RetrogeneDB ID: retro_chof_1165

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_216161:659..1612(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FYN
• Ensembl ID: ENSCHOG00000012780
• Aliases: None
• Description: FYN oncogene related to SRC, FGR, YES [Source:HGNC Symbol;Acc:4037]

Sequence

>retro_chof_1165
AAGAATGGTTATATCCCTAGCACTTATGTAGCACCAGCAGATTCCATTCAGGCAGAAGAATGGTATTTGGCAAAATGGGA
AGAAAAGATGCTGAAACATTACTTCTGAACCCTGGAAATCAAAGAGGTATTTTCTTGGTAAGAGAGAGTGAAACTACTAA
AGGTGCTTATTTCCTCTCTATTCGCGATTGGGATGAGATAAGAGGTGACAATGTGAAACACTACAAAATTAGGAAGCTTG
ACAATGGTGGATACTGTATCACAACCAGAGCACAATTTGATACTCTGCAGAAATTAGTGAAACACTACACAGAGCATGCT
GATGGTTTATGCCATGAGTTAACAACTGTGTGTCCAACTGTGAAACCCCAGACTCAAGGTCTAGCAAAAGATGCTTGGGA
AATCCCTCGAAAATCTTTGCAACTAGAGGTTAAACTAGGACAAGGATGTTTTGGTGAAGTATGGATGGGAACATGGAATG
GAACCACAAAAGTAGCAATTAAAACACTAAAACCAGGTACAATGATGCCAGAAGCTTTTATTCAAGAGGCTCAGATCATG
AAGAAATTAAGACATGATAAACTTGTTCCACTCTATGCAGTTGTTTCTGAAGAGCCAATTTATATTGTCACTTAATTTAT
GTCAAAAGGGAGTTTACTAGATTTCCTTAAGGAGGGAGATGGAAAGTATTTGAAGCTCCCACAACTGGTTGATATGGCTG
CTCAGATTGCTGATGGCATGGCATATATTGAAAGAATGAATTATATCCATCGTGACCTTCAGGCTGCTAATTTTCTTGTA
GGAGAAAACCTTGCATGCAAAATGGCAGATTTTGGTTTAGCAAGGTTAATTGAAGACAACGAATATACTGCAAGATAAGG
TGCAAAATTCCCAATCAAATGGACAGCTCCTGAGGCTGCACTGTATGGCTGATTTACAATAAAGTCTGATGTG

Alignment

ORF - retro_chof_1165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.71 %
• Parental protein coverage: 59.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ETGYIPSNYVAPVDSIQAEEWY-FGKLGRKDAERQLLSFGNPRGTFLIRESETTKGAYSLSIRDWDDMKG
          ..GYIPS.YVAP.DSIQAEEWY.FGK.GRKDAE..LL..GN.RG.FL.RESETTKGAY.LSIRDWD...G
Retrocopy KNGYIPSTYVAPADSIQAEEWY<FGKMGRKDAETLLLNPGNQRGIFLVRESETTKGAYFLSIRDWDEIRG

Parental  DHVKHYKIRKLDNGGYYITTRAQFETLQQLVQHYSERAAGLCCRLVVPCHKGMPRLTDLSVKTKDVWEIP
          D.VKHYKIRKLDNGGY.ITTRAQF.TLQ.LV.HY.E.A.GLC..L...C....P....L....KD.WEIP
Retrocopy DNVKHYKIRKLDNGGYCITTRAQFDTLQKLVKHYTEHADGLCHELTTVCPTVKPQTQGLA---KDAWEIP

Parental  RESLQLIKRLGNGQFGEVWMGTWNGNTKVAIKTLKPGTMSPESFLEEAQIMKKLKHDKLVQLYAVVSEEP
          R.SLQL...LG.G.FGEVWMGTWNG.TKVAIKTLKPGTM.PE.F..EAQIMKKL.HDKLV.LYAVVSEEP
Retrocopy RKSLQLEVKLGQGCFGEVWMGTWNGTTKVAIKTLKPGTMMPEAFIQEAQIMKKLRHDKLVPLYAVVSEEP

Parental  IYIVTEYMNKGSLLDFLKDGEGRALKLPNLVDMAAQVAAGMAYIERMNYIHRDLRSANILVGNGLICKIA
          IYIVT..M.KGSLLDFLK.G.G..LKLP.LVDMAAQ.A.GMAYIERMNYIHRDL..AN.LVG..L.CK.A
Retrocopy IYIVT*FMSKGSLLDFLKEGDGKYLKLPQLVDMAAQIADGMAYIERMNYIHRDLQAANFLVGENLACKMA

Parental  DFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDV
          DFGLARLIEDNEYTAR.GAKFPIKWTAPEAALYG.FTIKSDV
Retrocopy DFGLARLIEDNEYTAR*GAKFPIKWTAPEAALYG*FTIKSDV

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_1165 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012780	2 retrocopies	retro_chof_1165 , retro_chof_763,
Gorilla gorilla	ENSGGOG00000008065	1 retrocopy	retro_ggor_1595,