RetrogeneDB ID:

retro_hsap_1144

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:94914868..94915647(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000258357
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NSA2
Ensembl ID:ENSG00000164346
Aliases:NSA2, CDK105, HCL-G1, HCLG1, HUSSY29, TINP1
Description:NSA2 ribosome biogenesis homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:30728]


Retrocopy-Parental alignment summary:






>retro_hsap_1144
ATGCCACAGAACGAATATATTGAATTACACTGTAAACACTATGGATACCATTTGGATTACCATGAGAAAAAGGGAAAGAA
GGAAAGTCGAGAGGCTCATGAATGTTCAAAGAAGGGAAAGAAAATGATTGGTCTGAAGGCTAAGCTTTACCATAAACAGC
GCCATGCTGAGAAAATACAAATGAAAAGACTATCAAGATGCATGAAAAGAGAAACATCAAACAAAAGAATGATGAAAAGA
CTCCACAGGGAGCAGTACCTGCCTATCTGCTGGACAGAGAGGAACAATCTCGAGCTAAAGTACTTTCCAATAGGATTAAA
CAGAAACGAAAAGAGAAAGTGGGAAAATGGGAAGTCCCTCTGCCTAAAGTACGTGCCCAGGGAGAAACAGAAGTATTAAA
AGTTATTCGAACAGGAAAGAGAAAGAAGAAGGCATGGAAGAGGATGGTTACTAAAGTCTGCTTTGTTGGAGATGGGTTTA
CAAGAAAACCACCTAAATATGAAAGATTCATCAGGCCAATGGGCTTGCATTTCAAGAAAGCCCATGTAACACATCCTGAA
ATGAAAGCCACCTTTTGCCTACGAATACTTGGTGTAAAGAAGAGCCCCTTGTCCCCACTGTATACAACTTTCGATGTTAT
TACCAAAGGTACTGTCATTGAAGTAAATATGAGCGAATTGGGCCTTGTGATGCAAGGAGGCAAAGTTATTTGGGGAAATT
ATGCCCAGGTTACTAACAATCCTGAAAATGATGCATGCATAAATGCAGTCTTACTGATT

ORF - retro_hsap_1144 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.19 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMPQNEYIELHRKRYGYRLDYHEKKRKKESREAHERSKKAKKMIGLKAKLYHKQRHAEKIQMK-KTIKMHE
MPQNEYIELH.K.YGY.LDYHEKK.KKESREAHE.SKK.KKMIGLKAKLYHKQRHAEKIQMK.KTIKMHE
RetrocopyMPQNEYIELHCKHYGYHLDYHEKKGKKESREAHECSKKGKKMIGLKAKLYHKQRHAEKIQMK<KTIKMHE
ParentalKRNTKQKNDEKTPQGAVPAYLLDREGQSRAKVLSNMIKQKRKEKAGKWEVPLPKVRAQGETEVLKVIRTG
KRN.KQKNDEKTPQGAVPAYLLDRE.QSRAKVLSN.IKQKRKEK.GKWEVPLPKVRAQGETEVLKVIRTG
RetrocopyKRNIKQKNDEKTPQGAVPAYLLDREEQSRAKVLSNRIKQKRKEKVGKWEVPLPKVRAQGETEVLKVIRTG
ParentalKRKKKAWKRMVTKVCFVGDGFTRKPPKYERFIRPMGLRFKKAHVTHPELKATFCLPILGVKKNPSSPLYT
KRKKKAWKRMVTKVCFVGDGFTRKPPKYERFIRPMGL.FKKAHVTHPE.KATFCL.ILGVKK.P.SPLYT
RetrocopyKRKKKAWKRMVTKVCFVGDGFTRKPPKYERFIRPMGLHFKKAHVTHPEMKATFCLRILGVKKSPLSPLYT
ParentalTLGVITKGTVIEVNVSELGLVTQGGKVIWGKYAQVTNNPENDGCINAVLLV
T..VITKGTVIEVN.SELGLV.QGGKVIWG.YAQVTNNPEND.CINAVLL.
RetrocopyTFDVITKGTVIEVNMSELGLVMQGGKVIWGNYAQVTNNPENDACINAVLLI

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 .12 RPM 89 .09 RPM
bodymap2_adrenal 0 .06 RPM 88 .90 RPM
bodymap2_brain 0 .02 RPM 42 .43 RPM
bodymap2_breast 0 .00 RPM 71 .56 RPM
bodymap2_colon 0 .12 RPM 212 .44 RPM
bodymap2_heart 0 .00 RPM 33 .69 RPM
bodymap2_kidney 0 .00 RPM 56 .62 RPM
bodymap2_liver 0 .00 RPM 29 .78 RPM
bodymap2_lung 0 .00 RPM 69 .11 RPM
bodymap2_lymph_node 0 .00 RPM 121 .72 RPM
bodymap2_ovary 0 .33 RPM 263 .51 RPM
bodymap2_prostate 0 .00 RPM 136 .78 RPM
bodymap2_skeletal_muscle 0 .13 RPM 47 .76 RPM
bodymap2_testis 0 .23 RPM 177 .29 RPM
bodymap2_thyroid 0 .02 RPM 91 .90 RPM
bodymap2_white_blood_cells 0 .00 RPM 115 .88 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1144 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1144 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1144 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1144 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1144 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_779
Pongo abelii retro_pabe_950
Macaca mulatta retro_mmul_890
Parental genes homology:
Parental genes homology involve 24 parental genes, and 176 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000083114 retrocopies
retro_cfam_1292, retro_cfam_361, retro_cfam_49, retro_cfam_64,
Callithrix jacchus ENSCJAG000000168741 retrocopy
retro_cjac_116,
Cavia porcellus ENSCPOG000000066481 retrocopy
retro_cpor_672,
Dasypus novemcinctus ENSDNOG000000106151 retrocopy
retro_dnov_428,
Echinops telfairi ENSETEG0000000409513 retrocopies
retro_etel_1086, retro_etel_1479, retro_etel_1786, retro_etel_2030, retro_etel_2112, retro_etel_2116, retro_etel_2197, retro_etel_359, retro_etel_613, retro_etel_729, retro_etel_890, retro_etel_940, retro_etel_988,
Felis catus ENSFCAG000000119781 retrocopy
retro_fcat_98,
Homo sapiens ENSG00000164346 4 retrocopies
retro_hsap_1144 , retro_hsap_1577, retro_hsap_4731, retro_hsap_493,
Gorilla gorilla ENSGGOG000000143656 retrocopies
retro_ggor_1200, retro_ggor_2136, retro_ggor_2939, retro_ggor_463, retro_ggor_824, retro_ggor_891,
Loxodonta africana ENSLAFG000000099104 retrocopies
retro_lafr_253, retro_lafr_455, retro_lafr_620, retro_lafr_714,
Macropus eugenii ENSMEUG000000157983 retrocopies
retro_meug_1191, retro_meug_1408, retro_meug_161,
Microcebus murinus ENSMICG000000007523 retrocopies
retro_mmur_1074, retro_mmur_374, retro_mmur_925,
Macaca mulatta ENSMMUG000000111966 retrocopies
retro_mmul_1984, retro_mmul_2219, retro_mmul_2523, retro_mmul_408, retro_mmul_441, retro_mmul_890,
Monodelphis domestica ENSMODG000000019004 retrocopies
retro_mdom_115, retro_mdom_1702, retro_mdom_581, retro_mdom_592,
Mustela putorius furoENSMPUG000000057955 retrocopies
retro_mputfur_153, retro_mputfur_250, retro_mputfur_510, retro_mputfur_573, retro_mputfur_690,
Nomascus leucogenys ENSNLEG0000000504610 retrocopies
retro_nleu_1026, retro_nleu_1507, retro_nleu_1758, retro_nleu_1759, retro_nleu_1929, retro_nleu_2255, retro_nleu_2565, retro_nleu_2675, retro_nleu_768, retro_nleu_943,
Oryctolagus cuniculus ENSOCUG000000065366 retrocopies
retro_ocun_149, retro_ocun_1591, retro_ocun_1602, retro_ocun_306, retro_ocun_658, retro_ocun_76,
Ochotona princeps ENSOPRG000000018677 retrocopies
retro_opri_1145, retro_opri_1195, retro_opri_254, retro_opri_427, retro_opri_654, retro_opri_778, retro_opri_83,
Pongo abelii ENSPPYG000000259268 retrocopies
retro_pabe_1300, retro_pabe_1715, retro_pabe_240, retro_pabe_3434, retro_pabe_3570, retro_pabe_3678, retro_pabe_950, retro_pabe_976,
Pan troglodytes ENSPTRG000000169906 retrocopies
retro_ptro_1063, retro_ptro_1713, retro_ptro_2105, retro_ptro_3146, retro_ptro_372, retro_ptro_779,
Rattus norvegicus ENSRNOG0000001653015 retrocopies
retro_rnor_1074, retro_rnor_1317, retro_rnor_1366, retro_rnor_1921, retro_rnor_2630, retro_rnor_2745, retro_rnor_2767, retro_rnor_2817, retro_rnor_2820, retro_rnor_2852, retro_rnor_2877, retro_rnor_2964, retro_rnor_618, retro_rnor_945, retro_rnor_951,
Sorex araneus ENSSARG000000094244 retrocopies
retro_sara_555, retro_sara_589, retro_sara_620, retro_sara_703,
Sarcophilus harrisii ENSSHAG000000176545 retrocopies
retro_shar_292, retro_shar_336, retro_shar_495, retro_shar_679, retro_shar_745,
Ictidomys tridecemlineatus ENSSTOG000000079593 retrocopies
retro_itri_1630, retro_itri_1638, retro_itri_860,
Tupaia belangeri ENSTBEG0000001297856 retrocopies
retro_tbel_1062, retro_tbel_1078, retro_tbel_1141, retro_tbel_1317, retro_tbel_1329, retro_tbel_1476, retro_tbel_152, retro_tbel_1548, retro_tbel_1569, retro_tbel_1627, retro_tbel_1733, retro_tbel_1762, retro_tbel_1778, retro_tbel_179, retro_tbel_1845, retro_tbel_1940, retro_tbel_2102, retro_tbel_2113, retro_tbel_2138, retro_tbel_2220, retro_tbel_229, retro_tbel_254, retro_tbel_2586, retro_tbel_2757, retro_tbel_2784, retro_tbel_3016, retro_tbel_3040, retro_tbel_3116, retro_tbel_3264, retro_tbel_3298, retro_tbel_3417, retro_tbel_3514, retro_tbel_3601, retro_tbel_3650, retro_tbel_3724, retro_tbel_3736, retro_tbel_3763, retro_tbel_3795, retro_tbel_4028, retro_tbel_406, retro_tbel_4104, retro_tbel_4169, retro_tbel_4270, retro_tbel_430, retro_tbel_4401, retro_tbel_4422, retro_tbel_4491, retro_tbel_4503, retro_tbel_4513, retro_tbel_4642, retro_tbel_4689, retro_tbel_535, retro_tbel_670, retro_tbel_721, retro_tbel_897, retro_tbel_91,

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 = 0.09 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .07 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 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 .02 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .09 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .08 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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



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