RetrogeneDB ID: retro_tbel_3975

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_47207:484..1162(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000015946
• Aliases: None
• Description: None

Sequence

>retro_tbel_3975
GCAGCTTGTGCCGTTGTTGCCATTGAAAACCCTGCCCACGTCAGTGTCCTGACTTCCAGGAACACTGGACAGCGGGCTGT
GCTGAAGTTGGCTCCTGCCACTGGGGCCACTCCTATTGCTGGTCCTTCACTCCTGGAACCATCCCTAACCAGATCCAGGC
AGCCTTCCGGGAACCGCGTCTTCTGGTGGTGACTGATCCCAGGGCCGACCCCCAGCCTCTCACAGAGGTGTCTAGTGTTA
ATCCACCTCCCATTGCCCTGTGCAACACAGATTCTCCTCTGCGCTGTGTGGACTTGCATTCCCAGGCAACAAGGGAGCTC
ATTGGGTGGGTTTGATGTGGTGCGTGCTGGCCCGGGAAGTGCTACGCATGCGTGGCACCGTCTCCTGTGAACACCCGTGG
GAGGTCATACCTGACCTCTACTTCTGCAGAGATCCGGAAGAGATCGAAAGGAGGAGCAGGCTGCAGCTGAAAAGGCTGTG
ATGAAGGAAGAATTTCAGGTGAATGGACTGCTCCAGCTCGTGAGTTTACTGCTACTCAGCCTGAGTTGCAGACTGGTCCT
AAGGCGTGCAGATGCCCTCCGTGCCCACCGCGCAGTTCCTCACTGAAGACTGGAGTGCTCACCTGCCACCGAAGACTGGT
CTGCAGCCCCTACTGCTCAGGCCACTGAATGGATGGGA

Alignment

ORF - retro_tbel_3975 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.72 %
• Parental protein coverage: 77.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  AARAIVAIENPADVSVISSRNTGXRAVLKFAAATGATPIAG-RFTPGTFTNQIQAAFREPRLLVVTDPRA
          AA.A.VAIENPA.VSV..SRNTG.RAVLK.A.ATGATPIAG..FTPGT..NQIQAAFREPRLLVVTDPRA
Retrocopy AACAVVAIENPAHVSVLTSRNTGQRAVLKLAPATGATPIAG<SFTPGTIPNQIQAAFREPRLLVVTDPRA

Parental  DHQPLTEASYVNLPTIALCNTDSPLRYVD-IAIPCNNKVAGSLGLTWWMLAREVLRMRGTISREHPWEVM
          D.QPLTE.S.VN.P.IALCNTDSPLR.VD..A.P..NK.A...GL.W..LAREVLRMRGT.S.EHPWEV.
Retrocopy DPQPLTEVSSVNPPPIALCNTDSPLRCVD<LAFP-GNKGAHWVGLMWCVLAREVLRMRGTVSCEHPWEVI

Parental  PDLYFYRDPEEIE-KEEQAAAEKAVTKEEFQ-GEWAAPAPEFTATQPE-VADWSEGRQVPSVPIQQFPTG
          PDLYF.RDPEEIE.KEEQAAAEKAV.KEEFQ.GEW.APA.EFTATQPE.VADWS.G.Q.PSVP..QF.T.
Retrocopy PDLYFCRDPEEIE<KEEQAAAEKAVMKEEFQ<GEWTAPAREFTATQPE<VADWS*GVQMPSVPTAQFLTE

Parental  DWSA-QPATEDWSAAPTAQATEWAG
          DWSA..PATEDWSAAPTAQATEW.G
Retrocopy DWSA<SPATEDWSAAPTAQATEWMG

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_3975 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3975 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 281 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004183	1 retrocopy	retro_acar_140,
Ailuropoda melanoleuca	ENSAMEG00000008962	13 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	ENSCJAG00000009675	15 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	ENSCPOG00000008715	7 retrocopies	retro_cpor_1206, retro_cpor_1255, retro_cpor_1293, retro_cpor_594, retro_cpor_624, retro_cpor_806, retro_cpor_958,
Dasypus novemcinctus	ENSDNOG00000004048	27 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	ENSECAG00000013062	5 retrocopies	retro_ecab_193, retro_ecab_453, retro_ecab_46, retro_ecab_592, retro_ecab_71,
Erinaceus europaeus	ENSEEUG00000005292	2 retrocopies	retro_eeur_202, retro_eeur_679,
Echinops telfairi	ENSETEG00000018160	4 retrocopies	retro_etel_1399, retro_etel_1665, retro_etel_1960, retro_etel_92,
Homo sapiens	ENSG00000168028	2 retrocopies	retro_hsap_107, retro_hsap_3015,
Gorilla gorilla	ENSGGOG00000015038	11 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	ENSLAFG00000032009	5 retrocopies	retro_lafr_1234, retro_lafr_367, retro_lafr_806, retro_lafr_863, retro_lafr_997,
Macropus eugenii	ENSMEUG00000008169	14 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	ENSMMUG00000007930	2 retrocopies	retro_mmul_1789, retro_mmul_592,
Macaca mulatta	ENSMMUG00000022965	19 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 furo	ENSMPUG00000002463	21 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	ENSMUSG00000032518	1 retrocopy	retro_mmus_219,
Otolemur garnettii	ENSOGAG00000028830	8 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	ENSPPYG00000013993	4 retrocopies	retro_pabe_1085, retro_pabe_1142, retro_pabe_116, retro_pabe_818,
Pan troglodytes	ENSPTRG00000022841	1 retrocopy	retro_ptro_14,
Pteropus vampyrus	ENSPVAG00000007794	19 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	ENSRNOG00000018645	27 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	ENSSSCG00000011266	9 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	ENSTSYG00000004458	6 retrocopies	retro_tsyr_115, retro_tsyr_1290, retro_tsyr_156, retro_tsyr_38, retro_tsyr_456, retro_tsyr_807,
Vicugna pacos	ENSVPAG00000012307	4 retrocopies	retro_vpac_22, retro_vpac_293, retro_vpac_440, retro_vpac_553,