RetrogeneDB ID:

retro_hsap_2761

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:27256283..27256509(-)
Located in intron of:ENSG00000163491
Retrocopy
information
Ensembl ID:ENSG00000224237
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MINOS1
Ensembl ID:ENSG00000173436
Aliases:MINOS1, C1orf151, MIO10
Description:mitochondrial inner membrane organizing system 1 [Source:HGNC Symbol;Acc:32068]


Retrocopy-Parental alignment summary:






>retro_hsap_2761
TCGGAGTTGGAGCTTGGCCGGAAGTGGGACCGGTGCCTGGCGGATGTGGTCGTGAAGATAGGCACTGGTTTTGGATTAGG
AATTGTCTTCTCACCTTCTTTAAAAGAAGAATGTGGCCATTAGCCTTCCGTTCTGGCATGGGATTAGGAATGGCTTACTC
CAACTGTCACATGATTTCCAGGCTCCATATCTTCTACACGGAAAATATGTCAAAGAGCAGGAGCAG

ORF - retro_hsap_2761 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.08 %
Parental protein coverage: 98.72 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalSESELGRKWDRCLADAVVKIGTGFGLGIVFSLT-FFKRRMWPLAFGSGMGLGMAYSNC-QHDFQAPYLLH
SE.ELGRKWDRCLAD.VVKIGTGFGLGIVFS...F..R.MWPLAF.SGMGLGMAYSNC..HDFQAPYLLH
RetrocopySELELGRKWDRCLADVVVKIGTGFGLGIVFSPS<FKRR-MWPLAFRSGMGLGMAYSNC<SHDFQAPYLLH
ParentalGKYVKEQEQ
GKYVKEQEQ
RetrocopyGKYVKEQEQ

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 .16 RPM 14 .81 RPM
bodymap2_adrenal 0 .00 RPM 34 .20 RPM
bodymap2_brain 0 .28 RPM 26 .60 RPM
bodymap2_breast 1 .40 RPM 23 .93 RPM
bodymap2_colon 1 .12 RPM 36 .76 RPM
bodymap2_heart 0 .04 RPM 34 .73 RPM
bodymap2_kidney 0 .27 RPM 55 .55 RPM
bodymap2_liver 0 .00 RPM 10 .90 RPM
bodymap2_lung 0 .00 RPM 21 .94 RPM
bodymap2_lymph_node 0 .00 RPM 20 .48 RPM
bodymap2_ovary 0 .69 RPM 30 .90 RPM
bodymap2_prostate 0 .02 RPM 42 .80 RPM
bodymap2_skeletal_muscle 0 .00 RPM 16 .08 RPM
bodymap2_testis 0 .40 RPM 22 .85 RPM
bodymap2_thyroid 0 .00 RPM 26 .42 RPM
bodymap2_white_blood_cells 0 .00 RPM 20 .18 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2761 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2761 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2761 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2761 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2761 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1868
Gorilla gorilla retro_ggor_1920
Pongo abelii retro_pabe_2251
Parental genes homology:
Parental genes homology involve 12 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000067091 retrocopy
retro_cjac_2070,
Echinops telfairi ENSETEG000000109425 retrocopies
retro_etel_1360, retro_etel_1463, retro_etel_171, retro_etel_459, retro_etel_978,
Homo sapiens ENSG00000173436 3 retrocopies
retro_hsap_1857, retro_hsap_2761 , retro_hsap_2948,
Gallus gallus ENSGALG000000040391 retrocopy
retro_ggal_19,
Gorilla gorilla ENSGGOG000000073474 retrocopies
retro_ggor_1920, retro_ggor_2042, retro_ggor_2154, retro_ggor_979,
Macaca mulatta ENSMMUG000000058552 retrocopies
retro_mmul_1268, retro_mmul_1949,
Mus musculus ENSMUSG000000506081 retrocopy
retro_mmus_2357,
Nomascus leucogenys ENSNLEG000000078672 retrocopies
retro_nleu_1297, retro_nleu_665,
Pongo abelii ENSPPYG000000017883 retrocopies
retro_pabe_1513, retro_pabe_2251, retro_pabe_2445,
Pan troglodytes ENSPTRG000000002692 retrocopies
retro_ptro_1868, retro_ptro_2050,
Rattus norvegicus ENSRNOG000000426962 retrocopies
retro_rnor_16, retro_rnor_2460,
Tarsius syrichta ENSTSYG000000029031 retrocopy
retro_tsyr_825,

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 = 0.41 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .06 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .07 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 .05 RPM
FIN_HG00338 0 .06 RPM
FIN_HG00349 0 .11 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .11 RPM
GBR_HG00114 0 .03 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 .07 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .08 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .41 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .06 RPM
YRI_NA19093 0 .10 RPM
YRI_NA19099 0 .16 RPM
YRI_NA19114 0 .13 RPM
YRI_NA19118 0 .15 RPM
YRI_NA19213 0 .07 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .06 RPM

Indel association:

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





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