RetrogeneDB ID: retro_chof_774

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_14688:7737..8246(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FGF13
• Ensembl ID: ENSCHOG00000004376
• Aliases: None
• Description: fibroblast growth factor 13 [Source:HGNC Symbol;Acc:3670]

Sequence

>retro_chof_774
CCCCAGCTGAGAGGAATTGTGACAAGGTTATTCAGCCAGCAGGGACAGTTCCTGCAGATGCACCCAGATGGGATCATTGA
CAGGACCAAGGATGAAAACTGTTACTACAGCATCTTCAATCTAATCCCCGTGGGCCTGCGTGTGGTGGCCACCCAAGAGA
GAAGGCTGGCCTCTATGTGGCCGTGAGTGGTGAAGGCTATCTCTATAGCTCAGATGTTTTCACTCCAGAATGGAAACATA
AGGAATCTGTGTTTGAACTACACATGATCTATTCCGCCATACCATACCATCAGCAAGAATTAGGCCAAGTGTATTTTCTG
GGGCTCAATAAAGAAGGTCAAATTATGAAGGGAAATAGAGTGAAGAAAACCAAGCCCTCATCACATTTTGTACCAAAACC
TACTGAAGTGTGTATGTACAGAGAGACATCATTACATAAAATTGGAGAAAAACAAGGGTGTTCAAGGAAAAGTTCTGGAA
CACCAATCATGATCAGAGGCAAAGTTGGG

Alignment

ORF - retro_chof_774 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.56 %
• Parental protein coverage: 64.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PQLKGIVTKLYSRQGYHLQLQADGTIDGTKDEDSTYTLFNLIPVGLRVVAIQG-VQTKLYLLFSSEGYLY
          PQL.GIVT.L.S.QG..LQ...DG.ID.TKDE...Y..FNLIPVGLRVVA.Q......LY...S.EGYLY
Retrocopy PQLRGIVTRLFSQQGQFLQMHPDGIIDRTKDENCYYSIFNLIPVGLRVVATQE<EKAGLYVAVSGEGYLY

Parental  TSEHFTPECKFKESVFENYYVTYSSMIYRQQQSGRGWYLGLNKEGEIMKGNHVKKNKPAAHFLPKPLKVA
          .S..FTPE.K.KESVFE.....YS...Y.QQ..G....LGLNKEG.IMKGN.VKK.KP..HF.PKP..V.
Retrocopy SSDVFTPEWKHKESVFELHMI-YSAIPYHQQELGQVYFLGLNKEGQIMKGNRVKKTKPSSHFVPKPTEVC

Parental  MYKEPSLHDLTE---FSRSGSGTPTKSRSVSG
          MY.E.SLH...E....SR..SGTP...R...G
Retrocopy MYRETSLHKIGEKQGCSRKSSGTPIMIRGKVG

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_774 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004376	1 retrocopy	retro_chof_774 ,
Macaca mulatta	ENSMMUG00000012484	1 retrocopy	retro_mmul_301,