RetrogeneDB ID:

retro_hsap_3167

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:42972900..42973281(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000250711
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SLMO2
Ensembl ID:ENSG00000101166
Aliases:SLMO2, C20orf45, PRELID3B, dJ543J19.5
Description:slowmo homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:15892]


Retrocopy-Parental alignment summary:






>retro_hsap_3167
AAAACTCTTACTGGTGCAGCAAAACGCAAAACATATATACTAGAATATTCTGTAGTTAATCCTGTAGAGAAAACAATGGA
ACTTAAATCTACTAATATTTCACTTACAAATATGATTTCAGTAGATGAGAGATTTATACACAAACCACATCATCGGGACC
CCCCAAAAAACTATTTTGACTCAAGAAGCCATAATCACTGAAGAGAGGTAGCCTCAGCAGTTACCTTGAAGGACTGATGG
CAAGAACTATACCTTCAAATGCTAATAAAGGCCGAGAAGCACTGAAATGGGTCATACATAAATTACATGTTAAGACTGAA
GAATTGACAGCTTCCGCCAAGAGGAAGCATAAGAACTTCGATGGCAGCGGCGGCGGCAGCA

ORF - retro_hsap_3167 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.44 %
Parental protein coverage: 65.46 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalKSLIGAARTKTYVQEHSVVDPVEKTMELKSTNISFTNMVSVDERLIYKPHPQD-PEKTVLTQEAIITVKG
K.L.GAA..KTY..E.SVV.PVEKTMELKSTNIS.TNM.SVDER.I.KPH..D.P.K...........K.
RetrocopyKTLTGAAKRKTYILEYSVVNPVEKTMELKSTNISLTNMISVDERFIHKPHHRD<PPKKLF*LKKP*SLKR
ParentalVSLSSYLEGLMASTISSNASKGREAMEWVIHKLNAEIEELTASA-RGTIRTPMAAAAFA
.SLSSYLEGLMA.TI.SNA.KGREA..WVIHKL....EELTASA.RG.IRT.MAAAA.A
RetrocopyGSLSSYLEGLMARTIPSNANKGREALKWVIHKLHVKTEELTASA>RGSIRTSMAAAAAA

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 75 .34 RPM
bodymap2_adrenal 0 .06 RPM 68 .72 RPM
bodymap2_brain 0 .00 RPM 47 .09 RPM
bodymap2_breast 0 .04 RPM 73 .15 RPM
bodymap2_colon 0 .00 RPM 56 .89 RPM
bodymap2_heart 0 .02 RPM 42 .35 RPM
bodymap2_kidney 0 .00 RPM 86 .55 RPM
bodymap2_liver 0 .00 RPM 37 .35 RPM
bodymap2_lung 0 .00 RPM 61 .96 RPM
bodymap2_lymph_node 0 .00 RPM 56 .26 RPM
bodymap2_ovary 0 .02 RPM 70 .67 RPM
bodymap2_prostate 0 .00 RPM 52 .01 RPM
bodymap2_skeletal_muscle 0 .00 RPM 41 .41 RPM
bodymap2_testis 0 .08 RPM 59 .67 RPM
bodymap2_thyroid 0 .00 RPM 82 .63 RPM
bodymap2_white_blood_cells 0 .00 RPM 78 .06 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3167 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3167 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3167 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3167 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3167 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 26 parental genes, and 101 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000044023 retrocopies
retro_btau_1006, retro_btau_1346, retro_btau_996,
Canis familiaris ENSCAFG000000122201 retrocopy
retro_cfam_1293,
Callithrix jacchus ENSCJAG000000189054 retrocopies
retro_cjac_1286, retro_cjac_2921, retro_cjac_3171, retro_cjac_3236,
Cavia porcellus ENSCPOG000000123974 retrocopies
retro_cpor_1285, retro_cpor_1412, retro_cpor_456, retro_cpor_468,
Dasypus novemcinctus ENSDNOG000000145483 retrocopies
retro_dnov_1402, retro_dnov_2032, retro_dnov_2311,
Equus caballus ENSECAG000000005131 retrocopy
retro_ecab_409,
Erinaceus europaeus ENSEEUG000000036974 retrocopies
retro_eeur_244, retro_eeur_34, retro_eeur_389, retro_eeur_406,
Felis catus ENSFCAG000000314311 retrocopy
retro_fcat_1499,
Homo sapiens ENSG00000101166 6 retrocopies
retro_hsap_310, retro_hsap_3166, retro_hsap_3167 , retro_hsap_3311, retro_hsap_3783, retro_hsap_4227,
Gorilla gorilla ENSGGOG000000048035 retrocopies
retro_ggor_1349, retro_ggor_1350, retro_ggor_2544, retro_ggor_2545, retro_ggor_2830,
Microcebus murinus ENSMICG0000001490212 retrocopies
retro_mmur_101, retro_mmur_1111, retro_mmur_1143, retro_mmur_1299, retro_mmur_1304, retro_mmur_1318, retro_mmur_1391, retro_mmur_1400, retro_mmur_1604, retro_mmur_512, retro_mmur_659, retro_mmur_912,
Myotis lucifugus ENSMLUG000000149072 retrocopies
retro_mluc_1887, retro_mluc_845,
Macaca mulatta ENSMMUG000000075604 retrocopies
retro_mmul_1155, retro_mmul_1644, retro_mmul_2123, retro_mmul_539,
Monodelphis domestica ENSMODG000000166085 retrocopies
retro_mdom_1596, retro_mdom_1619, retro_mdom_1620, retro_mdom_1655, retro_mdom_405,
Mustela putorius furoENSMPUG000000070751 retrocopy
retro_mputfur_1586,
Nomascus leucogenys ENSNLEG000000095793 retrocopies
retro_nleu_1118, retro_nleu_2497, retro_nleu_2498,
Oryctolagus cuniculus ENSOCUG000000056218 retrocopies
retro_ocun_1944, retro_ocun_1954, retro_ocun_455, retro_ocun_486, retro_ocun_549, retro_ocun_619, retro_ocun_775, retro_ocun_926,
Otolemur garnettii ENSOGAG0000001338210 retrocopies
retro_ogar_1037, retro_ogar_1650, retro_ogar_2233, retro_ogar_2972, retro_ogar_3009, retro_ogar_3120, retro_ogar_3281, retro_ogar_3378, retro_ogar_3389, retro_ogar_3392,
Pongo abelii ENSPPYG000000111827 retrocopies
retro_pabe_1462, retro_pabe_2631, retro_pabe_2632, retro_pabe_2731, retro_pabe_3089, retro_pabe_3411, retro_pabe_371,
Pan troglodytes ENSPTRG000000136825 retrocopies
retro_ptro_2160, retro_ptro_2273, retro_ptro_251, retro_ptro_252, retro_ptro_2564,
Pteropus vampyrus ENSPVAG000000052262 retrocopies
retro_pvam_1075, retro_pvam_1445,
Sus scrofa ENSSSCG000000075253 retrocopies
retro_sscr_161, retro_sscr_258, retro_sscr_959,
Tupaia belangeri ENSTBEG000000004931 retrocopy
retro_tbel_1407,
Tarsius syrichta ENSTSYG000000125332 retrocopies
retro_tsyr_2061, retro_tsyr_250,
Tursiops truncatus ENSTTRG000000084172 retrocopies
retro_ttru_621, retro_ttru_818,
Vicugna pacos ENSVPAG000000010442 retrocopies
retro_vpac_224, retro_vpac_359,

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 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .02 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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