RetrogeneDB ID: retro_chof_318

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_7297:21395..21929(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DAPP1
• Ensembl ID: ENSCHOG00000005643
• Aliases: None
• Description: dual adaptor of phosphotyrosine and 3-phosphoinositides [Source:HGNC Symbol;Acc:16500]

Sequence

>retro_chof_318
ATGGGCAGAGCAGAACCTCTAGAAGGAAAGATGACTGCCCAGGATCCCTCAGATCTGTGGAGCAGATTGGATGGAGAAGT
TGAGCTGCTCCGAGACTTGGGATGTTATCATGGCAATCTCACCCGCCAAGCAGCAGAAGCTCTTCTCTCAAATGGATCTG
ATGGAAGCTACCTTCTAAGGGACAGTAACAAAAGGACCAGGCTGTACTCTCTCTCCGTAACAGCCAAAGACTCTGTCAAA
CATTTTCATGTTGAATATACTGGATATTTATTTAAATTTGGCTTTAATGAATTCTCATCTTTGAAGGATTTTGTCAAGCA
TTTTGCAAACCAGCCTCTGATTGGAAGCAAAACAGGCACTCTGATTGTTCTGAAACATCCTTATCCAAGAAAAGTGGAGG
AACCTTCCATTTATGAATCCATCCACGATTACACAGCAATGCAAACAGGAAGAATGGAAAATGACCTCGTGCCTATGGCT
CCTTCTCTGGGTACCAAAGTTGTTTACCTCATCAAACAAGGGGGCCTAGTCAAG

Alignment

ORF - retro_chof_318 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.8 %
• Parental protein coverage: 63.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRAEPLEGKMTAQDPSDLWSRSDGDAEEFXXXXWYHGNSTRHAAEALLLSNGSDGSYLLRDSNERTGLY
          MGRAEPLEGKMTAQDPSDLWSR.DG..E.......YHGN.TR.AAEALL.SNGSDGSYLLRDSN.RT.LY
Retrocopy MGRAEPLEGKMTAQDPSDLWSRLDGEVELLRDLGCYHGNLTRQAAEALL-SNGSDGSYLLRDSNKRTRLY

Parental  SLSVRAEDSVQHFHVEYTGYSFKFGFNEFSSLKDFVKHFANHPLIGSETGTLIVLKHPYPRKVEEPSIYE
          SLSV.A.DSV.HFHVEYTGY.FKFGFNEFSSLKDFVKHFAN.PLIGS.TGTLIVLKHPYPRKVEEPSIYE
Retrocopy SLSVTAKDSVKHFHVEYTGYLFKFGFNEFSSLKDFVKHFANQPLIGSKTGTLIVLKHPYPRKVEEPSIYE

Parental  SVRVHTAMQTGRTENDLVPTAPSLGTKEGYLIKQGGLVK
          S....TAMQTGR.ENDLVP.APSLGTK..YLIKQGGLVK
Retrocopy SIHDYTAMQTGRMENDLVPMAPSLGTKVVYLIKQGGLVK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_318 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni 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
Choloepus hoffmanni	ENSCHOG00000005643	2 retrocopies	retro_chof_1563, retro_chof_318 ,