RetrogeneDB ID: retro_chof_1383

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_27784:3815..4331(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000006159
• Aliases: None
• Description: None

Sequence

>retro_chof_1383
GTGGCTTCTTGTGGGATCCTTGGCATTTTCTTCCTCTCTGGTCCCCCCTCCCCTTGTGCCTGGAGCTCTGGAGTGGGATC
CCGGATCTAGGAATTAAAAATCTCATTTTGCTGTGTAGCTGGATTTTCTTATGGCTTGCTCTTCTTACTTTAATCATTTA
TGTGAATATCTCATGCCTTAACTCATTTAAATCTTCCCAAGTGTATCTGAAAGAAGAAGAGAAGAATGAGAAAAGGCAAA
AACTTGTGTGAAAAAACACAAGAGGCACAGGGTCAAAAGGCCAGCAGATACATAGAGGATATTTTAAAACCTCACCGGGA
AATGAAATTGAAAAAACTGGAAATGCTCCTTATCAAATGACGGGTAAAACCTGGAATTTAAGCAGCAGTCACAAACTTGG
GGTGATAAAGATTTGGTGCTTGGAAATGCCAGAAATCTTCTGAAACTTCCAACAGAGAAGCAGCGAAGAGACTGCATTTG
CCTAAGCCTGTAACCAAAGTTTCACCTCCTGAACAG

Alignment

ORF - retro_chof_1383 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.64 %
• Parental protein coverage: 64.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MASRAVVGIFLLSA-LPL-LCLELRRGIPDLGIKDLVLLCGRIFLLLALLTLIISVTTSWLNSFKSSQVY
          .AS....GIF.LS...PL.LCLEL..GIPDLGIK.L.LLC..IFL.LALLTLII.V..S.LNSFKSSQVY
Retrocopy VASCGILGIFFLSG<SPLPLCLELWSGIPDLGIKNLILLCSWIFLWLALLTLIIYVNISCLNSFKSSQVY

Parental  LKEEEEEKNGKRQ-KLVLNRQQETQSEKASRYIEKVLKPHQEMKLKKLEERF-YQMSGETWKLSNGHKLG
          L....EE.......K......QE.Q..KASRYIE..LKPH.EMKLKKLE....YQM.G.TW.LS..HKLG
Retrocopy L---KEEEKNEKR>KNLCEKTQEAQGQKASRYIEDILKPHREMKLKKLEMLL<YQMTGKTWNLSSSHKLG

Parental  -GDEGLVLENA-SQTSETSNREAARRRNLPEPVTKLSRPPDQ
          .GD..LVL.NA....SETSNREAA.R..LP.PVTK.S.PP.Q
Retrocopy <GDKDLVLGNA<QKSSETSNREAAKRLHLPKPVTKVS-PPEQ

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_1383 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 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001600	2 retrocopies	retro_amel_1272, retro_amel_1326,
Choloepus hoffmanni	ENSCHOG00000006159	4 retrocopies	retro_chof_1161, retro_chof_1175, retro_chof_1383 , retro_chof_1500,
Myotis lucifugus	ENSMLUG00000016846	1 retrocopy	retro_mluc_606,