RetrogeneDB ID:

retro_tbel_1960

Retrocopy
location
Organism:Treeshrew (Tupaia belangeri)
Coordinates:GeneScaffold_6064:287904..288612(-)
Located in intron of:ENSTBEG00000015170
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS3A
Ensembl ID:ENSTBEG00000002963
Aliases:None
Description:ribosomal protein S3A [Source:HGNC Symbol;Acc:10421]


Retrocopy-Parental alignment summary:






>retro_tbel_1960
GTTGGCAAGATCAAGTGCCTTACAAAAGGCAGCAGAAAGGGAGCCAAGAAGAAAGTGGTTGATCCATTTTCCAAGACTGG
TAATGCTGTGAAAGCACCTGCTATGTTCACTATAAGAAATACTGGAAAAACAGTAGTCGCCAGGACTCAGGGAACCGAAA
CTGCATCTTATGGCCTTAAGCACGGTATGTTTGAAGTGAGTCTTGCAGATCTACAGAATGATGAAGTTGCATTTAGGAAA
TTCAAGCTAATTACTGAGGGCGTTTAGGACAAAAATTTCCTGACTAACTTCCATGGCATGGATCTTACTCATGACGAAAT
GTATTTCACAGTCAAAAATGGCAGACCACGACTGAAGATCATGTTAATGTCACAACTATTGATGGTAATCTGCTTTGTTT
GTTCGGTGTTGGTTTTATTTAAAAAATGCAACAATCAGATACAGAAGACTTCCTATGCTCAGCTTTGGCAGGCCCACCAA
ATCTGGAAGATGATGATAGAAATCATGACCCAGGACATGCAGACAAATGACTTCAAAGAACTGGTCAATAAACTGATTCC
AGATAGCATTGGAAAGACACAGAAAAAAAGGCTTGCTAATCTATCTATCCTCTCCCATGATGTCTTCATCAGAAAAACAA
AAATGCTGAAGAAGTCCAAGTTTGAAATGAGAAAACTCATGGAGCTTCACAGTGAAAACATGAAAAGT

ORF - retro_tbel_1960 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.37 %
Parental protein coverage: 89.39 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalVGKNKRLTKGGKKGAKKKVXDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVSLA
VGK.K.LTKG..KGAKKKV.DPFSK.....VKAPAMF.IRN.GKT.V.RTQGT..AS.GLK...FEVSLA
RetrocopyVGKIKCLTKGSRKGAKKKVVDPFSKTG-NAVKAPAMFTIRNTGKTVVARTQGTETASYGLKHGMFEVSLA
ParentalDLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVK-KWQTMIEAHVDVKTTDGYLLRLFCVG
DLQNDEVAFRKFKLITE.V..KN.LTNFHGMDLT.D.M...VK.KWQT..E.HV.V.T.DG.LL.LF.VG
RetrocopyDLQNDEVAFRKFKLITEGV*DKNFLTNFHGMDLTHDEMYFTVK<KWQTTTEDHVNVTTIDGNLLCLFGVG
ParentalFT-KKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIG-KDIE-KACQSIYPL-
F..KK.NNQI.KTSYAQ..Q..QI.K.M.EIMT...QTND.KE.VNKLIPDSIG.KD.E.KAC.SIYPL.
RetrocopyFI>KKCNNQIQKTSYAQLWQAHQIWKMMIEIMTQDMQTNDFKELVNKLIPDSIG<KDTEKKAC*SIYPL>
ParentalHDVFVRKVKMLKKPKFELGKLMELHGEGSSS
HDVF.RK.KMLKK.KFE..KLMELH.E...S
RetrocopyHDVFIRKTKMLKKSKFEMRKLMELHSENMKS

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Tupaia belangeri was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_tbel_1960 retrocopy.

TSS - click to see more details

Tupaia belangeri was not studied using FANTOM5 data.

Lab - click to see more details

retro_tbel_1960 was not experimentally validated.

Retrocopy orthology:
Tupaia belangeri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 15 parental genes, and 211 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,
Dipodomys ordii ENSDORG0000000225010 retrocopies
retro_dord_142, retro_dord_168, retro_dord_193, retro_dord_209, retro_dord_229, retro_dord_314, retro_dord_380, retro_dord_752, retro_dord_757, retro_dord_95,
Erinaceus europaeus ENSEEUG000000049944 retrocopies
retro_eeur_297, retro_eeur_510, retro_eeur_517, retro_eeur_66,
Homo sapiens ENSG0000014542540 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 ENSTBEG00000002963 98 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,


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