RetrogeneDB ID:

retro_hsap_1817

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:17:25678886..25679316(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000265683
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SYPL1
Ensembl ID:ENSG00000008282
Aliases:SYPL1, H-SP1, SYPL
Description:synaptophysin-like 1 [Source:HGNC Symbol;Acc:11507]


Retrocopy-Parental alignment summary:






>retro_hsap_1817
ATTACATTTGCAGTCTCTGTCTTCCTGTACTGCATTGCTGTCGTGCTTTATGTTGGTTACAGGAACCTATATCAGGGTAG
TCATAAACTTCCCATGATTGGCTTTGTCATTACTCTTGTTGCCATCTTTTGCGATTGGTGAGCACTTCAAAAGCTCGCTT
GGGCAAAAGCTCTTGCAGATATTAAAATAACTACTGGTCAAAATATTGTTCAGGAACTTCTGCTTGTAAGAAATCATAAT
AATGTGTTATTTTGGCTCTGTGACCAGCATGGGATTCCTAAATGTATCTGTGATCTTTGTCTTTCTGAATATGATACTTT
GGAGGGGAAATGCTTGGCGTGTGTACAAGTATGAGGAGACCAACTTACACAACCCATCAAATACTTATGCTCCTCATAGC
CAAGGAGGTATTCCACCTCCTGCTGGAATG

ORF - retro_hsap_1817 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.39 %
Parental protein coverage: 54.44 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVTFAVFVFLYCIAALLLYVGYTSLYLDSRKLPMIDFVVTLVATFL-W-LVSTSAWAKALTDIKIATGHNI
.TFAV.VFLYCIA...LYVGY..LY..S.KLPMI.FV.TLVA.F..W......AWAKAL.DIKI.TG.NI
RetrocopyITFAVSVFLYCIA-VVLYVGYRNLYQGSHKLPMIGFVITLVAIFCDW*ALQKLAWAKALADIKITTGQNI
ParentalIDEL-PPCKKK-AVLCYFGSVTSMGSLNVSVIFGFLNMILWGGNAWFVYK--ETSLHSPSNTSAPHSQGG
..EL...CKK.....CYFGSVTSMG.LNVSVIF.FLNMILW.GNAW.VYK..ET.LH.PSNT.APHSQGG
RetrocopyVQEL<SACKKS<IIMCYFGSVTSMGFLNVSVIFVFLNMILWRGNAWRVYKYEETNLHNPSNTYAPHSQGG
ParentalIPPPTGI
IPPP.G.
RetrocopyIPPPAGM

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 138 .61 RPM
bodymap2_adrenal 0 .00 RPM 169 .65 RPM
bodymap2_brain 0 .23 RPM 90 .36 RPM
bodymap2_breast 0 .00 RPM 133 .72 RPM
bodymap2_colon 0 .14 RPM 209 .27 RPM
bodymap2_heart 0 .00 RPM 109 .14 RPM
bodymap2_kidney 0 .06 RPM 207 .45 RPM
bodymap2_liver 0 .00 RPM 54 .37 RPM
bodymap2_lung 0 .14 RPM 165 .44 RPM
bodymap2_lymph_node 0 .00 RPM 139 .25 RPM
bodymap2_ovary 0 .02 RPM 164 .95 RPM
bodymap2_prostate 0 .00 RPM 247 .61 RPM
bodymap2_skeletal_muscle 0 .22 RPM 237 .50 RPM
bodymap2_testis 0 .11 RPM 187 .91 RPM
bodymap2_thyroid 0 .53 RPM 176 .79 RPM
bodymap2_white_blood_cells 0 .00 RPM 102 .42 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_1817 in 6 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CLM POLR2A 17:25680166..25680706
ENCFF002CMI POLR2A 17:25679859..25681025
ENCFF002CXN POLR2A 17:25679791..25680287
ENCFF002CXQ POLR2A 17:25679794..25680444
ENCFF002CXR POLR2A 17:25679800..25680236
ENCFF002DBE POLR2A 17:25680178..25680674

EST - click to see more details

No EST(s) were mapped for retro_hsap_1817 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1817 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1817 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1817 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1173
Macaca mulatta retro_mmul_1251
Parental genes homology:
Parental genes homology involve 20 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000161762 retrocopies
retro_cjac_1588, retro_cjac_2483,
Cavia porcellus ENSCPOG000000092211 retrocopy
retro_cpor_239,
Equus caballus ENSECAG000000096951 retrocopy
retro_ecab_340,
Homo sapiens ENSG00000008282 1 retrocopy
retro_hsap_1817 ,
Gorilla gorilla ENSGGOG000000064971 retrocopy
retro_ggor_1984,
Myotis lucifugus ENSMLUG000000149803 retrocopies
retro_mluc_1884, retro_mluc_2083, retro_mluc_449,
Macaca mulatta ENSMMUG000000195932 retrocopies
retro_mmul_1251, retro_mmul_1464,
Mus musculus ENSMUSG000000205701 retrocopy
retro_mmus_3470,
Nomascus leucogenys ENSNLEG000000088611 retrocopy
retro_nleu_2720,
Oryctolagus cuniculus ENSOCUG000000151273 retrocopies
retro_ocun_1000, retro_ocun_1569, retro_ocun_331,
Otolemur garnettii ENSOGAG000000080792 retrocopies
retro_ogar_1970, retro_ogar_2520,
Ochotona princeps ENSOPRG000000067552 retrocopies
retro_opri_210, retro_opri_448,
Pongo abelii ENSPPYG000000182921 retrocopy
retro_pabe_2370,
Pan troglodytes ENSPTRG000000195702 retrocopies
retro_ptro_1173, retro_ptro_1939,
Rattus norvegicus ENSRNOG000000098562 retrocopies
retro_rnor_2273, retro_rnor_2992,
Sorex araneus ENSSARG000000139351 retrocopy
retro_sara_450,
Ictidomys tridecemlineatus ENSSTOG000000208711 retrocopy
retro_itri_1243,
Tupaia belangeri ENSTBEG000000090952 retrocopies
retro_tbel_2025, retro_tbel_2566,
Tarsius syrichta ENSTSYG000000132962 retrocopies
retro_tsyr_1768, retro_tsyr_775,
Tursiops truncatus ENSTTRG000000028481 retrocopy
retro_ttru_661,

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 = 0.19 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .14 RPM
CEU_NA11930 0 .13 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .19 RPM
CEU_NA12873 0 .13 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .15 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .09 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .11 RPM
GBR_HG00114 0 .16 RPM
GBR_HG00119 0 .14 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .07 RPM
GBR_HG00134 0 .09 RPM
GBR_HG00137 0 .19 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .12 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .09 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .06 RPM
TSI_NA20771 0 .11 RPM
TSI_NA20786 0 .05 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .07 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .13 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .11 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .17 RPM
YRI_NA19213 0 .07 RPM
YRI_NA19214 0 .10 RPM
YRI_NA19223 0 .16 RPM

Indel association:

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





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