RetrogeneDB ID: retro_tbel_2911

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_123369:104350..105010(-)
• 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_2911
ATGGCAGCCTCCTCACAGAATGGGCAAACTTCCAGGACTGGGAAAAGTGAATTTCAGAATCAGAAGTCAAAGCTAGAGAA
CCGAGATAAATTAGAGCTACTTACTGTTTCTGATGGTTAGAAGGGACCAGCCTTTTCCAAAGAAGACAATCCCAGAAGAC
ACTTGGAGGAAAGCAGTTTTGCAACCTGTTTCCAAAGTATAGAGAGGCTTACTTGAAAGAGTGTTGGTCTTTGGTGAAGA
AAATATTGAATGAACATCACGTTCATGCAACCTTGGACTTGATCAAGGGCAGTATGACTGTGTGTACTACAAAGAAGACT
TTTGATCTCTCTGTCCTCATTAGGGCCAGAGACTAACTAAAACTGTTAGCAAGGAGTGTTTCATTTGAACAGGCAGTACA
AATTCTTCAGGATGACATTGCATGTGATATCACTAAATTAGGTTTTTTAGGCAAGAAATAAAGAACAATTTGTAAAAAGA
AGACAATGGCTTATTGATCCCAAAGGATCTACATTGAAGGCTTTGAAACTCTTAACAAACTGTTACATTATGGTTCAAGG
AGACACTGTTTTAGCTGTTGGACCTTTTAGTGGATTAAAGGAGGTTTGAAAAGTAGTCATAGATACTATGAAGAATATTC
ATCCAATTTAGAACATTAAA

Alignment

ORF - retro_tbel_2911 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.63 %
• Parental protein coverage: 66.07 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAASSLNGPAAGTGKSEFRNQKSKVENRDESELLTVPDGWKEPAFSKEDNPRGLLEESSFAT-LFPKYRE
          MAASS.NG....TGKSEF.NQKSK.ENRD..ELLTV.DG.K.PAFSKEDNPR..LEESSFAT.LFPKYRE
Retrocopy MAASSQNGQTSRTGKSEFQNQKSKLENRDKLELLTVSDG*KGPAFSKEDNPRRHLEESSFAT<LFPKYRE

Parental  AYLKECWPLVQKALNEHHVKATLDLIEGSMTVCTTKKTFDPYIIIRARDLIKLLARSVSFEQAVRILQDD
          AYLKECW.LV.K.LNEHHV.ATLDLI.GSMTVCTTKKTFD....IRARD..KLLARSVSFEQAV.ILQDD
Retrocopy AYLKECWSLVKKILNEHHVHATLDLIKGSMTVCTTKKTFDLSVLIRARD*LKLLARSVSFEQAVQILQDD

Parental  IACDIIKIGSL-VRNKERFVKRRQRLIGPKGSTLKALELLTNCYIMVQGNTVSAIGPFNGLKEVRKVVLD
          IACDI.K.G.L..RNKE.FVKRRQ.LI.PKGSTLKAL.LLTNCYIMVQG.TV.A.GPF.GLKEV.KVV.D
Retrocopy IACDITKLGFL>ARNKEQFVKRRQWLIDPKGSTLKALKLLTNCYIMVQGDTVLAVGPFSGLKEV*KVVID

Parental  TMKNIHPIYNIK
          TMKNIHPI.NIK
Retrocopy TMKNIHPI*NIK

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_2911 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2911 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 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,