RetrogeneDB ID: retro_tbel_3726

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_149475:45887..46327(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DUSP12
• Ensembl ID: ENSTBEG00000015805
• Aliases: None
• Description: dual specificity phosphatase 12 [Source:HGNC Symbol;Acc:3067]

Sequence

>retro_tbel_3726
TTACAGAATTTAACTTAAGAACTCTTTGCTGTTGACCCAGCAAATCTCAAAAGATTGAGAGATAAGGGCTTCTCTACAAA
TGTAGAAAGTGCAGGCAATCCTTATTTCAAAGTTCTAGTATTTGGAGTCGTAATAAAGGAAGTGGGCCTACAGATTTTGC
CCACAAGCAAAAAAACCCCATCTTACGTGCATACCACAGAGACTCAGGGTCAATGTGTATCTTGTTTTATTGAACCTGTG
CATGGATCAAATCCACTTTGTTGGGAGAGATGGACTGACATCTTCTTTGCCCAAAATGCAGTGCTAGGTTGAGTTTCCTC
AATCTGTGTGGTGAACAGTGTTCCTGTGATAGATAGATAACACCTGCTTTTAAAATCCCTAAGCATATAGTGGATAAAAT
GTAAACACTGCTGGTTTGGGGACCACAAACAAGAAAAATC

Alignment

ORF - retro_tbel_3726 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.0 %
• Parental protein coverage: 54.44 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LQNLPQELFAVD-PTTISQGSKDEVLYKCRKCRRSLFRSSSILYHNEGNGPIAFAHK-RVTPALMPTRGS
          LQNL..ELFAVD.P...........LYKCRKCR.SLF.SSSI...N.G.GP..FAHK...TP....T...
Retrocopy LQNLT*ELFAVD<PSKSQKIER*GLLYKCRKCRQSLFQSSSIWSRNKGSGPTDFAHK>KKTPSYVHTTET

Parental  PAQCTSYFIEPVQ-WMESTLLGVMDGQLLCPKCGAKLGSFNWYGEQCSCGRWVTPAFQMHKNRVDEMKTL
          ..QC.S.FIEPV..W..STLLG.MD..LLCPKC.A.L...N..GEQCSC.R..TPAF...K..VD.M.TL
Retrocopy QGQCVSCFIEPVH<WIKSTLLGEMD*HLLCPKCSARLSFLNLCGEQCSCDR*ITPAFKIPKHIVDKM*TL

Parental  PVLGSQARKV
          .V.G.Q.RK.
Retrocopy LVWGPQTRKI

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_3726 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3726 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000000590	1 retrocopy	retro_ogar_2517,
Ictidomys tridecemlineatus	ENSSTOG00000025153	1 retrocopy	retro_itri_1224,
Tupaia belangeri	ENSTBEG00000015805	1 retrocopy	retro_tbel_3726 ,