RetrogeneDB ID: retro_chof_1090

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_197165:284..1058(+)
• 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_1090
GAGATGAGGTCGCGGGCGGAAAGCGCCGCGCTGTCCCTGCTGGCGCTGTTGGTGCTGCTGCTTCTCAGAGACGCCAAGTG
CAAGTTCAGGGCTCGGCACAAGCCATAGACTCAACACTACTACGCCCGGGACCGGATGAGTCTGGACTCCCGGCTACTGC
CGAGCTGGTTTGACGAGGCCACGTTCGGGGTTTTCGTGCACTGGGGCGTGTTCTTGGTGCCAGCCTGGGGCAGTGAGTGG
TTCTGATGGCACTGGAAGGAAGAGGGGCGGCCCCATACCAGTGCTTTATGAATGACAACTGCCCTCCTGGCTTCAGCTAT
GCTGACTTCGAGCCTCAGTTCACCGAAGGCTTCTTCCAGTCAGAAGACCAGGCTGAACTCTTGCAGGCCATGGGGCCAAG
TATGTGGTTCTGACCACGAAGTATCACGAAGGCTTCACAAACTGGCCAAGTCCTGTGTCTTGAAACTGGAACTCTCAGGA
CCTGGGGTCCCATTGTGGTTTGGTCGGTGAGAAGGGACCCGCTATCCCCAAGAGGAGCATATGTATGGACTCTTATCATT
CACTCTTAGAATGGTTCCATCTACTCTATCTGCTTGATAAGAAAAATGGCTTCAAAACACAGCATTTTGTCAGTGCAAAA
ACAATGCCAGAGCTATACGACCTAGTTGATGGTACAAACCAGACCTGATTTGGTCTGATGGAGAGTGGGACTGTCCTGAT
ACTTATTGGAACTCTACCAATTTTCTTTCTTGGTTCTATAATGATAGCCCTGTT

Alignment

ORF - retro_chof_1090 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.81 %
• Parental protein coverage: 54.87 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EMKLRGRRAALLQPGLLVLLVLGDAESNFGARRQPETQHRYTPDWPSLDSRPLPRWFDEAKFGVFVHWGV
          EM..R...AAL....LLVLL.L.DA...F.AR..P.TQH.Y..D..SLDSR.LP.WFDEA.FGVFVHWGV
Retrocopy EMRSRAESAALSLLALLVLLLLRDAKCKFRARHKP*TQHYYARDRMSLDSRLLPSWFDEATFGVFVHWGV

Parental  FSVPAWGSEWFWWHWKGEGLPQ-FQRFMKENYPPGFSYADFGPQFTAGFFQPEDWAELFQAAG-AKYVVL
          F.VPAWGSEWF.WHWK.EG.P...Q.FM..N.PPGFSYADF.PQFT.GFFQ.ED.AEL.QA.G.AKYVVL
Retrocopy FLVPAWGSEWF*WHWKEEGRPH<YQCFMNDNCPPGFSYADFEPQFTEGFFQSEDQAELLQAMG<AKYVVL

Parental  TTKHHEGFTNWPSPVSWNWNSQDLGPHRDLVGELGTALRKRNIRYGLYHSLLEWFHPLSLLDKKNGFKTQ
          TTK.HEGFTNWPSPVS.NWNSQDLG.H..LVGE.G.A..KR.I....YHSLLEWFH.L.LLDKKNGFKTQ
Retrocopy TTKYHEGFTNWPSPVS*NWNSQDLGSHCGLVGEKGPAIPKRSICMDSYHSLLEWFHLLYLLDKKNGFKTQ

Parental  HFVTAKTMPELYDLVNR-YKPDLIWSDGEWDCPYTYWNSTNFLSWLYNDSPV
          HFV.AKTMPELYDLV...YKPDLIWSDGEWDCP.TYWNSTNFLSW.YNDSPV
Retrocopy HFVSAKTMPELYDLVDG<YKPDLIWSDGEWDCPDTYWNSTNFLSWFYNDSPV

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_1090 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,