RetrogeneDB ID: retro_chof_2176

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_55549:3182..3452(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000002184
• Aliases: None
• Description: None

Sequence

>retro_chof_2176
CTTGGAGAAATTCAGTCAAGACTTTTAGATCACAGACCAGTTATTCAAGGTGAAACCCGTTATTTTGTGAAAGAATTTGA
AGAAAAATGTAGTCTCCAAGAAATGAAAGTTCTTGAAAATTTGAAGAATATGATCCACAAAACAAATGAACAGACTCTTC
CCAAATGTGGAGAGACAGTTCAGGACAACATAAACCAAGTTCTCCAGAGATTGCAAGCAGCTAATCACTCAGTCTGTAGA
CTCCAACAGAGGGAGCAGGAACAAAGAAAG

Alignment

ORF - retro_chof_2176 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 60.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGEIHSRLLDHRPVIQGEIRYFVKEFEEKRGLREMRVLENLKNMIHKTNEQTLPKCGETVQDNLNQILQR
          LGEI.SRLLDHRPVIQGE.RYFVKEFEEK..L.EM.VLENLKNMIHKTNEQTLPKCGETVQDN.NQ.LQR
Retrocopy LGEIQSRLLDHRPVIQGETRYFVKEFEEKCSLQEMKVLENLKNMIHKTNEQTLPKCGETVQDNINQVLQR

Parental  XXXXXXXVCRLQQREQEQRK
          .......VCRLQQREQEQRK
Retrocopy LQAANHSVCRLQQREQEQRK

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_2176 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
Choloepus hoffmanni	ENSCHOG00000002184	4 retrocopies	retro_chof_1163, retro_chof_2176 , retro_chof_2312, retro_chof_663,
Callithrix jacchus	ENSCJAG00000021322	2 retrocopies	retro_cjac_1041, retro_cjac_4180,
Microcebus murinus	ENSMICG00000005966	1 retrocopy	retro_mmur_31,