RetrogeneDB ID:

retro_hsap_645

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:10818181..10818530(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000228997
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ORMDL1
Ensembl ID:ENSG00000128699
Aliases:None
Description:ORM1-like 1 (S. cerevisiae) [Source:HGNC Symbol;Acc:16036]


Retrocopy-Parental alignment summary:






>retro_hsap_645
GTCTTACTCAGCATTCCTTCTTCCGTGTTCTCATTGCTTAGATCTTGACAAATATTATACATAATCTGGGGATGAATGAA
TTTTTCCATGCTTGAAAGGAACACCTTTGGAAACCCCTGACCAGGGTAAAGCAAGGATCCCAACGCACTGCGAACAGCTG
GGTGACGGAGTACCGTTTACATCTTCACAGAAGTTTTTCACCATTTCTCCAATCATTCTGTGTTTTCCAGCAAGTTTCTA
TAGAAGTATGCTCCAACTCACTCCGTCGTAAGCACGGCTTCTCTCCTGAGTATGCTAAACTCCCCAAACGCAGCAACAAC
ACAGCGTTCCGATCTTTGGAATTAATAAG

ORF - retro_hsap_645 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.42 %
Parental protein coverage: 76.47 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalVLLSIP-FFSVPVAWTLTNIIHNLGMYVFLHA-VKGTPFETPDQGKARLLTHWEQLDYGVQFTSSRKFFT
VLLSIP.FF.V..A..LTNIIHNLGM..F.HA..KGTP.ETPDQGKAR..TH.EQL..GV.FTSS.KFFT
RetrocopyVLLSIP<FFRVLIA*ILTNIIHNLGMNEFFHA<LKGTPLETPDQGKARIPTHCEQLGDGVPFTSSQKFFT
ParentalISPIILYFLASFYT-KYDPTHFILNTASLLSVL-IPKMPQLHGVRIFGINK
ISPIIL.F.ASFY..KY.PTH....TASLLS.L..P...Q.H.V.IFGINK
RetrocopyISPIILCFPASFYR<KYAPTHSVVSTASLLSML>TPQTQQQHSVPIFGINK

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 .14 RPM 22 .32 RPM
bodymap2_adrenal 0 .02 RPM 39 .34 RPM
bodymap2_brain 0 .00 RPM 27 .82 RPM
bodymap2_breast 0 .04 RPM 27 .96 RPM
bodymap2_colon 0 .00 RPM 24 .09 RPM
bodymap2_heart 0 .00 RPM 17 .45 RPM
bodymap2_kidney 0 .00 RPM 49 .28 RPM
bodymap2_liver 0 .00 RPM 19 .29 RPM
bodymap2_lung 0 .00 RPM 33 .02 RPM
bodymap2_lymph_node 0 .00 RPM 52 .56 RPM
bodymap2_ovary 0 .00 RPM 44 .26 RPM
bodymap2_prostate 0 .00 RPM 36 .63 RPM
bodymap2_skeletal_muscle 0 .00 RPM 10 .60 RPM
bodymap2_testis 0 .26 RPM 58 .14 RPM
bodymap2_thyroid 0 .00 RPM 34 .25 RPM
bodymap2_white_blood_cells 0 .00 RPM 46 .19 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_645 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_645 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_645 retrocopy 5' end.

Lab - click to see more details

retro_hsap_645 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_645 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_469
Gorilla gorilla retro_ggor_565
Macaca mulatta retro_mmul_2432
Parental genes homology:
Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000055791 retrocopy
retro_cjac_2962,
Homo sapiens ENSG00000128699 1 retrocopy
retro_hsap_645 ,
Gorilla gorilla ENSGGOG000000152591 retrocopy
retro_ggor_565,
Loxodonta africana ENSLAFG000000077691 retrocopy
retro_lafr_411,
Myotis lucifugus ENSMLUG000000143391 retrocopy
retro_mluc_2318,
Macaca mulatta ENSMMUG000000143161 retrocopy
retro_mmul_2432,
Nomascus leucogenys ENSNLEG000000066251 retrocopy
retro_nleu_730,
Pongo abelii ENSPPYG000000130172 retrocopies
retro_pabe_570, retro_pabe_571,
Pan troglodytes ENSPTRG000000127361 retrocopy
retro_ptro_469,
Sus scrofa ENSSSCG000000160441 retrocopy
retro_sscr_247,
Tupaia belangeri ENSTBEG000000129421 retrocopy
retro_tbel_10,
Tursiops truncatus ENSTTRG000000052402 retrocopies
retro_ttru_1846, retro_ttru_770,

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 = 0.03 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 .00 RPM
FIN_HG00328 0 .00 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 .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 .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 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 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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