RetrogeneDB ID: retro_tbel_4051

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_59573:1066..1300(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BLOC1S2
• Ensembl ID: ENSTBEG00000016889
• Aliases: None
• Description: biogenesis of lysosomal organelles complex-1, subunit 2 [Source:HGNC Symbol;Acc:20984]

Sequence

>retro_tbel_4051
TGCTGAGACATGTTCTCCAAGATGGCCACATACCTGACTGGGGAGCTGACGGCTACCAGTGAAGACTGTAAGCTTCTGGA
AAATATGAATAAACTAACCCAGCTTGAAGTACCTTGAAATGAAAGATATTGCTATAAACATTAGTAGAAATGTAAAGGAC
TTAAACCAGAAGTATGCTGACTGCAGCCTTATCTGGATCAGATCAGCGTCCTCACTGAGCAGGGAGCCGCTCTT

Alignment

ORF - retro_tbel_4051 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.5 %
• Parental protein coverage: 55.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CRDMFSKMATYLTGELTATSEDYKLLENMNKLT-SLKYLEMKDIAINISRNXXXXXXXXAG-LQPYLDQI
          C.DMFSKMATYLTGELTATSED.KLLENMNKLT.SLKYLEMKDIAINISRN........A..LQPYLDQI
Retrocopy C*DMFSKMATYLTGELTATSEDCKLLENMNKLT>SLKYLEMKDIAINISRNVKDLNQKYAD<LQPYLDQI

Parental  NAIEEQVAAL
          ....EQ.AAL
Retrocopy SVLTEQGAAL

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_4051 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4051 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 5 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000007299	1 retrocopy	retro_etel_861,
Macropus eugenii	ENSMEUG00000003630	57 retrocopies	retro_meug_1051, retro_meug_1098, retro_meug_1099, retro_meug_114, retro_meug_1152, retro_meug_1157, retro_meug_1175, retro_meug_1248, retro_meug_1276, retro_meug_1324, retro_meug_1353, retro_meug_1382, retro_meug_1405, retro_meug_1502, retro_meug_153, retro_meug_1592, retro_meug_1629, retro_meug_1687, retro_meug_1707, retro_meug_1715, retro_meug_1756, retro_meug_1785, retro_meug_1834, retro_meug_1844, retro_meug_1892, retro_meug_1925, retro_meug_1937, retro_meug_1955, retro_meug_1978, retro_meug_2007, retro_meug_2012, retro_meug_2083, retro_meug_2145, retro_meug_2177, retro_meug_2188, retro_meug_225, retro_meug_243, retro_meug_250, retro_meug_259, retro_meug_317, retro_meug_329, retro_meug_339, retro_meug_391, retro_meug_394, retro_meug_617, retro_meug_711, retro_meug_725, retro_meug_827, retro_meug_839, retro_meug_841, retro_meug_871, retro_meug_922, retro_meug_931, retro_meug_955, retro_meug_967, retro_meug_975, retro_meug_984,
Mus musculus	ENSMUSG00000057506	2 retrocopies	retro_mmus_1918, retro_mmus_363,
Otolemur garnettii	ENSOGAG00000001395	4 retrocopies	retro_ogar_2024, retro_ogar_3475, retro_ogar_671, retro_ogar_696,
Tupaia belangeri	ENSTBEG00000016889	1 retrocopy	retro_tbel_4051 ,