RetrogeneDB ID: retro_chof_1840

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_39990:7973..8304(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000004983
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000003286
• Aliases: None
• Description: None

Sequence

>retro_chof_1840
ACCCTTTTCTTGTGTAGCCTGCTCTGGGCTTTTTGTACCCCGGGTGCAAGGGCTGAGGAGCCCGGGGTCCGCTTCTCACA
TCCTGGCAACGCGGGCCTGGATAAGAACACAGTTCAAGACCAAGAGTCTGTCTTGGAGCCTCTAGAAAGTGGCATCAACA
AACCAGAGGCGGAAGTGTCCCCACAAAAACTGCAGCTCCATTATTTTCAAATGCATGATTATGATGGCAATAATTTACTG
GCAGGCTTAGAACTCTCCGCAGCCATCACTCATTCCACAGGAGGAAGGGAGTGAACAGACACCACCAAAGAATGAAGATG
ATCTGATTAAT

Alignment

ORF - retro_chof_1840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.48 %
• Parental protein coverage: 74.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TPFLCSLLWAFCTPGARAEEPGASFSHPGSAGLDRNTVHDQEHILEHLEGVINKPEAEMSPQELQLHYFK
          T.FLCSLLWAFCTPGARAEEPG..FSHPG.AGLD.NTV.DQE..LE.LE..INKPEAE.SPQ.LQLHYF.
Retrocopy TLFLCSLLWAFCTPGARAEEPGVRFSHPGNAGLDKNTVQDQESVLEPLESGINKPEAEVSPQKLQLHYFQ

Parental  MHDYDGNNLLDGLELSTAITHA-HKEGSDQTLPMKEEDLIN
          MHDYDGNNLL.GLELS.AITH....EGS.QT.P..E.DLIN
Retrocopy MHDYDGNNLLAGLELSAAITHS>QEEGSEQTPPKNEDDLIN

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_1840 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 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006097	2 retrocopies	retro_amel_720, retro_amel_906,
Bos taurus	ENSBTAG00000003358	1 retrocopy	retro_btau_629,
Canis familiaris	ENSCAFG00000032480	1 retrocopy	retro_cfam_797,
Choloepus hoffmanni	ENSCHOG00000003286	6 retrocopies	retro_chof_110, retro_chof_1840 , retro_chof_2447, retro_chof_3, retro_chof_41, retro_chof_581,
Felis catus	ENSFCAG00000009220	1 retrocopy	retro_fcat_42,
Macropus eugenii	ENSMEUG00000010002	1 retrocopy	retro_meug_2119,
Myotis lucifugus	ENSMLUG00000004210	1 retrocopy	retro_mluc_2396,
Mustela putorius furo	ENSMPUG00000012043	1 retrocopy	retro_mputfur_885,
Sus scrofa	ENSSSCG00000021325	2 retrocopies	retro_sscr_1129, retro_sscr_422,
Ictidomys tridecemlineatus	ENSSTOG00000003692	1 retrocopy	retro_itri_1118,
Vicugna pacos	ENSVPAG00000010692	1 retrocopy	retro_vpac_368,