RetrogeneDB ID:

retro_hsap_732

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:116261764..116262121(-)
Located in intron of:ENSG00000099204
Retrocopy
information
Ensembl ID:ENSG00000229668
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SNRPB2
Ensembl ID:ENSG00000125870
Aliases:SNRPB2, Msl1
Description:small nuclear ribonucleoprotein polypeptide B [Source:HGNC Symbol;Acc:11155]


Retrocopy-Parental alignment summary:






>retro_hsap_732
AAGAAAAGAAAAAACTCTATAGAACAGGATGTAGCAAGTGCAAAGGAAATGCCTGGTCAGGGAACATCAGATTCAGCTAA
CTCCCAAGGAAATTCAACACCACATCCTCAGGTCCCTGGTTACCCTCCAGACTGTGTTGTATTCCTGAATAACTTACCAG
AAGAGACTAATGAGAGGATGATGTTTCATGCTATCATATCAGTTCCCGCTTTCAACAAAGTATGTTTGGTACCTGGGAGA
CATGACATTGCTGTTGTTGAATTTGAAAATGATGGACAGGCCAAAGCTGTCAGGGATGCTTTGCAAGAATTCAGGATCAC
AGCATCCCATACCATGGGGGTCACCTATGTCAATAAA

ORF - retro_hsap_732 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.34 %
Parental protein coverage: 52.89 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKKKAKTVEQTATTTNKKPGQGTPNSANTQGNSTPNPQVPDYPPNYILFLNNLPEETNEMMLSMLFNQFPG
KK.....EQ........PGQGT..SAN.QGNSTP.PQVP.YPP....FLNNLPEETNE.M........P.
RetrocopyKKRKNSIEQDVASAKEMPGQGTSDSANSQGNSTPHPQVPGYPPDCVVFLNNLPEETNERMMFHAIISVPA
ParentalFKEVRLVPGRHDIAFVEFENDGQAGAARDALQGFKITPSHAMKITYAKK
F..V.LVPGRHDIA.VEFENDGQA.A.RDALQ.F.IT.SH.M..TY..K
RetrocopyFNKVCLVPGRHDIAVVEFENDGQAKAVRDALQEFRITASHTMGVTYVNK

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 37 .27 RPM
bodymap2_adrenal 0 .25 RPM 58 .83 RPM
bodymap2_brain 0 .00 RPM 40 .18 RPM
bodymap2_breast 0 .04 RPM 38 .64 RPM
bodymap2_colon 0 .00 RPM 54 .84 RPM
bodymap2_heart 0 .13 RPM 20 .69 RPM
bodymap2_kidney 0 .04 RPM 44 .52 RPM
bodymap2_liver 0 .00 RPM 19 .20 RPM
bodymap2_lung 0 .00 RPM 34 .63 RPM
bodymap2_lymph_node 0 .00 RPM 41 .35 RPM
bodymap2_ovary 0 .02 RPM 62 .67 RPM
bodymap2_prostate 0 .05 RPM 44 .65 RPM
bodymap2_skeletal_muscle 0 .00 RPM 23 .34 RPM
bodymap2_testis 0 .00 RPM 62 .14 RPM
bodymap2_thyroid 0 .04 RPM 57 .55 RPM
bodymap2_white_blood_cells 0 .00 RPM 64 .93 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_732 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_732 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_732 retrocopy 5' end.

Lab - click to see more details

retro_hsap_732 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_732 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_520
Gorilla gorilla retro_ggor_617
Pongo abelii retro_pabe_630
Equus caballus retro_ecab_118
Parental genes homology:
Parental genes homology involve 27 parental genes, and 118 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000165002 retrocopies
retro_amel_235, retro_amel_490,
Bos taurus ENSBTAG000000275061 retrocopy
retro_btau_1172,
Canis familiaris ENSCAFG000000055204 retrocopies
retro_cfam_1097, retro_cfam_1661, retro_cfam_1689, retro_cfam_264,
Callithrix jacchus ENSCJAG000000048111 retrocopy
retro_cjac_269,
Equus caballus ENSECAG000000184072 retrocopies
retro_ecab_118, retro_ecab_372,
Echinops telfairi ENSETEG000000010853 retrocopies
retro_etel_1283, retro_etel_1723, retro_etel_2031,
Felis catus ENSFCAG000000261151 retrocopy
retro_fcat_1513,
Homo sapiens ENSG00000125870 2 retrocopies
retro_hsap_3678, retro_hsap_732 ,
Gorilla gorilla ENSGGOG000000039372 retrocopies
retro_ggor_2487, retro_ggor_617,
Macropus eugenii ENSMEUG000000165522 retrocopies
retro_meug_465, retro_meug_482,
Microcebus murinus ENSMICG000000154041 retrocopy
retro_mmur_762,
Myotis lucifugus ENSMLUG000000081635 retrocopies
retro_mluc_1450, retro_mluc_1451, retro_mluc_1452, retro_mluc_2268, retro_mluc_586,
Macaca mulatta ENSMMUG000000144931 retrocopy
retro_mmul_1788,
Mus musculus ENSMUSG000000083334 retrocopies
retro_mmus_1496, retro_mmus_1497, retro_mmus_2378, retro_mmus_3325,
Nomascus leucogenys ENSNLEG000000096232 retrocopies
retro_nleu_477, retro_nleu_527,
Oryctolagus cuniculus ENSOCUG000000014273 retrocopies
retro_ocun_1069, retro_ocun_380, retro_ocun_485,
Otolemur garnettii ENSOGAG000000151461 retrocopy
retro_ogar_2042,
Ochotona princeps ENSOPRG000000115872 retrocopies
retro_opri_59, retro_opri_776,
Pongo abelii ENSPPYG000000107231 retrocopy
retro_pabe_630,
Pan troglodytes ENSPTRG000000132712 retrocopies
retro_ptro_2492, retro_ptro_520,
Rattus norvegicus ENSRNOG000000049671 retrocopy
retro_rnor_962,
Sorex araneus ENSSARG0000000268114 retrocopies
retro_sara_197, retro_sara_209, retro_sara_289, retro_sara_290, retro_sara_328, retro_sara_374, retro_sara_514, retro_sara_546, retro_sara_548, retro_sara_604, retro_sara_670, retro_sara_724, retro_sara_733, retro_sara_770,
Ictidomys tridecemlineatus ENSSTOG000000091981 retrocopy
retro_itri_1895,
Tupaia belangeri ENSTBEG000000128926 retrocopies
retro_tbel_1123, retro_tbel_2350, retro_tbel_3126, retro_tbel_3534, retro_tbel_3754, retro_tbel_530,
Tarsius syrichta ENSTSYG0000000885752 retrocopies
retro_tsyr_1067, retro_tsyr_1072, retro_tsyr_1083, retro_tsyr_1124, retro_tsyr_1158, retro_tsyr_1175, retro_tsyr_1216, retro_tsyr_1223, retro_tsyr_1242, retro_tsyr_1244, retro_tsyr_1245, retro_tsyr_1247, retro_tsyr_1261, retro_tsyr_1279, retro_tsyr_1323, retro_tsyr_1339, retro_tsyr_1361, retro_tsyr_1386, retro_tsyr_1434, retro_tsyr_1438, retro_tsyr_1461, retro_tsyr_1468, retro_tsyr_1469, retro_tsyr_1470, retro_tsyr_1501, retro_tsyr_1503, retro_tsyr_1513, retro_tsyr_1533, retro_tsyr_1586, retro_tsyr_1599, retro_tsyr_1616, retro_tsyr_1619, retro_tsyr_1629, retro_tsyr_1699, retro_tsyr_1720, retro_tsyr_1724, retro_tsyr_1776, retro_tsyr_1872, retro_tsyr_1930, retro_tsyr_1962, retro_tsyr_286, retro_tsyr_384, retro_tsyr_397, retro_tsyr_500, retro_tsyr_584, retro_tsyr_629, retro_tsyr_695, retro_tsyr_805, retro_tsyr_835, retro_tsyr_899, retro_tsyr_977, retro_tsyr_979,
Tursiops truncatus ENSTTRG000000063951 retrocopy
retro_ttru_1545,
Vicugna pacos ENSVPAG000000045571 retrocopy
retro_vpac_67,

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 .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 .03 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 .02 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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