...FTR.GNKL.HQKDT.Q.TFL
RetrocopyPRLSDKNTEHYFPVLKRKASLLKQNEVHRKPVAVLKRPNQLNRKNNIMSSFTRRGNKLSHQKDTSQVTFL
ParentalFRRGL-KVQAQLNTEQLLDDVVAKRTRQWRTSTTNGGI-LTVSIDNPGAVQCPVTQKPRLTRTAVPSFLT
F.RGL.KVQAQLNTEQLL.DVVAKRT.Q..TS.TN.GI.LTVSIDNPGAVQCP.T.KP.L..TA.PSF..
RetrocopyFGRGLKKVQAQLNTEQLL-DVVAKRTSQCQTSITNAGI<LTVSIDNPGAVQCPATEKP*LIHTAIPSFFK
ParentalKREQSDVKKVPKGVPLQFDINSVGKQTGMTLNERFGILKEQRATLTYNKGGSRFVTV
.R.Q..VKKVP.GVPLQFDINSVGKQT.M.LNE.FGIL..Q.ATLTYNKGGS.F.TV
RetrocopyTRQQENVKKVPTGVPLQFDINSVGKQTEMALNEHFGILRKQTATLTYNKGGSHFLTV

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 .06 RPM 118 .87 RPM
bodymap2_adrenal 0 .10 RPM 100 .08 RPM
bodymap2_brain 0 .00 RPM 81 .83 RPM
bodymap2_breast 0 .00 RPM 124 .59 RPM
bodymap2_colon 0 .00 RPM 156 .04 RPM
bodymap2_heart 0 .02 RPM 110 .53 RPM
bodymap2_kidney 0 .27 RPM 96 .95 RPM
bodymap2_liver 0 .00 RPM 43 .58 RPM
bodymap2_lung 0 .00 RPM 146 .08 RPM
bodymap2_lymph_node 0 .00 RPM 112 .60 RPM
bodymap2_ovary 0 .00 RPM 151 .23 RPM
bodymap2_prostate 0 .09 RPM 128 .84 RPM
bodymap2_skeletal_muscle 0 .00 RPM 199 .61 RPM
bodymap2_testis 0 .02 RPM 200 .11 RPM
bodymap2_thyroid 0 .00 RPM 187 .09 RPM
bodymap2_white_blood_cells 0 .00 RPM 119 .09 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_476 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_476 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_476 retrocopy 5' end.

Lab - click to see more details

retro_hsap_476 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_476 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_357
Gorilla gorilla retro_ggor_450
Pongo abelii retro_pabe_258
Macaca mulatta retro_mmul_577
Callithrix jacchus retro_cjac_1639
Parental genes homology:
Parental genes homology involve 17 parental genes, and 31 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000148741 retrocopy
retro_btau_1572,
Canis familiaris ENSCAFG000000296951 retrocopy
retro_cfam_70,
Choloepus hoffmanni ENSCHOG000000028812 retrocopies
retro_chof_1068, retro_chof_114,
Callithrix jacchus ENSCJAG000000164882 retrocopies
retro_cjac_1639, retro_cjac_623,
Cavia porcellus ENSCPOG000000114632 retrocopies
retro_cpor_1039, retro_cpor_586,
Dasypus novemcinctus ENSDNOG000000078076 retrocopies
retro_dnov_1010, retro_dnov_1224, retro_dnov_1311, retro_dnov_2013, retro_dnov_442, retro_dnov_570,
Erinaceus europaeus ENSEEUG000000014331 retrocopy
retro_eeur_13,
Echinops telfairi ENSETEG000000007001 retrocopy
retro_etel_765,
Homo sapiens ENSG00000122068 2 retrocopies
retro_hsap_4291, retro_hsap_476 ,
Gorilla gorilla ENSGGOG000000116651 retrocopy
retro_ggor_450,
Macaca mulatta ENSMMUG000000066261 retrocopy
retro_mmul_577,
Nomascus leucogenys ENSNLEG000000155472 retrocopies
retro_nleu_1047, retro_nleu_889,
Pongo abelii ENSPPYG000000144562 retrocopies
retro_pabe_258, retro_pabe_3497,
Pan troglodytes ENSPTRG000000157961 retrocopy
retro_ptro_357,
Sorex araneus ENSSARG000000099961 retrocopy
retro_sara_148,
Sarcophilus harrisii ENSSHAG000000057041 retrocopy
retro_shar_242,
Tupaia belangeri ENSTBEG000000055954 retrocopies
retro_tbel_2469, retro_tbel_2943, retro_tbel_4257, retro_tbel_791,

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 = 0.14 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .14 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .02 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 .07 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .07 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 .02 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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



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