RetrogeneDB ID: retro_tbel_1641

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5353:929..1409(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000001371
• Aliases: None
• Description: None

Sequence

>retro_tbel_1641
AAAGTTGATCTTGCCAGTGTTTTAGATATTCATGCCTTTGACAGTCTCTCTGGAATAAGTTTGCAGAAAAAACTTCAGCA
TGTGCCAGCAATACAACCTCACCTTGATCAGAGTATTATTACAATCACATTTGAAGTACCAGGAAATGCACATGAAGAAA
ATCTAAATGTATTTATTCACAGTCTTCTGAGGGAAAAGAATGTGCCGAGCAAGGACAATCACTGAATGGAGGTCATAGGG
CTAAAGGGTCTGGTGTCAATCAAAGATAAACCACAGCAGGTGGTTGTCCAAGGTGTCCCTAAGCTATATGACTTGGAATA
GACTTCAGTGAGCTGGAAGGATGACACTGAGAAAACATATCAGTTGGTCTTTATTGGCAGGAATTTAGATAAGGATAGCC
TTAAACAACTATTTGTAGCTACCGTGACAGAAACAGGAAAACAGAGGACAACACATTTCAAAGAAGATCGAATTTGTCTG

Alignment

ORF - retro_tbel_1641 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.38 %
• Parental protein coverage: 80. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVDLASVLDLHAFDSLSGIGLQKKLHHVPATQPHLDQSIVTITFEVPGNAHEENLNVFIQNLLWEKNVRS
          .VDLASVLD.HAFDSLSGI.LQKKL.HVPA.QPHLDQSI.TITFEVPGNAHEENLNVFI..LL.EKNV.S
Retrocopy KVDLASVLDIHAFDSLSGISLQKKLQHVPAIQPHLDQSIITITFEVPGNAHEENLNVFIHSLLREKNVPS

Parental  KDNRCMEVIRLKGLVSIKDKPQQVVVQGVHELYDLEETPVSWKDDTERTNRLVFIGRNLDKDILKQLFIA
          KDN..MEVI.LKGLVSIKDKPQQVVVQGV..LYDLE.T.VSWKDDTE.T..LVFIGRNLDKD.LKQLF.A
Retrocopy KDNH*MEVIGLKGLVSIKDKPQQVVVQGVPKLYDLE*TSVSWKDDTEKTYQLVFIGRNLDKDSLKQLFVA

Parental  TVTETGKQWTTHMKEDGICL
          TVTETGKQ.TTH.KED.ICL
Retrocopy TVTETGKQRTTHFKEDRICL

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_1641 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1641 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
Canis familiaris	ENSCAFG00000001943	1 retrocopy	retro_cfam_354,
Sarcophilus harrisii	ENSSHAG00000001103	1 retrocopy	retro_shar_244,
Tupaia belangeri	ENSTBEG00000001371	1 retrocopy	retro_tbel_1641 ,