RetrogeneDB ID: retro_tbel_2297

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_108698:42922..43810(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000007004
• Aliases: None
• Description: None

Sequence

>retro_tbel_2297
CATGAACAGTCAGTCAAAAGAGAATTTATCCTCTTGGGATTGACAGATGACTCACAACTGCAATTTGTGATTTTCATATT
TCTCTTTCTCAACTACATCCTGAGCATGATGGGAAACCTATCTATCATCCTCCTTACGCAGCTGGATCCCCGTCTCAAAA
CTCCAATATATTTTTTCCTCAGAAATTTCTCCTTCCTGGAAATCTCATTAACAACTGTCTGTATTCCCAGATTCCTAATA
GCCATAATAACTAAAAACAAAGTCATTTCCTACAATGAGTGTGCATCTCAGTTATTCTTTTTCCTTTTGCTAGGCGTTAC
TGAATTTTACCTGCTGGCTGCCATGTCTTTTGATCGCTATGTAGCAATCTGTAAACCCCTACATTACCCAAGCATCATGA
GCAACAGACTGTGCTACCAGCTTGTACTCAGCTCATGGACAGCTGGCTTTCTGATTACGTTTCCACCGCTGGTCTTGGGA
CTGAAACTGGAATTCTGTGCCTCCACAGAAATTGATCATTTCATATGTGACACATCCCCTGTCTTGCAGATTTCTTGCTC
AGACACTCATCTGCTAGAACTGATTTCATTTGTCTCTGCGGTTGTAACACTGGTGATGACATTTCTGTTAGTGATTCTTT
CCTACTCGTACATTATCAAGACCATTCTAAAAATCCCCTCTGCCCAGAAAAGAACCAAAGCTTTTTCTACTTGTTCCTCT
CACATGGTCGTCGTCTCCCTAACCTATGGCAGCTGTATCTTTATTTACATGAAGCCATCAGCAAAGGAAAGAGTGACTTT
ATCCAAAGGTGTAGCTGTCATGTGCGCTCTATATATACAAAATATTAAACCCTTTTATTTACACTCTAAGGAACCAGCAA
GTGAAACA

Alignment

ORF - retro_tbel_2297 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.18 %
• Parental protein coverage: 97.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NNQSKEIEFILLGLTDDPQLQFVIFIFLFLNYILSVMGNLSIILLTQLDPRLKTPMYFFLRNFSFLEISL
          ..QS...EFILLGLTDD.QLQFVIFIFLFLNYILS.MGNLSIILLTQLDPRLKTP.YFFLRNFSFLEISL
Retrocopy HEQSVKREFILLGLTDDSQLQFVIFIFLFLNYILSMMGNLSIILLTQLDPRLKTPIYFFLRNFSFLEISL

Parental  TTVCIPRFLIAKITKNRVISYNECASQLFFFLLLGVTEFYLLAAMSFDRYVAICKPLHYPSIMSNRLCYQ
          TTVCIPRFLIA.ITKN.VISYNECASQLFFFLLLGVTEFYLLAAMSFDRYVAICKPLHYPSIMSNRLCYQ
Retrocopy TTVCIPRFLIAIITKNKVISYNECASQLFFFLLLGVTEFYLLAAMSFDRYVAICKPLHYPSIMSNRLCYQ

Parental  LVLSSWTAGFLITFPPLVLGLKLEFCASTEIDHFICDTSPVLQISCSDTHLLELISFVSAVVTLVMTFLL
          LVLSSWTAGFLITFPPLVLGLKLEFCASTEIDHFICDTSPVLQISCSDTHLLELISFVSAVVTLVMTFLL
Retrocopy LVLSSWTAGFLITFPPLVLGLKLEFCASTEIDHFICDTSPVLQISCSDTHLLELISFVSAVVTLVMTFLL

Parental  VILSYTYIIKTILKIPSAQKRTKAFSTCSSHMIVVSLTYGSCIFIYMKPSAKERVTLSKGXXILNNSALM
          VILSY.YIIKTILKIPSAQKRTKAFSTCSSHM.VVSLTYGSCIFIYMKPSAKERVTLSKG..........
Retrocopy VILSYSYIIKTILKIPSAQKRTKAFSTCSSHMVVVSLTYGSCIFIYMKPSAKERVTLSKGVAVMCALYIQ

Parental  -LNPIYIPRNQQVKES
          ...P.Y........E.
Retrocopy NIKPFYLHSKEPASET

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_2297 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2297 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Tupaia belangeri	ENSTBEG00000007004	2 retrocopies	retro_tbel_1917, retro_tbel_2297 ,