RetrogeneDB ID: retro_chof_2254

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_61244:9842..10143(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC25
• Ensembl ID: ENSCHOG00000012971
• Aliases: None
• Description: coiled-coil domain containing 25 [Source:HGNC Symbol;Acc:25591]

Sequence

>retro_chof_2254
GGGGAGAAGATAGAGACATCTCAAAGGAAGTGCTGATGGTCTGTGCTCATCTTGTGAAGGCCAATAGCATTCAATTTGCA
AGATGAACAACGTCATTGTGGTATATACACCGTGATCTAACCTGAAGAAAACAGCTGACATGGATGTGGGACAGATAGGC
TTTCACAGGCAAAAGGATGTTAAAATTGTGACAGTGGAGAAGAAAGTGAATGAGATACTGAATCGATAAGAAAAGACCAA
AATGGAGCGAATCCCAGACCTAGCAGCAGAGGAAGAACGCAGAGACCGTGAAGAGAGGAAT

Alignment

ORF - retro_chof_2254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.32 %
• Parental protein coverage: 55.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GEKIE-DIPKEVLMDCAHLVKANSIQG-CKMNNVNVVYTPWSNLKKTADMDVGQIGFHRQKDVKIVTVEK
          GEKIE.DI.KEVLM.CAHLVKANSIQ..CKMNNV.VVYTP.SNLKKTADMDVGQIGFHRQKDVKIVTVEK
Retrocopy GEKIE<DISKEVLMVCAHLVKANSIQF<CKMNNVIVVYTP*SNLKKTADMDVGQIGFHRQKDVKIVTVEK

Parental  KVNEILNRLEKTKMERFPDLAAEKECRDREERN
          KVNEILNR.EKTKMER.PDLAAE.E.RDREERN
Retrocopy KVNEILNR*EKTKMERIPDLAAEEERRDREERN

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_2254 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012971	2 retrocopies	retro_chof_2254 , retro_chof_847,
Dipodomys ordii	ENSDORG00000006595	1 retrocopy	retro_dord_491,
Echinops telfairi	ENSETEG00000006478	1 retrocopy	retro_etel_434,
Homo sapiens	ENSG00000147419	1 retrocopy	retro_hsap_1701,
Gorilla gorilla	ENSGGOG00000009685	1 retrocopy	retro_ggor_1274,
Monodelphis domestica	ENSMODG00000015976	1 retrocopy	retro_mdom_511,
Pongo abelii	ENSPPYG00000018468	2 retrocopies	retro_pabe_1364, retro_pabe_477,
Pan troglodytes	ENSPTRG00000020109	1 retrocopy	retro_ptro_141,
Tarsius syrichta	ENSTSYG00000000732	1 retrocopy	retro_tsyr_1364,