RetrogeneDB ID: retro_tbel_474

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_2175:112507..112936(-)
• Located in intron of: ENSTBEG00000012293

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000007749
• Aliases: None
• Description: None

Sequence

>retro_tbel_474
ATGAAGTTCAATCCTTTTGTGACTTCTGACCGAAGCAAGAACCGTAAAAGGCATTTCAATGCACCTTCCCACATCCGAAG
GAAGATAATGTCTTCCCCCCTTTCCAAAGAGCTGAGGCAGAAGTACAACGTGCGATCTATGCCCATCCGAGAAGATGAAG
TTCAGGTTGTGCGAGGACACTATAAAGGGCAGCACATTGGCAAAGTGGTCCAAGTGTACAGGAAGAAATATGTCACCTAC
ACTGAGCAGGTGCAGCGGGAAAAGGCTAACGGCACAGCGGTCCACGTGGGGATTCGCCCCAGCAAGGCGGTTACCATAGA
CTAAAGCTGGACAAAGACCGCAAAAAGATCCTTGAACGGAAAGCCAAGTCTTGCCAAGTAGGAAAAGAAAAGGGCAAACA
TAAAAAAACAATTGAGAAGATGCAGGAGT

Alignment

ORF - retro_tbel_474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.99 %
• Parental protein coverage: 93.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKFNPFVTSDRSKNRKRHFNAPSHIRRKIMSS-LSKELRQKYNVRSMPIRKDDEVQVVRGHYKGQQIGKV
          MKFNPFVTSDRSKNRKRHFNAPSHIRRKIMSS.LSKELRQKYNVRSMPIR..DEVQVVRGHYKGQ.IGKV
Retrocopy MKFNPFVTSDRSKNRKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIR-EDEVQVVRGHYKGQHIGKV

Parental  VQVYRKKYVIYIERVQREKANGTTVHVGIHPSKVVIT-RLKLDKDRKKILERKAKSRQVGKEKNIR-KKQ
          VQVYRKKYV.Y.E.VQREKANGT.VHVGI.PSK.V...RLKLDKDRKKILERKAKS.QVGKEK....KKQ
Retrocopy VQVYRKKYVTYTEQVQREKANGTAVHVGIRPSKAVTI<RLKLDKDRKKILERKAKSCQVGKEKGKH>KKQ

Parental  SRRCRS
          .RRCRS
Retrocopy LRRCRS

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_474 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_474 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 14 parental genes, and 153 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002453	7 retrocopies	retro_amel_1175, retro_amel_1535, retro_amel_1885, retro_amel_1934, retro_amel_360, retro_amel_499, retro_amel_900,
Bos taurus	ENSBTAG00000012344	2 retrocopies	retro_btau_1090, retro_btau_230,
Callithrix jacchus	ENSCJAG00000014372	8 retrocopies	retro_cjac_110, retro_cjac_119, retro_cjac_240, retro_cjac_250, retro_cjac_270, retro_cjac_297, retro_cjac_321, retro_cjac_362,
Felis catus	ENSFCAG00000011259	13 retrocopies	retro_fcat_1090, retro_fcat_1151, retro_fcat_1198, retro_fcat_1236, retro_fcat_1257, retro_fcat_1309, retro_fcat_1412, retro_fcat_1652, retro_fcat_1801, retro_fcat_1845, retro_fcat_1965, retro_fcat_497, retro_fcat_801,
Homo sapiens	ENSG00000161970	27 retrocopies	retro_hsap_1137, retro_hsap_1309, retro_hsap_1376, retro_hsap_1394, retro_hsap_191, retro_hsap_2108, retro_hsap_2165, retro_hsap_2253, retro_hsap_253, retro_hsap_267, retro_hsap_2946, retro_hsap_3118, retro_hsap_3260, retro_hsap_3324, retro_hsap_3490, retro_hsap_3700, retro_hsap_3803, retro_hsap_3813, retro_hsap_3914, retro_hsap_4043, retro_hsap_4061, retro_hsap_4874, retro_hsap_4932, retro_hsap_642, retro_hsap_691, retro_hsap_915, retro_hsap_998,
Gorilla gorilla	ENSGGOG00000023944	4 retrocopies	retro_ggor_2565, retro_ggor_270, retro_ggor_51, retro_ggor_974,
Myotis lucifugus	ENSMLUG00000002176	1 retrocopy	retro_mluc_232,
Macaca mulatta	ENSMMUG00000003448	22 retrocopies	retro_mmul_1117, retro_mmul_1361, retro_mmul_1398, retro_mmul_1497, retro_mmul_1710, retro_mmul_1773, retro_mmul_1899, retro_mmul_1986, retro_mmul_2052, retro_mmul_2163, retro_mmul_2332, retro_mmul_2344, retro_mmul_325, retro_mmul_360, retro_mmul_398, retro_mmul_405, retro_mmul_448, retro_mmul_548, retro_mmul_805, retro_mmul_903, retro_mmul_920, retro_mmul_992,
Monodelphis domestica	ENSMODG00000006201	2 retrocopies	retro_mdom_36, retro_mdom_64,
Nomascus leucogenys	ENSNLEG00000009981	1 retrocopy	retro_nleu_76,
Otolemur garnettii	ENSOGAG00000017070	3 retrocopies	retro_ogar_118, retro_ogar_255, retro_ogar_66,
Sarcophilus harrisii	ENSSHAG00000006890	1 retrocopy	retro_shar_458,
Sus scrofa	ENSSSCG00000028850	9 retrocopies	retro_sscr_261, retro_sscr_363, retro_sscr_426, retro_sscr_427, retro_sscr_471, retro_sscr_485, retro_sscr_508, retro_sscr_609, retro_sscr_736,
Tupaia belangeri	ENSTBEG00000007749	53 retrocopies	retro_tbel_1053, retro_tbel_1088, retro_tbel_1103, retro_tbel_1140, retro_tbel_1366, retro_tbel_1389, retro_tbel_1390, retro_tbel_1391, retro_tbel_1433, retro_tbel_1497, retro_tbel_1512, retro_tbel_1767, retro_tbel_1793, retro_tbel_1928, retro_tbel_1930, retro_tbel_2005, retro_tbel_2033, retro_tbel_2053, retro_tbel_2057, retro_tbel_2099, retro_tbel_2105, retro_tbel_2332, retro_tbel_2416, retro_tbel_2465, retro_tbel_2500, retro_tbel_268, retro_tbel_2727, retro_tbel_2778, retro_tbel_2806, retro_tbel_2884, retro_tbel_3020, retro_tbel_3187, retro_tbel_3300, retro_tbel_3332, retro_tbel_3704, retro_tbel_3711, retro_tbel_3790, retro_tbel_3964, retro_tbel_404, retro_tbel_4162, retro_tbel_4200, retro_tbel_4381, retro_tbel_4416, retro_tbel_446, retro_tbel_4480, retro_tbel_470, retro_tbel_474 , retro_tbel_495, retro_tbel_573, retro_tbel_863, retro_tbel_906, retro_tbel_964, retro_tbel_99,