RetrogeneDB ID: retro_chof_763

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_144644:1391..2448(+)
• 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_763
ATAGGCTGCATTAAAAGTAAAGAGAACAAAAGTCCAGCCATTAAATATAGAACTGAAAACACTCCAGATCCTGTGAGCAA
GAGTATCACCCATTATGGAGCAGAACACACTGCAATGTCACCATCATCATCAGCTAAGGGAACATCTGTTAATTTTAGCA
ATCTTTCCATAAAACCATTTGGAGGATTCTCAGGGGTGACACCTTTTGGAGGAGCATCTTCCTCATTTTTGGTGGTGTCA
ACTTCATATCCTACTGGTTTAAAAGGCGATGTTACTGTATTTGTCACCTTATATGATTATGAAGCTAGAACTACAGAAGA
CCTTTCATTTAAGAAGGGTGAAAGATTCCAGGTAATTAACAATATGGAAGGAGACTGGTGGGAAGCAAGAGCAATTGCTA
CAGGAAAGAATGGCTATATCCCTAGCAATTATGTAGCACCAGCAGATTCCATTCAGGCAGAAGAATGGTATTTTGGCAAA
ATGGGGAGAAAAGATGCTGAAAGATTACTTCTGAACCCTGGAAATCAATGAGGTATTTTCTTGGTAAGAGAGAGTGAAAC
TACTAAAGGTGCTTATTCCCTCTCTATTTGTGATTGGGATGAGATAAGAGGTGACAATGTGAAACATTACTAAAATTAGG
AAACTTGACAATGGTGGATACTATATCACAGCCAGAGCACAATTTGATACTCTGCAGAAATTGGTGAAACACTACACAGA
GCATGCTGATGGTTTATGCCATAAGTTAACAACTGTGTGTCCAACTGTGAAACCGCAGACTCAAGGTCTAGCAAAAGATG
CTTGGGAAATCCCTTGAGAATCTTTGCGACTAGAGGTTAAACTAGGACAAGGATGTTTTGGTGAAGTATGGATGGGAACA
GGGAATGGAACCACAAAAGTAGCAATTAAAACACTAAAACCAGGTACAATGATGCCAGAAGCCTTTCTTCAAGAGTCTCA
AATCATGAAGAAATTAAGACATGATAAACTTGTTCCACTCTATGCGGTTGTTTCTGAAGAGCCGATTTACATTGTCACTG
AATTTATGTCAAAGGGA

Alignment

ORF - retro_chof_763 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.67 %
• Parental protein coverage: 64.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGCVQCKDKE--ATKLTEERDGSLTQSSGYRYGTDPTPQHYPSFGVTSIPNYNNFHA---AGGQGLTVF-
          .GC...K.....A.K...E........S...YG...T.....S.......N..N.......G..G.T.F.
Retrocopy IGCIKSKENKSPAIKYRTENTPDPVSKSITHYGAEHTAMSPSSSAKGTSVNFSNLSIKPFGGFSGVTPFG

Parental  GGVNSSSHTGTLRTRGGTG-VTLFVALYDYEARTEDDLSFHKGEKFQILNSSEGDWWEARSLTTGETGYI
          G...S.....T....G..G.VT.FV.LYDYEART..DLSF.KGE.FQ..N..EGDWWEAR...TG..GYI
Retrocopy GASSSFLVVSTSYPTGLKGDVTVFVTLYDYEARTTEDLSFKKGERFQVINNMEGDWWEARAIATGKNGYI

Parental  PSNYVAPVDSIQAEEWYFGKLGRKDAERQLLSFGNPRGTFLIRESETTKGAYSLSIRDWDDMKGDHVKHY
          PSNYVAP.DSIQAEEWYFGK.GRKDAER.LL..GN..G.FL.RESETTKGAYSLSI.DWD...GD.VKHY
Retrocopy PSNYVAPADSIQAEEWYFGKMGRKDAERLLLNPGNQ*GIFLVRESETTKGAYSLSICDWDEIRGDNVKHY

Parental  -KIRKLDNGGYYITTRAQFETLQQLVQHYSERAAGLCCRLVVPCHKGMPRLTDLSVKTKDVWEIPRESLQ
          .KIRKLDNGGYYIT.RAQF.TLQ.LV.HY.E.A.GLC..L...C....P....L....KD.WEIP.ESL.
Retrocopy >KIRKLDNGGYYITARAQFDTLQKLVKHYTEHADGLCHKLTTVCPTVKPQTQGLA---KDAWEIP*ESLR

Parental  LIKRLGNGQFGEVWMGTWNGNTKVAIKTLKPGTMSPESFLEEAQIMKKLKHDKLVQLYAVVSEEPIYIVT
          L...LG.G.FGEVWMGT.NG.TKVAIKTLKPGTM.PE.FL.E.QIMKKL.HDKLV.LYAVVSEEPIYIVT
Retrocopy LEVKLGQGCFGEVWMGTGNGTTKVAIKTLKPGTMMPEAFLQESQIMKKLRHDKLVPLYAVVSEEPIYIVT

Parental  EYMNKG
          E.M.KG
Retrocopy EFMSKG

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_763 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,