RetrogeneDB ID:

retro_hsap_2073

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:8743211..8743486(+)
Located in intron of:ENSG00000231083
Retrocopy
information
Ensembl ID:ENSG00000225642
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SNRPE
Ensembl ID:ENSG00000182004
Aliases:None
Description:small nuclear ribonucleoprotein polypeptide E [Source:HGNC Symbol;Acc:11161]


Retrocopy-Parental alignment summary:






>retro_hsap_2073
ATGGTGTACCATGGCCAGGGCCAGAAAGTGCAAAGGGTTATGGTGCAGCCCATCAACCTCATCTTCAGATACTTACAAAA
TAGATCACGGATTCAAGTGTAGCTCTATGAGCAAGTGAATATGAGGATAGAAGGCTGTATCATTGGTTTTGATGAGTATA
TGAACCTTGTATTAGATTATGCGAAGAGATTCATTCTAAAACAAAGTCAAGAAAACAACTGGGTCGGCTCATGCTAAAAG
GAGATAATATTCCTCTGCTGCAAAGTGTCTCCAAC

ORF - retro_hsap_2073 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.4 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMAYRGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDA-EEIHSKTK
M.Y.GQGQKVQ.VMVQPINLIFRYLQNRSRIQV.LYEQVNMRIEGCIIGFDEYMNLVLD.A.EEIHSKTK
RetrocopyMVYHGQGQKVQRVMVQPINLIFRYLQNRSRIQV*LYEQVNMRIEGCIIGFDEYMNLVLDYA<EEIHSKTK
ParentalSRKQLGRIMLKGDNITLLQSVSN
SRKQLGR.MLKGDNI.LLQSVSN
RetrocopySRKQLGRLMLKGDNIPLLQSVSN

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 49 .97 RPM
bodymap2_adrenal 0 .00 RPM 67 .04 RPM
bodymap2_brain 0 .00 RPM 35 .72 RPM
bodymap2_breast 0 .00 RPM 45 .27 RPM
bodymap2_colon 0 .00 RPM 71 .19 RPM
bodymap2_heart 0 .00 RPM 10 .67 RPM
bodymap2_kidney 0 .00 RPM 30 .42 RPM
bodymap2_liver 0 .00 RPM 19 .77 RPM
bodymap2_lung 0 .00 RPM 20 .29 RPM
bodymap2_lymph_node 0 .00 RPM 28 .18 RPM
bodymap2_ovary 0 .00 RPM 91 .89 RPM
bodymap2_prostate 0 .00 RPM 36 .72 RPM
bodymap2_skeletal_muscle 0 .00 RPM 12 .99 RPM
bodymap2_testis 0 .00 RPM 73 .21 RPM
bodymap2_thyroid 0 .00 RPM 59 .64 RPM
bodymap2_white_blood_cells 0 .00 RPM 30 .28 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_2073 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2073 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2073 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2073 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2073 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 13 parental genes, and 115 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000091586 retrocopies
retro_chof_139, retro_chof_1870, retro_chof_1897, retro_chof_1981, retro_chof_2652, retro_chof_450,
Callithrix jacchus ENSCJAG000000067351 retrocopy
retro_cjac_3163,
Dasypus novemcinctus ENSDNOG0000000449024 retrocopies
retro_dnov_1009, retro_dnov_1141, retro_dnov_122, retro_dnov_1223, retro_dnov_1312, retro_dnov_1314, retro_dnov_1362, retro_dnov_1438, retro_dnov_163, retro_dnov_191, retro_dnov_2398, retro_dnov_2671, retro_dnov_360, retro_dnov_414, retro_dnov_513, retro_dnov_579, retro_dnov_796, retro_dnov_828, retro_dnov_898, retro_dnov_900, retro_dnov_902, retro_dnov_93, retro_dnov_967, retro_dnov_983,
Echinops telfairi ENSETEG0000001401524 retrocopies
retro_etel_1136, retro_etel_1244, retro_etel_138, retro_etel_1443, retro_etel_1530, retro_etel_1636, retro_etel_1739, retro_etel_1781, retro_etel_1947, retro_etel_2143, retro_etel_234, retro_etel_258, retro_etel_310, retro_etel_377, retro_etel_466, retro_etel_546, retro_etel_56, retro_etel_579, retro_etel_581, retro_etel_582, retro_etel_76, retro_etel_776, retro_etel_799, retro_etel_80,
Felis catus ENSFCAG000000008732 retrocopies
retro_fcat_1836, retro_fcat_554,
Homo sapiens ENSG00000182004 10 retrocopies
retro_hsap_130, retro_hsap_1668, retro_hsap_2022, retro_hsap_2073 , retro_hsap_2287, retro_hsap_3262, retro_hsap_4228, retro_hsap_4660, retro_hsap_516, retro_hsap_576,
Gorilla gorilla ENSGGOG000000007557 retrocopies
retro_ggor_1462, retro_ggor_1626, retro_ggor_1700, retro_ggor_2221, retro_ggor_228, retro_ggor_2892, retro_ggor_91,
Microcebus murinus ENSMICG000000155373 retrocopies
retro_mmur_1406, retro_mmur_453, retro_mmur_58,
Monodelphis domestica ENSMODG000000283943 retrocopies
retro_mdom_1164, retro_mdom_1790, retro_mdom_1865,
Mustela putorius furoENSMPUG000000116427 retrocopies
retro_mputfur_1078, retro_mputfur_1527, retro_mputfur_1634, retro_mputfur_53, retro_mputfur_638, retro_mputfur_729, retro_mputfur_949,
Pongo abelii ENSPPYG000000003268 retrocopies
retro_pabe_1375, retro_pabe_20, retro_pabe_2023, retro_pabe_228, retro_pabe_3015, retro_pabe_3620, retro_pabe_56, retro_pabe_610,
Pan troglodytes ENSPTRG0000003022411 retrocopies
retro_ptro_1131, retro_ptro_134, retro_ptro_1345, retro_ptro_1346, retro_ptro_1526, retro_ptro_1620, retro_ptro_2206, retro_ptro_2872, retro_ptro_3096, retro_ptro_385, retro_ptro_426,
Sorex araneus ENSSARG000000033119 retrocopies
retro_sara_171, retro_sara_173, retro_sara_183, retro_sara_214, retro_sara_219, retro_sara_37, retro_sara_664, retro_sara_697, retro_sara_750,

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 = 0.02 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 .00 RPM
FIN_HG00375 0 .02 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 .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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