RetrogeneDB ID: retro_tbel_4560

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_902:9248..9976(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000001510
• Aliases: None
• Description: None

Sequence

>retro_tbel_4560
ATGGTGAAGGTCGGAATAAAGGGATTTGGCCGTATTGGGTGCCTGGTCACCAGGGCTGCCTTCACCTGTGGCAAAGTGGA
TGTTGTGGCCATCAACGACCCCTTCATTGACTTGAACTACATGGTTACATGTCCTAGTATGGCAAGTTCAATGGCACCGT
CAAGGCCGAGAACGGGAAGCTTATCATCAACGGGAAGTCCATCAACACCTTCCAGGAGCGAGATCCCGCCAACATCAGAG
GGGGTGATGCTGGTGCTGAGTGTGTTGTGGAGTCCACTGGTGTCTTCACCACCGTGGAGAAGGCTGGGGCTCACTTGAAG
GGTGGAGCCAAAAGGGTCTACATCTCTGCCCCTTCTGCCGACGCCCCCATGTTTGTGATGGGCGTGAACCACGAGAAGTA
ACGACAACTCCCTTAGCAATGCCTCCTGCACCACCAACTGCTTGGCCCCCCTGGCCAAGGTCATCCATGACAATTTTGGC
ATCATGGAAGGACTCATGACCACAGTCCACGCCATCACTGCCACCCAGAAGACTGTGGACGGCCCTCGGGGAAGCTGTGG
CGTGATGGCTGTGGGGCTGCCCAGAACATCATCCCAGCATTGACCGGGGCTGCCAAGGCTGTGGGCAAGGTCATCTCAGA
GCTGAACGGGAAGCTCACCGGCATGGCTTTCCATGTCCCCACCCGCAACGTGTCGGTCGTGGACTTGACCTGCCACCTGG
AGAAAGCT

Alignment

ORF - retro_tbel_4560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.38 %
• Parental protein coverage: 94.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVKVGVNGFGRIGRLVTRAAFNSGKVDVVAINDPFIDLNYMV-YMFQYDSTHGKFNGTVKAENGKLVING
          MVKVG..GFGRIG.LVTRAAF..GKVDVVAINDPFIDLNYMV.YM..Y....G....TVKAENGKL.ING
Retrocopy MVKVGIKGFGRIGCLVTRAAFTCGKVDVVAINDPFIDLNYMV<YMS*YGKFNG----TVKAENGKLIING

Parental  KSITIFQERDPANIKWGDAGAEYVVESTGVFTTMEKAGAHLKGGAKRVIISAPSADAPMFVMGVNHEK-Y
          KSI..FQERDPANI..GDAGAE.VVESTGVFTT.EKAGAHLKGGAKRV.ISAPSADAPMFVMGVNHEK..
Retrocopy KSINTFQERDPANIRGGDAGAECVVESTGVFTTVEKAGAHLKGGAKRVYISAPSADAPMFVMGVNHEK>N

Parental  DNSLKIVSNASCTTNCLAPLAKVIHDNFGIVEGLMTTVHAITATQKTVDG-PSGKLWRDGRGAAQNIIPA
          DNSL...SNASCTTNCLAPLAKVIHDNFGI.EGLMTTVHAITATQKTVDG.PSGKLWRDG.GAAQNIIPA
Retrocopy DNSL---SNASCTTNCLAPLAKVIHDNFGIMEGLMTTVHAITATQKTVDG<PSGKLWRDGCGAAQNIIPA

Parental  STGAAKAVGKVIPELNGKLTGMAFRVPTPNVSVVDLTCRLEKA
          .TGAAKAVGKVI.ELNGKLTGMAF.VPT.NVSVVDLTC.LEKA
Retrocopy LTGAAKAVGKVISELNGKLTGMAFHVPTRNVSVVDLTCHLEKA

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_4560 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4560 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 3 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002325	1 retrocopy	retro_cfam_1407,
Tupaia belangeri	ENSTBEG00000001510	27 retrocopies	retro_tbel_1055, retro_tbel_1149, retro_tbel_1315, retro_tbel_1359, retro_tbel_1519, retro_tbel_1684, retro_tbel_232, retro_tbel_2380, retro_tbel_2442, retro_tbel_2731, retro_tbel_2992, retro_tbel_3109, retro_tbel_3205, retro_tbel_3418, retro_tbel_3463, retro_tbel_3826, retro_tbel_3829, retro_tbel_393, retro_tbel_4036, retro_tbel_4094, retro_tbel_4310, retro_tbel_4377, retro_tbel_441, retro_tbel_4560 , retro_tbel_4635, retro_tbel_4706, retro_tbel_480,
Tupaia belangeri	ENSTBEG00000008617	16 retrocopies	retro_tbel_1017, retro_tbel_1193, retro_tbel_124, retro_tbel_1650, retro_tbel_1685, retro_tbel_2010, retro_tbel_2486, retro_tbel_249, retro_tbel_2793, retro_tbel_2832, retro_tbel_2873, retro_tbel_2929, retro_tbel_3117, retro_tbel_425, retro_tbel_4292, retro_tbel_4346,