RetrogeneDB ID: retro_chof_542

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_119414:417..1205(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FUCA1
• Ensembl ID: ENSCHOG00000012304
• Aliases: None
• Description: fucosidase, alpha-L- 1, tissue [Source:HGNC Symbol;Acc:4006]

Sequence

>retro_chof_542
CCCGAGATGAGATCACGGGCGGGAAAGAGCACGCCGCTGCTGCTGCCGGCGCTGTTGGTGCTGCTGGTTCTCGGAGATGC
CGAGTTCCCAGTTCGGGGCGCGGCGCCAGCCCGAGACCCAGGCACCGCTACACCCCGGACTGGCCGAGTCTGGGCTCCCG
GGCCGCTGCCGCGCTGCTTCCACGAGGCCAAAGTTCGGGGTGTTCGTGCACTGGGGCGTGTTCTCGGTGCCGGCCTGGGG
CAGCGAGTGGTCCTGGTGGCCCTGGAAGGGTGAGGGGTGGCCCCAGTACCAGCGCTTTATGAACCAATACTACCCACCCA
GCTTCAGCTACGCCGACCGCAGGCAGCAGTTCACGGCGGGCTTCTTCCGGCGGAAGCCTGGGCTGAGCTCTTCCGGGCCG
CGGGGGCCAAGTAAGTGGTTCTGACCACGAAGCATCACGAAGGCTTCACAAACTGGCGGAGTCCTGTGTCTTGGAACTAG
AACTCTCAGGACCTGGGGCCCCGTCGTGATTTGGTCGGGGAGCTGGGAACTGCTCTCTGGAAGAGGAACATACGCTATGA
ACTCTATCACTCACTCCTAGAACGGTTCCACCACTCTACCTGCTTGATAAGAAAAACAGCTTCAAAAGACAGCATTTTGT
CAGGGCAAAAACAATGCCAGAGCTATATGACCTAGTTAACAGGTACAAACCAGATCTGATTGCATCTGATGGAGAGTGAG
ACTGTCCTTATACTTACTGCAACTCTACCAATTTTCTTTCTTGGCTCTACAATGATAGCCCAGTCAAG

Alignment

ORF - retro_chof_542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.09 %
• Parental protein coverage: 55.3 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  PEMKLR-GRRAALLQPGLLVLLVLGDAE-SNFGARRQPETQ-HRYTPDWPSLDSR-PLPRWFDEAK-FGV
          PEM..R.G....LL.P.LLVLLVLGDAE.S.FGARRQPETQ.HRYTPDWPSL.SR.PLPR.F.EAK.FGV
Retrocopy PEMRSRAGKSTPLLLPALLVLLVLGDAE>SQFGARRQPETQ>HRYTPDWPSLGSR>PLPRCFHEAK>FGV

Parental  FVHWGVFSVPAWGSEWFWWHWKGEGLPQFQRFMKENYPPGFSYADFGPQFTAGFFQ-PEDWAELFQAAGA
          FVHWGVFSVPAWGSEW.WW.WKGEG.PQ.QRFM...YPP.FSYAD...QFTAGFF...E.WAELF.AAGA
Retrocopy FVHWGVFSVPAWGSEWSWWPWKGEGWPQYQRFMNQYYPPSFSYADRRQQFTAGFFR<AEAWAELFRAAGA

Parental  KYVVLTTKHHEGFTNWPSPVSWNWNSQDLGPHRDLVGELGTALRKRNIRYGLYHSLLEWFH-PLSLLDKK
          K.VVLTTKHHEGFTNW.SPVSWN.NSQDLGP.RDLVGELGTAL.KRNIRY.LYHSLLE.FH.PL.LLDKK
Retrocopy K*VVLTTKHHEGFTNWRSPVSWN*NSQDLGPRRDLVGELGTALWKRNIRYELYHSLLERFH<PLYLLDKK

Parental  NGFKTQHFVTAKTMPELYDLVNRYKPDLIWSDGEWDCPYTYWNSTNFLSWLYNDSPVK
          N.FK.QHFV.AKTMPELYDLVNRYKPDLI.SDGE.DCPYTY.NSTNFLSWLYNDSPVK
Retrocopy NSFKRQHFVRAKTMPELYDLVNRYKPDLIASDGE*DCPYTYCNSTNFLSWLYNDSPVK

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_542 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012304	2 retrocopies	retro_chof_1090, retro_chof_542 ,
Equus caballus	ENSECAG00000024652	1 retrocopy	retro_ecab_450,
Loxodonta africana	ENSLAFG00000015305	1 retrocopy	retro_lafr_252,
Microcebus murinus	ENSMICG00000007213	1 retrocopy	retro_mmur_542,
Tupaia belangeri	ENSTBEG00000013160	1 retrocopy	retro_tbel_3390,