RetrogeneDB ID: retro_tbel_3590

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_145520:57438..57903(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YBX1
• Ensembl ID: ENSTBEG00000015642
• Aliases: None
• Description: Y box binding protein 1 [Source:HGNC Symbol;Acc:8014]

Sequence

>retro_tbel_3590
ACTGCCATAAAGAAGAATAACCCCAGGAAGTACCTTCGCAGTGTAGGAGACGGAGAGACTGTGGAGTTCCATGCTGAAGG
AGAAAAGGGTGCGGAGGCAGCAGATGTTACAGGCCCTGGTGGAGCTCCAGTTCAAGGCAGTAAATATGCAGCAGACCGTA
ACCATTATAGACGCTGTCCACGTCCTAGGGGTCCTCCACGCAGTTACCAGCCAAATGACCAGAATAGAGTGGGGAAAAGA
ACAAGGGATCGCAGAGCGCTCCCGAAGGCCAGGCCCAACAACGCCGGCCCTCCCGCAGGCGAAGGTTCCCCCCTTACTAC
ATGCGGAGGTCCTATGGGCGTTGACCACAGTATTCCAACCTCCTGTGCAGGGAGAAGTGATGGGGGTGCTGACAACCAGG
GTGCAGGAGCACAAGGTAGACCAGTGAGGCAGAATATGTATCGGGGTTATAGACCGCTATTTCGC

Alignment

ORF - retro_tbel_3590 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.25 %
• Parental protein coverage: 64.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPGGVPVQGSKYAADRNHYRRYPRRRGPPRNY
          TAIKKNNPRKYLRSVGDGETVEF...EGEKGAEAA.VTGPGG.PVQGSKYAADRNHYRR.PR.RGPPR.Y
Retrocopy TAIKKNNPRKYLRSVGDGETVEFHA-EGEKGAEAADVTGPGGAPVQGSKYAADRNHYRRCPRPRGPPRSY

Parental  QPNYQNSESGEKNEGSESAP-EGQAQQRRPYRRRRFPPYYMRRPYGRRPQYSN-PPVQGEVM-EGADNQG
          QPN.QN...G.........P.EGQAQQRRP.RRRRFPPYYMRR.YGR.PQYSN.PPVQGEVM..GADNQG
Retrocopy QPNDQN-RVGKRTRDRRALP<EGQAQQRRPSRRRRFPPYYMRRSYGR*PQYSN<PPVQGEVM<GGADNQG

Parental  ARELQGRPVRQNMYRGYRPRFR
          A...QGRPVRQNMYRGYRP.FR
Retrocopy A-GAQGRPVRQNMYRGYRPLFR

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_3590 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3590 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 11 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002541	4 retrocopies	retro_cfam_1312, retro_cfam_2118, retro_cfam_758, retro_cfam_91,
Callithrix jacchus	ENSCJAG00000003155	6 retrocopies	retro_cjac_1261, retro_cjac_1701, retro_cjac_2718, retro_cjac_3156, retro_cjac_4172, retro_cjac_817,
Echinops telfairi	ENSETEG00000004125	3 retrocopies	retro_etel_1772, retro_etel_1980, retro_etel_2134,
Felis catus	ENSFCAG00000022604	6 retrocopies	retro_fcat_145, retro_fcat_1554, retro_fcat_1956, retro_fcat_241, retro_fcat_503, retro_fcat_631,
Loxodonta africana	ENSLAFG00000007597	1 retrocopy	retro_lafr_804,
Macaca mulatta	ENSMMUG00000013136	5 retrocopies	retro_mmul_1139, retro_mmul_1423, retro_mmul_2017, retro_mmul_423, retro_mmul_861,
Oryctolagus cuniculus	ENSOCUG00000028047	2 retrocopies	retro_ocun_1519, retro_ocun_1953,
Otolemur garnettii	ENSOGAG00000006784	25 retrocopies	retro_ogar_1127, retro_ogar_1246, retro_ogar_1350, retro_ogar_1371, retro_ogar_1497, retro_ogar_2011, retro_ogar_2018, retro_ogar_2302, retro_ogar_2359, retro_ogar_2607, retro_ogar_2654, retro_ogar_3170, retro_ogar_3225, retro_ogar_324, retro_ogar_3303, retro_ogar_3316, retro_ogar_3317, retro_ogar_3366, retro_ogar_3416, retro_ogar_3474, retro_ogar_448, retro_ogar_572, retro_ogar_678, retro_ogar_690, retro_ogar_753,
Sorex araneus	ENSSARG00000007896	1 retrocopy	retro_sara_559,
Tupaia belangeri	ENSTBEG00000012570	1 retrocopy	retro_tbel_996,
Tupaia belangeri	ENSTBEG00000015642	9 retrocopies	retro_tbel_1183, retro_tbel_1955, retro_tbel_2347, retro_tbel_2694, retro_tbel_2702, retro_tbel_2961, retro_tbel_3590 , retro_tbel_4037, retro_tbel_4478,