RetrogeneDB ID: retro_chof_1727

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_36897:5392..5746(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS18
• Ensembl ID: ENSCHOG00000003746
• Aliases: None
• Description: ribosomal protein S18 [Source:HGNC Symbol;Acc:10401]

Sequence

>retro_chof_1727
GGTGAGGGGTGAAGGTATGCTTGTGTGGTGTTGAAGAAAGCAGACATCAACCTCACCAAGAGGGCAGGAGAACTCATGGA
GGATGAAGTGGAATGTGTAGCCAACTTTATGCAGAATCCACACCAGTGCGAGATCCCAGGCCGGTTCTTGAACTGACAGA
AGGATGTCAAGGATGCAAAATACAGCCAGGTCCTGACCAGTGGCCTGCACAATAAGCTCCACGAAGACCTGGAGCAACTG
AAGAAGATTCAGGCCCACATAGGGCTGCACCACTTCTGGGGTCTTTTTGTCTGAGGCCAGTACACCTAGATCATGGGCTG
CTGTGGTTGCACTGTGGGTGTATCCAAGAAGAAG

Alignment

ORF - retro_chof_1727 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.19 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLD
          G.G.RYA.VVL.KADI.LTKRAGEL.EDEVE.V...MQNP.Q..IP..FLN.QKDVKD.KYSQVL..GL.
Retrocopy GEG*RYACVVLKKADINLTKRAGELMEDEVECVANFMQNPHQCEIPGRFLN*QKDVKDAKYSQVLTSGLH

Parental  NKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKTTGRRGRTVGVSKKK
          NKL.EDLE.LKKI.AH.GL.HFWGL.V.GQ.T...G..G.TVGVSKKK
Retrocopy NKLHEDLEQLKKIQAHIGLHHFWGLFV*GQYT*IMGCCGCTVGVSKKK

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_1727 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 10 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003746	5 retrocopies	retro_chof_1248, retro_chof_1727 , retro_chof_1768, retro_chof_1968, retro_chof_444,
Gorilla gorilla	ENSGGOG00000006571	5 retrocopies	retro_ggor_1496, retro_ggor_2310, retro_ggor_344, retro_ggor_77, retro_ggor_93,
Loxodonta africana	ENSLAFG00000032173	1 retrocopy	retro_lafr_1171,
Macaca mulatta	ENSMMUG00000003867	1 retrocopy	retro_mmul_2198,
Oryctolagus cuniculus	ENSOCUG00000010546	1 retrocopy	retro_ocun_31,
Pongo abelii	ENSPPYG00000025953	14 retrocopies	retro_pabe_1138, retro_pabe_128, retro_pabe_1481, retro_pabe_1482, retro_pabe_1813, retro_pabe_1881, retro_pabe_2303, retro_pabe_2407, retro_pabe_2663, retro_pabe_2833, retro_pabe_2967, retro_pabe_3013, retro_pabe_3070, retro_pabe_368,
Pan troglodytes	ENSPTRG00000018039	1 retrocopy	retro_ptro_121,
Rattus norvegicus	ENSRNOG00000028505	4 retrocopies	retro_rnor_102, retro_rnor_234, retro_rnor_29, retro_rnor_70,
Sarcophilus harrisii	ENSSHAG00000006857	2 retrocopies	retro_shar_265, retro_shar_563,
Sarcophilus harrisii	ENSSHAG00000008658	1 retrocopy	retro_shar_618,