RetrogeneDB ID: retro_chof_730

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_141319:778..1413(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBXO28
• Ensembl ID: ENSCHOG00000010255
• Aliases: None
• Description: F-box protein 28 [Source:HGNC Symbol;Acc:29046]

Sequence

>retro_chof_730
AACACGCTGTTGGCGCTGCCCATCGTAGCTATAGAGAACATCCTCAGCTTTATGTCCTACGACCAAATTAGCCAGCTCCG
CTTGGTTTGTAGAACAATGGACTTGATCTGCCAGAGAATGTTGAATCAGGGATTTCTGAAAGTGGAGCGGTACCACAGTC
TACGCCAGAAACAAGTTAAAGCACAGCTCCCAAGGAGAGAGTCGGAAAGGCGAAACTATCCATTAGCCCGTCATGCCGAT
ATCCTTGCTGCTGTTGAAACCCGACTATCACTGTTACATATGACTTTCATGAAGTATGTGGAACCCAGTCTCTGTTGCTT
CATCCCAGGAAAGGTCATTGATGAAATTTATCGTGTGTTGAGATATGTCAGTTCTACCAGAGCCCCTCAACGAGCTCACG
AAGTGCTTAAAGAATTAAGGGATGTTTCCTCCATGGCAATGGAATACTTTGATGAGAAAATTGCTCCAGTACTAAAGAGG
AAATTACCAGGATCAGATGTGAATGGAAGACTCACGGGCTTTGCTCCAGCCCCAGGACCTTCCGCGGACGTAAGGAGGAT
ACAGCTGTTCTCCATGCAAGCCCTGCAAGGCAAGAGCTCTCCACGCTCCAGCAGCACGTTAAAACAAATGCTGCT

Alignment

ORF - retro_chof_730 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.65 %
• Parental protein coverage: 68.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NNTVALPIVAIENILSM--YDEISQLRLVCKRMDLVCQRMLNQGFLKVERYHNLCQKQVKAQLPRRESER
          N...ALPIVAIENILS...YD.ISQLRLVC..MDL.CQRMLNQGFLKVERYH.L.QKQVKAQLPRRESER
Retrocopy NTLLALPIVAIENILSFMSYDQISQLRLVCRTMDLICQRMLNQGFLKVERYHSLRQKQVKAQLPRRESER

Parental  RNHSLARHADILAAVETILSLLNMTFMXXXXXXXXXXXXXXVIDEIYRVLRYVSSTRAPQRAHEVLQELR
          RN..LARHADILAAVET.LSLL.MTFM..............VIDEIYRVLRYVSSTRAPQRAHEVL.ELR
Retrocopy RNYPLARHADILAAVETRLSLLHMTFMKYVEPSLCCFIPGKVIDEIYRVLRYVSSTRAPQRAHEVLKELR

Parental  DISSMAMEYFDENIVPILKRKLPGSDVSGRLMGSPPAPGPSATLTTMQLSSKQ-NPSRQEVTKLQQQVKT
          D.SSMAMEYFDE.I.P.LKRKLPGSDV.GRL.G..PAPGPSA.....QL.S.Q..P.RQE...LQQ.VKT
Retrocopy DVSSMAMEYFDEKIAPVLKRKLPGSDVNGRLTGFAPAPGPSADVRRIQLFSMQ<SPARQELSTLQQHVKT

Parental  NGA
          N.A
Retrocopy NAA

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_730 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 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010255	5 retrocopies	retro_chof_1637, retro_chof_2403, retro_chof_247, retro_chof_730 , retro_chof_903,
Dipodomys ordii	ENSDORG00000004351	1 retrocopy	retro_dord_773,
Tursiops truncatus	ENSTTRG00000013708	1 retrocopy	retro_ttru_1359,