RetrogeneDB ID: retro_tbel_3679

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_148290:3194..3853(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRR1
• Ensembl ID: ENSTBEG00000008145
• Aliases: None
• Description: KRR1, small subunit (SSU) processome component, homolog (yeast) [Source:HGNC Symbol;Acc:5176]

Sequence

>retro_tbel_3679
ATGGCTGCTCCCTCACAGAACGGGCTGACTGCCGGGACTGGGAAAAGTGAATTTCAGAATCAGAAGTCAAAGGTAGAGAA
CTGAGATGAATCAGAGCTACTTACTGTTCCTGATGGTTGGAAGGAACCAGCCTTTTCCAAAGAAGACAATCCCGAAGGAC
TCTGGGAAGAGAGCAGTTTTGCAACCTTATTTCCAAAGAATAGAGAGGCTTACTTGAAATAGTGTTGGCCTTTGGTGCAG
AAAGCATTGAATGAACATCATGTTAATGCAACCTTGGACCTGATCGAGGCAGCATGACTGTTTGTATTACAAAGAAGACT
TTTGATCCATACATCATCATTAGGGTCAGAGACTTAATAAAACTATTAGCAAGGAGTGTTTCATTTGAACAGGCACTACG
AATTCTTCAGGATGACATTGCATGTGACAACATCAAAATAGATTCTTTGGTAAGAAATAAAGAACGAGTTGTAAAAAGAA
GACAACGGCTTATTTGTCCCAAAGGATCTATATTGAAGGCATTGGAACTCTTAACAAGCTGTTACATTATGGTTCAAGGA
AACACAGTTTCAGCCATCAGACCTTGTAGTGGATTAAAGGAGGTTTGAAAAGTAGTCCTAGATACTATGAAGAATATTCA
CCCAATTTATAACATTAAA

Alignment

ORF - retro_tbel_3679 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.69 %
• Parental protein coverage: 66.07 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAASSLNGPAAGTGKSEFRNQKSKVENRDESELLTVPDGWKEPAFSKEDNPRGLLEESSFATLFPKYREA
          MAA.S.NG..AGTGKSEF.NQKSKVEN.DESELLTVPDGWKEPAFSKEDNP.GL.EESSFATLFPK.REA
Retrocopy MAAPSQNGLTAGTGKSEFQNQKSKVEN*DESELLTVPDGWKEPAFSKEDNPEGLWEESSFATLFPKNREA

Parental  YLKECWPLVQKALNEHHVKATLDLIE-GSMTVCTTKKTFDPYIIIRARDLIKLLARSVSFEQAVRILQDD
          YLK.CWPLVQKALNEHHV.ATLDLIE.GSMTVC.TKKTFDPYIIIR.RDLIKLLARSVSFEQA.RILQDD
Retrocopy YLK*CWPLVQKALNEHHVNATLDLIE<GSMTVCITKKTFDPYIIIRVRDLIKLLARSVSFEQALRILQDD

Parental  IACDIIKIGSLVRNKERFVKRRQRLIGPKGSTLKALELLTNCYIMVQGNTVSAIGPFNGLKEVRKVVLDT
          IACD.IKI.SLVRNKER.VKRRQRLI.PKGS.LKALELLT.CYIMVQGNTVSAI.P..GLKEV.KVVLDT
Retrocopy IACDNIKIDSLVRNKERVVKRRQRLICPKGSILKALELLTSCYIMVQGNTVSAIRPCSGLKEV*KVVLDT

Parental  MKNIHPIYNIK
          MKNIHPIYNIK
Retrocopy MKNIHPIYNIK

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_3679 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3679 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006437	1 retrocopy	retro_amel_1292,
Canis familiaris	ENSCAFG00000005665	1 retrocopy	retro_cfam_1091,
Choloepus hoffmanni	ENSCHOG00000009636	5 retrocopies	retro_chof_1030, retro_chof_1826, retro_chof_2438, retro_chof_2452, retro_chof_365,
Monodelphis domestica	ENSMODG00000020451	1 retrocopy	retro_mdom_791,
Tupaia belangeri	ENSTBEG00000008145	5 retrocopies	retro_tbel_1056, retro_tbel_2060, retro_tbel_2911, retro_tbel_2915, retro_tbel_3679 ,