RetrogeneDB ID:

retro_hsap_2908

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:9032011..9032621(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000251313
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS3A
Ensembl ID:ENSG00000145425
Aliases:RPS3A, FTE1, MFTL, S3A
Description:ribosomal protein S3A [Source:HGNC Symbol;Acc:10421]


Retrocopy-Parental alignment summary:






>retro_hsap_2908
ATGGCGGTTGTTAAGAACAAGTGCCTTATAAAAGGTGGCAAAAAGGGAGTTAAGGAGAAAATAGTTGATCCATTTTCTAA
GAAAGATCAGTATGATGTGAAAGCACCTGCTATGTTCAATATAAGAAATATTGGAAAGACTTGGTCACCAGGACCCAAGG
AACCCAAATTGCATCTGATGGTCTCAAGAGTCTTGTGTTTGAAGTGAGTCTGGCTGATTTGCAAAATGATAAAGTTGCAT
TTAGAAAATTCAAGCTGATTACTGAAGATGTTCAGGGCAAAAACTGCCTGACTAACTTCTATGGCATGGGTCTTACCTGT
GACAAAATATGTTCCATGGTTGAAAAATGTTCAACAATGATTGAAGCTCATGTTGATGTCAAGACTACCGATGGTTACTT
CTTTCATCTGTTTTGTGTTGGTTTTACCAAAAAACACAACAATCAGATACAGAAGACCTCTTATGCTCAGCACAAACAGT
CCCCCAAATCCAGAAGAAGATGATGGAAATCATGACCTGAGAGGTGCAGACAAATGACTTGAAAGAAGTGGTCAATAAAT
TGATTCCAGACAACATTGGAAAAGATGTAGAAGAGGCTTGCCAATCTATC

ORF - retro_hsap_2908 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.47 %
Parental protein coverage: 77.27 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKT-LVTRTQGTKIASDGLKGRVFEV
MAV.KNK.L.KGGKKG.K.K.VDPFSKKD.YDVKAPAMFNIRNIGKT.LVTRTQGT.IASDGLK..VFEV
RetrocopyMAVVKNKCLIKGGKKGVKEKIVDPFSKKDQYDVKAPAMFNIRNIGKT<LVTRTQGTQIASDGLKSLVFEV
ParentalSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFC
SLADLQND.VAFRKFKLITEDVQGKNCLTNF.GM.LT.DK.CSMV.K..TMIEAHVDVKTTDGY...LFC
RetrocopySLADLQNDKVAFRKFKLITEDVQGKNCLTNFYGMGLTCDKICSMVEKCSTMIEAHVDVKTTDGYFFHLFC
ParentalVGFTKKRNNQIRKTSYAQHQQ-VRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSI
VGFTKK.NNQI.KTSYAQH.Q.V.QI.KKMMEIMT.EVQTNDLKEVVNKLIPD.IGKD.E.ACQSI
RetrocopyVGFTKKHNNQIQKTSYAQHKQ<VPQIQKKMMEIMT*EVQTNDLKEVVNKLIPDNIGKDVEEACQSI

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 165 .82 RPM
bodymap2_adrenal 0 .00 RPM 364 .03 RPM
bodymap2_brain 0 .07 RPM 75 .31 RPM
bodymap2_breast 0 .00 RPM 171 .42 RPM
bodymap2_colon 0 .00 RPM 412 .69 RPM
bodymap2_heart 0 .00 RPM 106 .78 RPM
bodymap2_kidney 0 .00 RPM 159 .90 RPM
bodymap2_liver 0 .00 RPM 109 .78 RPM
bodymap2_lung 0 .00 RPM 488 .03 RPM
bodymap2_lymph_node 0 .00 RPM 443 .21 RPM
bodymap2_ovary 0 .10 RPM 526 .47 RPM
bodymap2_prostate 0 .07 RPM 540 .27 RPM
bodymap2_skeletal_muscle 0 .00 RPM 86 .34 RPM
bodymap2_testis 0 .00 RPM 259 .98 RPM
bodymap2_thyroid 0 .00 RPM 233 .87 RPM
bodymap2_white_blood_cells 0 .00 RPM 665 .11 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2908 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2908 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2908 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2908 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2908 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 13 parental genes, and 197 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000022687 retrocopies
retro_cjac_2, retro_cjac_21, retro_cjac_249, retro_cjac_312, retro_cjac_337, retro_cjac_368, retro_cjac_78,
Homo sapiens ENSG00000145425 40 retrocopies
retro_hsap_1080, retro_hsap_1178, retro_hsap_1320, retro_hsap_144, retro_hsap_1507, retro_hsap_1559, retro_hsap_1620, retro_hsap_1891, retro_hsap_1994, retro_hsap_2575, retro_hsap_2578, retro_hsap_2607, retro_hsap_2700, retro_hsap_274, retro_hsap_2803, retro_hsap_2908 , retro_hsap_2909, retro_hsap_3020, retro_hsap_3112, retro_hsap_313, retro_hsap_3213, retro_hsap_3366, retro_hsap_3675, retro_hsap_3876, retro_hsap_3878, retro_hsap_3879, retro_hsap_3910, retro_hsap_3929, retro_hsap_3931, retro_hsap_4017, retro_hsap_4020, retro_hsap_4021, retro_hsap_588, retro_hsap_602, retro_hsap_613, retro_hsap_683, retro_hsap_789, retro_hsap_838, retro_hsap_888, retro_hsap_914,
Gorilla gorilla ENSGGOG000000031822 retrocopies
retro_ggor_70, retro_ggor_97,
Myotis lucifugus ENSMLUG000000147888 retrocopies
retro_mluc_1197, retro_mluc_1397, retro_mluc_1568, retro_mluc_1846, retro_mluc_2130, retro_mluc_2158, retro_mluc_2388, retro_mluc_862,
Macaca mulatta ENSMMUG000000218211 retrocopy
retro_mmul_2297,
Monodelphis domestica ENSMODG000000009696 retrocopies
retro_mdom_1040, retro_mdom_1229, retro_mdom_1396, retro_mdom_1480, retro_mdom_627, retro_mdom_694,
Mus musculus ENSMUSG000000280812 retrocopies
retro_mmus_218, retro_mmus_254,
Nomascus leucogenys ENSNLEG0000000581526 retrocopies
retro_nleu_1160, retro_nleu_1177, retro_nleu_1402, retro_nleu_1472, retro_nleu_1483, retro_nleu_1487, retro_nleu_1816, retro_nleu_1878, retro_nleu_1992, retro_nleu_209, retro_nleu_2437, retro_nleu_2567, retro_nleu_2571, retro_nleu_2753, retro_nleu_281, retro_nleu_2979, retro_nleu_3087, retro_nleu_443, retro_nleu_526, retro_nleu_654, retro_nleu_658, retro_nleu_758, retro_nleu_767, retro_nleu_799, retro_nleu_942, retro_nleu_962,
Oryctolagus cuniculus ENSOCUG000000070111 retrocopy
retro_ocun_257,
Rattus norvegicus ENSRNOG000000118931 retrocopy
retro_rnor_198,
Sarcophilus harrisii ENSSHAG000000150882 retrocopies
retro_shar_777, retro_shar_95,
Sus scrofa ENSSSCG000000090193 retrocopies
retro_sscr_27, retro_sscr_749, retro_sscr_762,
Tupaia belangeri ENSTBEG0000000296398 retrocopies
retro_tbel_1005, retro_tbel_11, retro_tbel_1119, retro_tbel_116, retro_tbel_1232, retro_tbel_1318, retro_tbel_133, retro_tbel_137, retro_tbel_1375, retro_tbel_1378, retro_tbel_1383, retro_tbel_1417, retro_tbel_1421, retro_tbel_1509, retro_tbel_1686, retro_tbel_1698, retro_tbel_172, retro_tbel_1720, retro_tbel_1721, retro_tbel_1744, retro_tbel_1814, retro_tbel_1829, retro_tbel_1856, retro_tbel_1896, retro_tbel_1948, retro_tbel_1960, retro_tbel_1999, retro_tbel_206, retro_tbel_2200, retro_tbel_2306, retro_tbel_2463, retro_tbel_2483, retro_tbel_2510, retro_tbel_2626, retro_tbel_2654, retro_tbel_2657, retro_tbel_2745, retro_tbel_2759, retro_tbel_2760, retro_tbel_2764, retro_tbel_281, retro_tbel_2857, retro_tbel_2957, retro_tbel_2959, retro_tbel_3114, retro_tbel_317, retro_tbel_3212, retro_tbel_3255, retro_tbel_3259, retro_tbel_3299, retro_tbel_336, retro_tbel_3372, retro_tbel_3416, retro_tbel_3471, retro_tbel_3486, retro_tbel_3513, retro_tbel_3558, retro_tbel_3613, retro_tbel_3631, retro_tbel_3655, retro_tbel_3705, retro_tbel_373, retro_tbel_375, retro_tbel_3755, retro_tbel_3786, retro_tbel_3815, retro_tbel_3823, retro_tbel_3832, retro_tbel_386, retro_tbel_3882, retro_tbel_39, retro_tbel_3947, retro_tbel_3966, retro_tbel_399, retro_tbel_4116, retro_tbel_4144, retro_tbel_4147, retro_tbel_4211, retro_tbel_4220, retro_tbel_423, retro_tbel_4294, retro_tbel_4304, retro_tbel_4347, retro_tbel_438, retro_tbel_4428, retro_tbel_445, retro_tbel_4579, retro_tbel_598, retro_tbel_619, retro_tbel_623, retro_tbel_671, retro_tbel_859, retro_tbel_90, retro_tbel_912, retro_tbel_92, retro_tbel_928, retro_tbel_956, retro_tbel_973,

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 .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 .03 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 .02 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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