RetrogeneDB ID:

retro_hsap_215

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:146059942..146060341(+)
Located in intron of:ENSG00000232637
Retrocopy
information
Ensembl ID:ENSG00000227216
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PFN1
Ensembl ID:ENSG00000108518
Aliases:PFN1, ALS18
Description:profilin 1 [Source:HGNC Symbol;Acc:8881]


Retrocopy-Parental alignment summary:






>retro_hsap_215
ATCTACAGCCTCGTGGCGGACGGGACCTGTTAGGACACGGCCATTGTGGGCAACAAGGACCCACCTTCCATCTGTGCCAC
CGTCCCAGGGAAAACCTTCCTCAACATCACGCCAGCTGAGGTTGGTGTCCTGGTTGGCAAAGACTGGTCAAGCTTTGTCA
TGAATGGGCTGACACTGGGGGGCCAGAAATATACTGTGGTCCTGGACTCACTGCTGCAGGATGGGGAATTGACCACGGAT
CTTTGTATGAAGAGCATCGGTGGAGCCCCCACCTTCAACGTCATTGTCACCATGACTGCCAAGACGCTAGGCCTGCTGAT
GGGCAAAGAAGGTATCCATGGCAATTTCATCAACAAGTAATGTTATGAAATGGCCTCCCACCTTCAGCGTTCCCAGTAC

ORF - retro_hsap_215 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.19 %
Parental protein coverage: 95. %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalIDNLMADGTCQDAAIVGYKDSPSVWAAVPGKTFVNITPAEVGVLVGKDRSSFYVNGLTLGGQKCSVIRDS
I..L.ADGTC.D.AIVG.KD.PS..A.VPGKTF.NITPAEVGVLVGKD.SSF..NGLTLGGQK..V..DS
RetrocopyIYSLVADGTC*DTAIVGNKDPPSICATVPGKTFLNITPAEVGVLVGKDWSSFVMNGLTLGGQKYTVVLDS
ParentalLLQDGEFSMDLRTKSTGGAPTFNVTVTKTDKTLVLLMGKEGVHGGLINKKCYEMASHLRRSQY
LLQDGE...DL..KS.GGAPTFNV.VT.T.KTL.LLMGKEG.HG..INK.CYEMASHL.RSQY
RetrocopyLLQDGELTTDLCMKSIGGAPTFNVIVTMTAKTLGLLMGKEGIHGNFINK*CYEMASHLQRSQY

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 337 .55 RPM
bodymap2_adrenal 0 .00 RPM 548 .44 RPM
bodymap2_brain 0 .00 RPM 78 .20 RPM
bodymap2_breast 0 .00 RPM 232 .32 RPM
bodymap2_colon 0 .00 RPM 381 .67 RPM
bodymap2_heart 0 .00 RPM 82 .54 RPM
bodymap2_kidney 0 .00 RPM 230 .30 RPM
bodymap2_liver 0 .00 RPM 224 .00 RPM
bodymap2_lung 0 .00 RPM 363 .01 RPM
bodymap2_lymph_node 0 .00 RPM 391 .06 RPM
bodymap2_ovary 0 .00 RPM 213 .76 RPM
bodymap2_prostate 0 .00 RPM 385 .65 RPM
bodymap2_skeletal_muscle 0 .00 RPM 163 .65 RPM
bodymap2_testis 0 .04 RPM 200 .07 RPM
bodymap2_thyroid 0 .00 RPM 167 .90 RPM
bodymap2_white_blood_cells 0 .00 RPM 932 .91 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_215 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_215 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_215 retrocopy 5' end.

Lab - click to see more details

retro_hsap_215 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_215 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 19 parental genes, and 51 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000061932 retrocopies
retro_amel_1712, retro_amel_1781,
Bos taurus ENSBTAG000000049151 retrocopy
retro_btau_141,
Callithrix jacchus ENSCJAG000000117192 retrocopies
retro_cjac_1023, retro_cjac_1641,
Cavia porcellus ENSCPOG000000131361 retrocopy
retro_cpor_1216,
Equus caballus ENSECAG000000211163 retrocopies
retro_ecab_171, retro_ecab_28, retro_ecab_559,
Homo sapiens ENSG00000108518 10 retrocopies
retro_hsap_214, retro_hsap_215 , retro_hsap_221, retro_hsap_223, retro_hsap_224, retro_hsap_352, retro_hsap_446, retro_hsap_447, retro_hsap_450, retro_hsap_451,
Gorilla gorilla ENSGGOG000000223943 retrocopies
retro_ggor_285, retro_ggor_289, retro_ggor_366,
Macaca mulatta ENSMMUG000000027725 retrocopies
retro_mmul_407, retro_mmul_527, retro_mmul_528, retro_mmul_574, retro_mmul_732,
Mus musculus ENSMUSG000000182931 retrocopy
retro_mmus_1326,
Nomascus leucogenys ENSNLEG000000174466 retrocopies
retro_nleu_16, retro_nleu_1870, retro_nleu_2425, retro_nleu_2429, retro_nleu_848, retro_nleu_886,
Otolemur garnettii ENSOGAG000000313953 retrocopies
retro_ogar_1680, retro_ogar_2143, retro_ogar_3351,
Procavia capensis ENSPCAG000000002911 retrocopy
retro_pcap_27,
Pelodiscus sinensis ENSPSIG000000041241 retrocopy
retro_psin_8,
Pan troglodytes ENSPTRG000000086165 retrocopies
retro_ptro_185, retro_ptro_196, retro_ptro_276, retro_ptro_332, retro_ptro_333,
Rattus norvegicus ENSRNOG000000039751 retrocopy
retro_rnor_1623,
Sus scrofa ENSSSCG000000179051 retrocopy
retro_sscr_275,
Ictidomys tridecemlineatus ENSSTOG000000289501 retrocopy
retro_itri_129,
Tursiops truncatus ENSTTRG000000012991 retrocopy
retro_ttru_14,
Vicugna pacos ENSVPAG000000053273 retrocopies
retro_vpac_389, retro_vpac_395, retro_vpac_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 = 0.05 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 .05 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .04 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 .00 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 .02 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 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .03 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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