RetrogeneDB ID:

retro_hsap_4199

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:99717295..99717740(+)
Located in intron of:ENSG00000196312
Retrocopy
information
Ensembl ID:ENSG00000236745
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:YRDC
Ensembl ID:ENSG00000196449
Aliases:YRDC, DRIP3, IRIP, SUA5
Description:yrdC domain containing (E. coli) [Source:HGNC Symbol;Acc:28905]


Retrocopy-Parental alignment summary:






>retro_hsap_4199
TGTATGAGAGTAGTACCCCAGGAGCTCCTCAAAGACCTAGTGCCAGGACGAGTGTCCCTGGTGATGGAACGTTCAGAGGA
GCTCAACAACGACCTAAACCCCTTTACTCCTCTTACAAGGTATCCGGATTCCTGATTATGCCTTTATGCAAGACTTGGCC
AAGATGTATGAGCATCCTCTTGCTCTCACTAGTGCCAACCTCAGCTCCCAGGACAGTTCTCTGAATGCCATGGAGTTATA
AGACCTCTGGCCTCAGTTGTCCTTGGTCATTGATGGGGGACAAGCTAGGGATAGCCAGATCCCTGAGTGTTACCTTGGCT
CAACTGTGGTTGACTTATCTGTGCATAGAAAGTTTGGCATCATTCGTCCAGGCTGTGTCCTGGAAAGTACTACAGCCTTT
CTTCAACAGAGGTATGGGTTGCACCCCTCATGTGCATCCTACTTG

ORF - retro_hsap_4199 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.52 %
Parental protein coverage: 53.05 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalCRVRVPEGLLKDLLPGPVTLVMERSEELNKDLNPFTPLV-GIRIPDHAFMQDLAQMFEGPLALTSANLSS
C...VP..LLKDL.PG.V.LVMERSEELN.DLNPFTPL..GIRIPD.AFMQDLA.M.E.PLALTSANLSS
RetrocopyCMRVVPQELLKDLVPGRVSLVMERSEELNNDLNPFTPLT>GIRIPDYAFMQDLAKMYEHPLALTSANLSS
ParentalQASSLNVEEFQDLWPQLSLVIDGGQIGDGQSPECRLGSTVVDLSVPGKFGIIRPGCALESTTAILQQKYG
Q.SSLN..E..DLWPQLSLVIDGGQ..D.Q.PEC.LGSTVVDLSV..KFGIIRPGC.LESTTA.LQQ.YG
RetrocopyQDSSLNAMEL*DLWPQLSLVIDGGQARDSQIPECYLGSTVVDLSVHRKFGIIRPGCVLESTTAFLQQRYG
ParentalLLPSHASYL
L.PS.ASYL
RetrocopyLHPSCASYL

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 .10 RPM 6 .20 RPM
bodymap2_adrenal 0 .20 RPM 14 .92 RPM
bodymap2_brain 0 .02 RPM 11 .86 RPM
bodymap2_breast 0 .06 RPM 7 .20 RPM
bodymap2_colon 0 .00 RPM 4 .97 RPM
bodymap2_heart 0 .00 RPM 4 .01 RPM
bodymap2_kidney 0 .00 RPM 12 .88 RPM
bodymap2_liver 0 .04 RPM 12 .19 RPM
bodymap2_lung 0 .00 RPM 13 .94 RPM
bodymap2_lymph_node 0 .00 RPM 10 .98 RPM
bodymap2_ovary 0 .00 RPM 5 .59 RPM
bodymap2_prostate 0 .00 RPM 10 .36 RPM
bodymap2_skeletal_muscle 0 .00 RPM 3 .98 RPM
bodymap2_testis 0 .00 RPM 22 .76 RPM
bodymap2_thyroid 0 .00 RPM 8 .53 RPM
bodymap2_white_blood_cells 0 .00 RPM 11 .03 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4199 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4199 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4199 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4199 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4199 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 16 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000011731 retrocopy
retro_amel_350,
Dasypus novemcinctus ENSDNOG000000091112 retrocopies
retro_dnov_1774, retro_dnov_2232,
Equus caballus ENSECAG000000225221 retrocopy
retro_ecab_534,
Felis catus ENSFCAG000000110181 retrocopy
retro_fcat_375,
Homo sapiens ENSG00000196449 2 retrocopies
retro_hsap_4199 , retro_hsap_4289,
Gorilla gorilla ENSGGOG000000076191 retrocopy
retro_ggor_2866,
Macropus eugenii ENSMEUG000000050681 retrocopy
retro_meug_452,
Microcebus murinus ENSMICG000000119531 retrocopy
retro_mmur_188,
Myotis lucifugus ENSMLUG000000009551 retrocopy
retro_mluc_367,
Macaca mulatta ENSMMUG000000053722 retrocopies
retro_mmul_1206, retro_mmul_1662,
Nomascus leucogenys ENSNLEG000000116652 retrocopies
retro_nleu_1045, retro_nleu_1046,
Otolemur garnettii ENSOGAG000000304742 retrocopies
retro_ogar_1107, retro_ogar_2342,
Pongo abelii ENSPPYG000000015231 retrocopy
retro_pabe_3495,
Pan troglodytes ENSPTRG000000005574 retrocopies
retro_ptro_2850, retro_ptro_2906, retro_ptro_2907, retro_ptro_2999,
Tupaia belangeri ENSTBEG000000088631 retrocopy
retro_tbel_1817,
Tarsius syrichta ENSTSYG000000055553 retrocopies
retro_tsyr_1108, retro_tsyr_1420, retro_tsyr_874,

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 = 0.1 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 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 .05 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 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 .02 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .10 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 .03 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 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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