RetrogeneDB ID: retro_chof_1438

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_29438:13744..14205(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000010717
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HUS1
• Ensembl ID: ENSCHOG00000001764
• Aliases: None
• Description: HUS1 checkpoint homolog (S. pombe) [Source:HGNC Symbol;Acc:5309]

Sequence

>retro_chof_1438
ATGAAGTTTAGGGCCAAGATCGTGGCCGGGGCCTGTCTCAACCACTTCACGCGAGTCAGTAACATGACATGGAAACTTGC
CAAAACCTGTACCCTCCGCATCAGCCGGATAAACTGAGCTTCATCCTTTCAGACAGGGTGGCTGATGGAGGGGTGAGCAT
GTGGTGTGAACTAGAACAGGAGAACTTCAGTGAATTTCAAATGGAAGTTGTTTCTGCAGAAAACAATGAGATTTATTTAG
AGCTGACATCGGAAAACTTCTCTCGAGCCTTGAAAACTGCTCAAAATGCCAGTACTTTGAAGATCGAGCTGACCAATAAA
CACTTTCCCGGCCTCACAGTCTCTGTAGAACTGCTATCTCTATTAAGCATTAGTCGCATTGTAACACATGACATCCCCTT
AAAGGTTATTCCAAGAAAACTGTGGAAGGATTTACAAGAGCCTGCAATCGCAGACTCTGAT

Alignment

ORF - retro_chof_1438 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.82 %
• Parental protein coverage: 56.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKFRAKIVDGACLNHFTRVSNMISKLAKTCTLRIS-PDKLNFILSDRVANGGVSMWCELEQENYFSEFQM
          MKFRAKIV.GACLNHFTRVSNM..KLAKTCTLRIS.PDKL.FILSDRVA.GGVSMWCELEQEN.FSEFQM
Retrocopy MKFRAKIVAGACLNHFTRVSNMTWKLAKTCTLRIS<PDKLSFILSDRVADGGVSMWCELEQEN-FSEFQM

Parental  EGVSAENNEIYLELTSENLSRALKTAQNARTLKIKLTNKHFPCLTVSVELLSLSSTSRIVTHDIPIKVI-
          E.VSAENNEIYLELTSEN.SRALKTAQNA.TLKI.LTNKHFP.LTVSVELLSL.S.SRIVTHDIP.KVI.
Retrocopy EVVSAENNEIYLELTSENFSRALKTAQNASTLKIELTNKHFPGLTVSVELLSLLSISRIVTHDIPLKVIP

Parental  KKLWKDLQEPTIPDSD
          .KLWKDLQEP.I.DSD
Retrocopy RKLWKDLQEPAIADSD

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_1438 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001764	4 retrocopies	retro_chof_1438 , retro_chof_1958, retro_chof_2084, retro_chof_898,
Dipodomys ordii	ENSDORG00000006582	1 retrocopy	retro_dord_182,
Echinops telfairi	ENSETEG00000009941	2 retrocopies	retro_etel_1764, retro_etel_1797,
Nomascus leucogenys	ENSNLEG00000004497	1 retrocopy	retro_nleu_2321,
Oryctolagus cuniculus	ENSOCUG00000027263	1 retrocopy	retro_ocun_761,
Otolemur garnettii	ENSOGAG00000012683	1 retrocopy	retro_ogar_1,
Pongo abelii	ENSPPYG00000025821	1 retrocopy	retro_pabe_151,
Sorex araneus	ENSSARG00000012348	1 retrocopy	retro_sara_391,
Ictidomys tridecemlineatus	ENSSTOG00000027204	1 retrocopy	retro_itri_151,