RetrogeneDB ID:

retro_hsap_786

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:63399693..63400192(+)
Located in intron of:ENSG00000184743
Retrocopy
information
Ensembl ID:ENSG00000270269
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:IMMP1L
Ensembl ID:ENSG00000148950
Aliases:IMMP1L, IMP1, IMP1-LIKE
Description:IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae) [Source:HGNC Symbol;Acc:26317]


Retrocopy-Parental alignment summary:






>retro_hsap_786
ATGCTTCGTGGTGCTCTGGGGAAACCTTCTGACTTGTTGGCTATGCTATTCAGTATGGCTGTATAGCTCACTGTGCTTCT
GAATACGTTGGTGGTGTTGTCATGTGTTCTGGACCATCAATGGAGCCTACAATTCAAAATTCAGATACTGTCTTTGCACA
AAATCTTAGTCGACATTTTGATAGTATCCAAAGAGGTGACATTGTGATTGCAAAAAGCCCAAGTGATCCAACATCAAATA
TTTGTAAAAGAGTAACTGGTTTGGAAGGAGACAAAATCCTCACCACTAGTCCATCAGATTTCTTTAAAAGCTACAGTTAT
GTCCCAGTGGGTCATGTTTGGTTAGAAGGTGATAAATCTACAGAATTCTACAGATTCCAGTTACTATGGACCTATTCCAT
ATGAACTAATAAGAGGACGAATCTTCTTTTAAGATTCGGCCTCTGAGTGATTTTGGATTTTTATGTGCCAGCCTTAATGG
CCACAGATTTTCTGATGAT

ORF - retro_hsap_786 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.57 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMLRGVLGK-TFRLVGYTIQYGCIAHCAFEYVGGVVMCSGPSMEPTIQNSDIVFAENLSRHFYGIQRGDIV
MLRG.LGK.TF.LVGY.IQYGCIAHCA.EYVGGVVMCSGPSMEPTIQNSD.VFA.NLSRHF..IQRGDIV
RetrocopyMLRGALGK<TF*LVGYAIQYGCIAHCASEYVGGVVMCSGPSMEPTIQNSDTVFAQNLSRHFDSIQRGDIV
ParentalIAKSPSDPKSNICKRVIGLEGDKILTTSPSDFFKSHSYVPMGHVWLEGD-NLQNSTDSRCYGPIPYGLIR
IAKSPSDP.SNICKRV.GLEGDKILTTSPSDFFKS.SYVP.GHVWLEGD.NLQNSTDS..YGPIPY.LIR
RetrocopyIAKSPSDPTSNICKRVTGLEGDKILTTSPSDFFKSYSYVPVGHVWLEGD>NLQNSTDSSYYGPIPYELIR
ParentalGRIF-FKIWPLSDFGFLRASPNGHRFSDD
GRIF.FKI.PLSDFGFL.AS.NGHRFSDD
RetrocopyGRIF>FKIRPLSDFGFLCASLNGHRFSDD

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 .40 RPM 3 .84 RPM
bodymap2_adrenal 0 .37 RPM 9 .33 RPM
bodymap2_brain 0 .21 RPM 8 .88 RPM
bodymap2_breast 0 .35 RPM 9 .84 RPM
bodymap2_colon 0 .00 RPM 8 .24 RPM
bodymap2_heart 0 .02 RPM 7 .16 RPM
bodymap2_kidney 0 .00 RPM 11 .89 RPM
bodymap2_liver 0 .04 RPM 4 .33 RPM
bodymap2_lung 0 .09 RPM 4 .43 RPM
bodymap2_lymph_node 0 .00 RPM 8 .79 RPM
bodymap2_ovary 0 .35 RPM 9 .18 RPM
bodymap2_prostate 0 .10 RPM 11 .21 RPM
bodymap2_skeletal_muscle 0 .09 RPM 6 .44 RPM
bodymap2_testis 0 .15 RPM 14 .14 RPM
bodymap2_thyroid 0 .24 RPM 9 .06 RPM
bodymap2_white_blood_cells 0 .00 RPM 6 .44 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_786 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_786 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_786 retrocopy 5' end.

Lab - click to see more details

retro_hsap_786 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_786 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 27 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000068761 retrocopy
retro_amel_623,
Bos taurus ENSBTAG000000004751 retrocopy
retro_btau_528,
Canis familiaris ENSCAFG000000075142 retrocopies
retro_cfam_1757, retro_cfam_548,
Choloepus hoffmanni ENSCHOG000000101064 retrocopies
retro_chof_1157, retro_chof_1665, retro_chof_2427, retro_chof_358,
Callithrix jacchus ENSCJAG000000060421 retrocopy
retro_cjac_1240,
Dipodomys ordii ENSDORG000000002504 retrocopies
retro_dord_144, retro_dord_205, retro_dord_243, retro_dord_726,
Equus caballus ENSECAG000000205123 retrocopies
retro_ecab_1019, retro_ecab_159, retro_ecab_920,
Echinops telfairi ENSETEG000000030571 retrocopy
retro_etel_1971,
Homo sapiens ENSG00000148950 1 retrocopy
retro_hsap_786 ,
Gorilla gorilla ENSGGOG000000148971 retrocopy
retro_ggor_651,
Myotis lucifugus ENSMLUG000000065042 retrocopies
retro_mluc_2105, retro_mluc_385,
Macaca mulatta ENSMMUG000000168061 retrocopy
retro_mmul_1092,
Mus musculus ENSMUSG000000426702 retrocopies
retro_mmus_2571, retro_mmus_591,
Nomascus leucogenys ENSNLEG000000178821 retrocopy
retro_nleu_2484,
Oryctolagus cuniculus ENSOCUG000000296121 retrocopy
retro_ocun_388,
Otolemur garnettii ENSOGAG000000078533 retrocopies
retro_ogar_1202, retro_ogar_2006, retro_ogar_2643,
Pongo abelii ENSPPYG000000033891 retrocopy
retro_pabe_747,
Pan troglodytes ENSPTRG000000034721 retrocopy
retro_ptro_547,
Pteropus vampyrus ENSPVAG000000155351 retrocopy
retro_pvam_932,
Rattus norvegicus ENSRNOG000000048291 retrocopy
retro_rnor_2450,
Sarcophilus harrisii ENSSHAG000000154072 retrocopies
retro_shar_396, retro_shar_491,
Sus scrofa ENSSSCG000000133221 retrocopy
retro_sscr_1178,
Ictidomys tridecemlineatus ENSSTOG000000031792 retrocopies
retro_itri_489, retro_itri_623,
Tupaia belangeri ENSTBEG000000021266 retrocopies
retro_tbel_1510, retro_tbel_2503, retro_tbel_315, retro_tbel_3504, retro_tbel_4049, retro_tbel_878,
Tarsius syrichta ENSTSYG000000092571 retrocopy
retro_tsyr_2139,
Tursiops truncatus ENSTTRG000000023952 retrocopies
retro_ttru_1862, retro_ttru_966,
Vicugna pacos ENSVPAG000000019401 retrocopy
retro_vpac_126,

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 .02 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .08 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .09 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 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 .08 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .10 RPM
GBR_HG00134 0 .04 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 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .06 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 .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 .00 RPM

Indel association:

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



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