RetrogeneDB ID: retro_tbel_3406

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_139441:16116..16543(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDO1
• Ensembl ID: ENSTBEG00000003937
• Aliases: None
• Description: cysteine dioxygenase type 1 [Source:HGNC Symbol;Acc:1795]

Sequence

>retro_tbel_3406
TATACCCGAAATCTTGTGGATCAAGGAAATGGAAAATTTAACCTGATGATTCTCTGTTGGAGTGAAGGGCATGGCGGCAG
TATTCATGATCACACGGGCTCCCACTGCTTCCTGAAGATGCTGCAGGGAAACCTGAAGGAGACGTTGTTTGCCTGGCCTG
ACAAAAAAGCCAATGAGATGACCAAGAAGTCCGAAAGAATCTTGAGGGAAAACCAGTGTGCCTACATCAACGATTCTATG
GCTTACATGGAGCGAGAACATTAGCAGCACAGAGCCCGCTGTGAGCCTTCACCTGTACAGTCCGCCTTTTGACACCTGCT
ATACTTTTGATCAAAAGACAGGACATACAAACAAAGTCACCATGACATTCCATAGCAAATTTGGAACCAGGACTCCATTA
ACAATTTCAGGTTCACTGGAAAACAAC

Alignment

ORF - retro_tbel_3406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.66 %
• Parental protein coverage: 72.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YTRNLVDLGNGKFNLMILCWGEGHGSSIHDHTDSHCFLKMLQGNLKETLFAWPDKKANEMTKKSERILRE
          YTRNLVD.GNGKFNLMILCW.EGHG.SIHDHT.SHCFLKMLQGNLKETLFAWPDKKANEMTKKSERILRE
Retrocopy YTRNLVDQGNGKFNLMILCWSEGHGGSIHDHTGSHCFLKMLQGNLKETLFAWPDKKANEMTKKSERILRE

Parental  NQCAYINDSI-GLHRV-ENISHTEPAVSLHLYSPPFDSCHTFDQRTGHKNKVTMTFHSKFGTRTPLTTSG
          NQCAYINDS..GLH...ENIS.TEPAVSLHLYSPPFD.C.TFDQ.TGH.NKVTMTFHSKFGTRTPLT.SG
Retrocopy NQCAYINDSM<GLHGA<ENISSTEPAVSLHLYSPPFDTCYTFDQKTGHTNKVTMTFHSKFGTRTPLTISG

Parental  SLENN
          SLENN
Retrocopy SLENN

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_3406 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3406 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009577	1 retrocopy	retro_dnov_2171,
Microcebus murinus	ENSMICG00000009005	1 retrocopy	retro_mmur_1405,
Otolemur garnettii	ENSOGAG00000009306	1 retrocopy	retro_ogar_660,
Tupaia belangeri	ENSTBEG00000003937	2 retrocopies	retro_tbel_3406 , retro_tbel_4269,