RetrogeneDB ID: retro_chof_568

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_122371:2553..3113(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000008668
• Aliases: None
• Description: None

Sequence

>retro_chof_568
CATTGTGTATAGCTAAATGATGGTCACATCATTCCTATCCTGGCATTTGGAACTGGTGCACATGCAGAGGTTCCTAAGAG
TGAAGCAGAGGAGGCCACCAAATTAGCTATGATGCTGGGTTTCACCATATTGATGCTACGCATGTGTACAAAAATGAAGA
GGAGGTTGGACAGGCCATCTGAAGCAAGACTGTAGAAGACATTATGAAGAGGAAAGATATATTCTACACTTCAAAGCTTT
GGGTCACTTTCTTTTGACCAGAGTTGGTCCGGCCGGCCTTGGAAAGATCACTGAAAAAACTTCAGCTGGACTATGTGGAC
CTCTACATTATTCATTTCCCAACAGCTCTGAAGCCTGGGGAGGATCTTTTACCTAAAGATGAACATAGAAAATACATATT
TGACACAGTGGATCTCTGTGCCACCTGGGAGGCCCAGGAGAAGGGAAAGGATGCAGCATTGACCAAGTCCATTGATGTGT
CCAATTTTAATCACAAGCAGCTTGAGATGATCCTGAACAAGCCAGGGCTCAAGTACAGGCCTGTTTGCAACCAAGTAGAA

Alignment

ORF - retro_chof_568 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.72 %
• Parental protein coverage: 57.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HCVQLNDGHFMPILGFGTAVPAEVPKTEAEEATKIAI-DAGYRHIDAAYVYENEEEVGRAIRSKIADGTV
          HCV.LNDGH..PIL.FGT...AEVPK.EAEEATK.A..DAG..HIDA..VY.NEEEVG.AI.SK......
Retrocopy HCV*LNDGHIIPILAFGTGAHAEVPKSEAEEATKLAM<DAGFHHIDATHVYKNEEEVGQAI*SKTVEDIM

Parental  KREDIFYTSKLWATFFRPELVRPALERSLKKLQLDYMDLYIIHFPLALKPGEDILPMDEHGKCIFDTVDF
          KR.DIFYTSKLW.TFF.PELVRPALERSLKKLQLDY.DLYIIHFP.ALKPGED.LP.DEH.K.IFDTVD.
Retrocopy KRKDIFYTSKLWVTFF*PELVRPALERSLKKLQLDYVDLYIIHFPTALKPGEDLLPKDEHRKYIFDTVDL

Parental  CATWEALEKCKDAGLTKSIGVSNFNHKQLERILNKPGLKYKPVCNQVE
          CATWEA.EK.KDA.LTKSI.VSNFNHKQLE.ILNKPGLKY.PVCNQVE
Retrocopy CATWEAQEKGKDAALTKSIDVSNFNHKQLEMILNKPGLKYRPVCNQVE

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_568 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000166	1 retrocopy	retro_chof_400,
Choloepus hoffmanni	ENSCHOG00000008668	1 retrocopy	retro_chof_568 ,
Echinops telfairi	ENSETEG00000009155	1 retrocopy	retro_etel_352,
Rattus norvegicus	ENSRNOG00000038361	1 retrocopy	retro_rnor_2046,
Sarcophilus harrisii	ENSSHAG00000006005	1 retrocopy	retro_shar_520,