RetrogeneDB ID: retro_tbel_117

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1186:75889..76302(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000016853
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000010726
• Aliases: None
• Description: None

Sequence

>retro_tbel_117
ATAATCAAGAGCCTTGGTTACGACCGACTTACCCTCCAAATTGGTAGAGGAACAGTGGCACCTGAACCATTCAGCACCGA
GTCCTTTACTCTGGATGTTTACAGGCACAAGGATTCCTTGAAAGAAGACCTTCAGAATGCAGATCTTGTTATTAGTCACG
CAGGTCCTGGAAGCTGTTTAGAGACTCTGGAGAGAGGAAAGCCACTCGTGGTGGTTATAAATGAAAAGTTGATGAATAAT
CATCAGCTGGAATTGGCAAAACAGCTACACAAAGAGGGACATCTCTTCTACTGTACCTGCAGCAGCTTTCTGGGCTGTTA
CAGTCAATGGATTTATCAACACTGAAATGTTATCCTCCTGGCCAGCCAGAAAAATTTTCTGCATTTTTCGATAAAGTTGT
TGGATTACAAAAA

Alignment

ORF - retro_tbel_117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IIKSLGYDRLTLQIGRGTVAPEPFSTESFTLDVYRYKDSLKEDLQNADLVISHAGAGSCLETLERGKPLV
          IIKSLGYDRLTLQIGRGTVAPEPFSTESFTLDVYR.KDSLKEDLQNADLVISHAG.GSCLETLERGKPLV
Retrocopy IIKSLGYDRLTLQIGRGTVAPEPFSTESFTLDVYRHKDSLKEDLQNADLVISHAGPGSCLETLERGKPLV

Parental  VVINEKLMNNHQLELAKQLHKEGHLFYCTCST-LPGLLQSMDLSTLKCYPPGQPEKFSAFLDKVVGLQK
          VVINEKLMNNHQLELAKQLHKEGHLFYCTCS..L.GLLQSMDLSTLKCYPPGQPEKFSAF.DKVVGLQK
Retrocopy VVINEKLMNNHQLELAKQLHKEGHLFYCTCSS<LSGLLQSMDLSTLKCYPPGQPEKFSAFFDKVVGLQK

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_117 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_117 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000005613	1 retrocopy	retro_etel_1023,
Monodelphis domestica	ENSMODG00000005175	1 retrocopy	retro_mdom_1156,
Mus musculus	ENSMUSG00000041718	1 retrocopy	retro_mmus_256,
Oryctolagus cuniculus	ENSOCUG00000000232	2 retrocopies	retro_ocun_1459, retro_ocun_477,
Otolemur garnettii	ENSOGAG00000031713	2 retrocopies	retro_ogar_2864, retro_ogar_3363,
Tupaia belangeri	ENSTBEG00000010726	2 retrocopies	retro_tbel_117 , retro_tbel_6,