RetrogeneDB ID:

retro_tbel_4219

Retrocopy
location
Organism:Treeshrew (Tupaia belangeri)
Coordinates:scaffold_72186:4642..5274(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSTBEG00000002931
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSTBEG00000015946
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_tbel_4219
AGGGCTGTGCTGAAGTTCGCTGCTGCCCCTGGAGCCACTCCTATTGCTGGTCCTTCACTCCTGGAACCTTCACTAACCAG
ATCCAGGCAGCCTTCCGGGAGCCGCGTCTTCTGGTGGTGACTGATCCCAGGGCCGACCCCCAGCCCCTCACAGAGGCGTC
TTAGGTTAATCCACCTACCATTGCCCTGTGCAACACGGATTCTCCTCTGCGCTATGTGGACATTGCCATCCCATGCAACA
ACAAGGGAGCTCATTCGGTGGGTCTGATGTGGTGGATGCTGGCCAGGGAAGTGCTGCGCATGCGTGGCACCATCTCCCGT
GAACACCCGTGGGAGGTCATGCCTGATCTCTACTTCTACAGAGATCCTGAAGAGATTGAAAAGGAGGAACAGGCTGCAGC
TGAAAAGGCTCTGACCAAGGAGGAATTTCAGGGTGAATGGACTGCTCCCGCTCCTGAGTTTACTGCCGCTCAGCCTGAGG
TTGCAGACTGATCTGAAGGCGTGCAGGTGCCCTCCGTGCCCATCCAGCAGTTCCCTACTGAAGACTGGAGTGCTCAGCCT
GCCACCCAAGACTGGTCTGCAGCCCCCACTGCTCAGGCCACTGAACGGGTGGGAACAACCACTGAGTGGTCT

ORF - retro_tbel_4219 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.04 %
Parental protein coverage: 71.53 %
Number of stop codons detected: 2
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalRAVLKFAAATGATPIAG-RFTPGTFTNQIQAAFREPRLLVVTDPRADHQPLTEASYVNLPTIALCNTDSP
RAVLKFAAA.GATPIAG..FTPGTFTNQIQAAFREPRLLVVTDPRAD.QPLTEAS.VN.PTIALCNTDSP
RetrocopyRAVLKFAAAPGATPIAG<SFTPGTFTNQIQAAFREPRLLVVTDPRADPQPLTEAS*VNPPTIALCNTDSP
ParentalLRYVDIAIPCNNKVAGSLGLTWWMLAREVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVT
LRYVDIAIPCNNK.A.S.GL.WWMLAREVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKA.T
RetrocopyLRYVDIAIPCNNKGAHSVGLMWWMLAREVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKALT
ParentalKEEFQGEWAAPAPEFTATQPEVADWSEGRQVPSVPIQQFPTGDWSAQPATEDWSAAPTAQATEWAGTTTE
KEEFQGEW.APAPEFTA.QPEVAD.SEG.QVPSVPIQQFPT.DWSAQPAT.DWSAAPTAQATE..GTTTE
RetrocopyKEEFQGEWTAPAPEFTAAQPEVAD*SEGVQVPSVPIQQFPTEDWSAQPATQDWSAAPTAQATERVGTTTE
ParentalWS
WS
RetrocopyWS

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_4219 retrocopy.

TSS - click to see more details

Tupaia belangeri was not studied using FANTOM5 data.

Lab - click to see more details

retro_tbel_4219 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 25 parental genes, and 281 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000041831 retrocopy
retro_acar_140,
Ailuropoda melanoleuca ENSAMEG0000000896213 retrocopies
retro_amel_1091, retro_amel_1276, retro_amel_1357, retro_amel_1432, retro_amel_1446, retro_amel_1497, retro_amel_1634, retro_amel_1817, retro_amel_1857, retro_amel_196, retro_amel_430, retro_amel_808, retro_amel_943,
Callithrix jacchus ENSCJAG0000000967515 retrocopies
retro_cjac_1113, retro_cjac_1572, retro_cjac_1595, retro_cjac_2265, retro_cjac_2438, retro_cjac_2500, retro_cjac_2502, retro_cjac_2750, retro_cjac_2897, retro_cjac_305, retro_cjac_3160, retro_cjac_4124, retro_cjac_53, retro_cjac_732, retro_cjac_958,
Cavia porcellus ENSCPOG000000087157 retrocopies
retro_cpor_1206, retro_cpor_1255, retro_cpor_1293, retro_cpor_594, retro_cpor_624, retro_cpor_806, retro_cpor_958,
Dasypus novemcinctus ENSDNOG0000000404827 retrocopies
retro_dnov_1022, retro_dnov_108, retro_dnov_1099, retro_dnov_1219, retro_dnov_1372, retro_dnov_1431, retro_dnov_1614, retro_dnov_184, retro_dnov_1913, retro_dnov_1974, retro_dnov_1987, retro_dnov_1988, retro_dnov_2067, retro_dnov_2200, retro_dnov_2224, retro_dnov_2309, retro_dnov_2339, retro_dnov_2469, retro_dnov_2480, retro_dnov_375, retro_dnov_42, retro_dnov_456, retro_dnov_465, retro_dnov_663, retro_dnov_800, retro_dnov_895, retro_dnov_940,
Equus caballus ENSECAG000000130625 retrocopies
retro_ecab_193, retro_ecab_453, retro_ecab_46, retro_ecab_592, retro_ecab_71,
Erinaceus europaeus ENSEEUG000000052922 retrocopies
retro_eeur_202, retro_eeur_679,
Echinops telfairi ENSETEG000000181604 retrocopies
retro_etel_1399, retro_etel_1665, retro_etel_1960, retro_etel_92,
Homo sapiens ENSG000001680282 retrocopies
retro_hsap_107, retro_hsap_3015,
Gorilla gorilla ENSGGOG0000001503811 retrocopies
retro_ggor_1069, retro_ggor_1095, retro_ggor_1110, retro_ggor_1277, retro_ggor_1729, retro_ggor_2325, retro_ggor_2461, retro_ggor_2671, retro_ggor_2804, retro_ggor_2811, retro_ggor_62,
Loxodonta africana ENSLAFG000000320095 retrocopies
retro_lafr_1234, retro_lafr_367, retro_lafr_806, retro_lafr_863, retro_lafr_997,
Macropus eugenii ENSMEUG0000000816914 retrocopies
retro_meug_1123, retro_meug_1137, retro_meug_1643, retro_meug_1722, retro_meug_1923, retro_meug_1933, retro_meug_1936, retro_meug_343, retro_meug_429, retro_meug_684, retro_meug_810, retro_meug_847, retro_meug_957, retro_meug_990,
Macaca mulatta ENSMMUG000000079302 retrocopies
retro_mmul_1789, retro_mmul_592,
Macaca mulatta ENSMMUG0000002296519 retrocopies
retro_mmul_1008, retro_mmul_1167, retro_mmul_120, retro_mmul_1237, retro_mmul_136, retro_mmul_1527, retro_mmul_1678, retro_mmul_1755, retro_mmul_1879, retro_mmul_1909, retro_mmul_2274, retro_mmul_2388, retro_mmul_2538, retro_mmul_2541, retro_mmul_2622, retro_mmul_378, retro_mmul_789, retro_mmul_876, retro_mmul_911,
Mustela putorius furoENSMPUG0000000246321 retrocopies
retro_mputfur_1045, retro_mputfur_1143, retro_mputfur_1194, retro_mputfur_1227, retro_mputfur_1311, retro_mputfur_1318, retro_mputfur_1427, retro_mputfur_1502, retro_mputfur_1558, retro_mputfur_1584, retro_mputfur_288, retro_mputfur_358, retro_mputfur_423, retro_mputfur_477, retro_mputfur_515, retro_mputfur_560, retro_mputfur_576, retro_mputfur_712, retro_mputfur_733, retro_mputfur_932, retro_mputfur_953,
Mus musculus ENSMUSG000000325181 retrocopy
retro_mmus_219,
Otolemur garnettii ENSOGAG000000288308 retrocopies
retro_ogar_1507, retro_ogar_1548, retro_ogar_2094, retro_ogar_2258, retro_ogar_3126, retro_ogar_327, retro_ogar_457, retro_ogar_567,
Pongo abelii ENSPPYG000000139934 retrocopies
retro_pabe_1085, retro_pabe_1142, retro_pabe_116, retro_pabe_818,
Pan troglodytes ENSPTRG000000228411 retrocopy
retro_ptro_14,
Pteropus vampyrus ENSPVAG0000000779419 retrocopies
retro_pvam_1189, retro_pvam_1249, retro_pvam_1335, retro_pvam_1403, retro_pvam_1406, retro_pvam_1443, retro_pvam_1446, retro_pvam_396, retro_pvam_499, retro_pvam_532, retro_pvam_548, retro_pvam_60, retro_pvam_635, retro_pvam_650, retro_pvam_789, retro_pvam_889, retro_pvam_896, retro_pvam_898, retro_pvam_98,
Rattus norvegicus ENSRNOG0000001864527 retrocopies
retro_rnor_1004, retro_rnor_1114, retro_rnor_1119, retro_rnor_1213, retro_rnor_1301, retro_rnor_1396, retro_rnor_1481, retro_rnor_1634, retro_rnor_1778, retro_rnor_1840, retro_rnor_1886, retro_rnor_2068, retro_rnor_2153, retro_rnor_2329, retro_rnor_2384, retro_rnor_2444, retro_rnor_2553, retro_rnor_2554, retro_rnor_2589, retro_rnor_2637, retro_rnor_2649, retro_rnor_2701, retro_rnor_2810, retro_rnor_2912, retro_rnor_2958, retro_rnor_645, retro_rnor_702,
Sus scrofa ENSSSCG000000112669 retrocopies
retro_sscr_1022, retro_sscr_1180, retro_sscr_22, retro_sscr_269, retro_sscr_890, retro_sscr_926, retro_sscr_966, retro_sscr_967, retro_sscr_982,
Tupaia belangeri ENSTBEG00000015946 54 retrocopies
retro_tbel_1001, retro_tbel_1007, retro_tbel_1069, retro_tbel_1257, retro_tbel_1303, retro_tbel_1319, retro_tbel_1324, retro_tbel_1354, retro_tbel_1355, retro_tbel_1382, retro_tbel_1395, retro_tbel_1531, retro_tbel_1563, retro_tbel_1616, retro_tbel_1682, retro_tbel_1712, retro_tbel_1723, retro_tbel_1935, retro_tbel_2006, retro_tbel_245, retro_tbel_2511, retro_tbel_2518, retro_tbel_2544, retro_tbel_2735, retro_tbel_2827, retro_tbel_2906, retro_tbel_3198, retro_tbel_3218, retro_tbel_3241, retro_tbel_3272, retro_tbel_3325, retro_tbel_3351, retro_tbel_341, retro_tbel_3431, retro_tbel_3444, retro_tbel_3555, retro_tbel_3640, retro_tbel_3695, retro_tbel_3915, retro_tbel_3975, retro_tbel_4026, retro_tbel_4219 , retro_tbel_4252, retro_tbel_4259, retro_tbel_4355, retro_tbel_4423, retro_tbel_4479, retro_tbel_496, retro_tbel_565, retro_tbel_645, retro_tbel_666, retro_tbel_782, retro_tbel_802, retro_tbel_916,
Tarsius syrichta ENSTSYG000000044586 retrocopies
retro_tsyr_115, retro_tsyr_1290, retro_tsyr_156, retro_tsyr_38, retro_tsyr_456, retro_tsyr_807,
Vicugna pacos ENSVPAG000000123074 retrocopies
retro_vpac_22, retro_vpac_293, retro_vpac_440, retro_vpac_553,


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