RetrogeneDB ID: retro_chof_1139

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_2095:34595..34909(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: N6AMT1
• Ensembl ID: ENSCHOG00000005227
• Aliases: None
• Description: N-6 adenine-specific DNA methyltransferase 1 (putative) [Source:HGNC Symbol;Acc:16021]

Sequence

>retro_chof_1139
GAGCCCGCGGAGGGCACGTTCCAGCTCAGCGCGGCCGTGGAGGAACTCGCGGGAATGGAAAAACGCGTTGAAGTTGGGTC
AGGGTCTGGAGTGGTAGCTGTATTCCTGACTCAACAGTAGGTCCTCAGGCATTGTACGTGTGCACCGAGATCAAGCCCAA
CACAGGGGCTTGTACCCTGGAGACAGCACATGGTAACCAAGTCCACATTCAAGCAGGAATTACAGATTTGATCAGAAGCT
TGCTCCCAAGATTGAAGGAAAAAGTTGACATTCTGGTGTTTAATCACCCCTAAGTAGTGACTCCACCTGAAGAG

Alignment

ORF - retro_chof_1139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.09 %
• Parental protein coverage: 50.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EPAEDTFLLLDALEAAAAELAGVEICLEVGSGSGVVSVFLA-SMIGPQALCMCTEINPNAAACTLETARC
          EPAE.TF.....L.AA..ELAG.E...EVGSGSGVV.VFL..S..GPQAL..CTEI.PN..ACTLETA..
Retrocopy EPAEGTF----QLSAAVEELAGMEKRVEVGSGSGVVAVFLT<STVGPQALYVCTEIKPNTGACTLETAHG

Parental  NKVHIQPVITDLVKGLLPRLKEKVDLLVFNPPYVVTPPEE
          N.VHIQ..ITDL...LLPRLKEKVD.LVFN.P.VVTPPEE
Retrocopy NQVHIQAGITDLIRSLLPRLKEKVDILVFNHP*VVTPPEE

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_1139 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005227	1 retrocopy	retro_chof_1139 ,
Homo sapiens	ENSG00000156239	1 retrocopy	retro_hsap_916,
Gorilla gorilla	ENSGGOG00000022382	1 retrocopy	retro_ggor_739,
Nomascus leucogenys	ENSNLEG00000002845	1 retrocopy	retro_nleu_282,
Oryctolagus cuniculus	ENSOCUG00000001084	1 retrocopy	retro_ocun_521,
Ochotona princeps	ENSOPRG00000001551	3 retrocopies	retro_opri_200, retro_opri_867, retro_opri_925,
Pongo abelii	ENSPPYG00000011314	1 retrocopy	retro_pabe_790,
Pan troglodytes	ENSPTRG00000013817	1 retrocopy	retro_ptro_635,
Pteropus vampyrus	ENSPVAG00000012777	2 retrocopies	retro_pvam_1166, retro_pvam_1200,
Sus scrofa	ENSSSCG00000026046	1 retrocopy	retro_sscr_130,
Ictidomys tridecemlineatus	ENSSTOG00000021743	1 retrocopy	retro_itri_497,
Tupaia belangeri	ENSTBEG00000001269	1 retrocopy	retro_tbel_777,