RetrogeneDB ID: retro_chof_1459

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_299874:186..760(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000012815
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000008485
• Aliases: None
• Description: None

Sequence

>retro_chof_1459
ATGAGCATGCAGGGGCAGATAAAAGATTTAAATATTAAGTGAGATTTTACATCCTCAAGTCCAAACTTTAGATCTACGGA
GCTGTGATATTTCAGATGCTGCTCTCCTGCACCTATGTAACTGCAGAAAACTGAAGAAATTAAACTCAAATTCCTCAAAA
GAAAACAGAATGTCCATAACTTCAAAAGGAATAAAAGCTGTGGCTTCATCTTATTTCTACCTGCATGAAGCTTCTTTGAA
AACATACTTCAATCTTACCGATGAAGGAGTCCTTGTTCTTACACTCAATTGCCGGCGCTAAAGACCACTGGTTTGGGTAG
TTGCTTAGATATTACAGATGTGCCCTTACATGCATTAGGAGAAAACTGCCCAGTTTTGCAGTGTGTTGACTTTCAGCTAC
TCAGGTGTCTGACAATGGTGTGGTCATGCTTGTGAGAGGACCTTGTGCCAAGAAATTAGAGGAGATTCATATAAGACATT
GTGTAAACCTCACTGATGAGTCTGTGGAAGCTGTACTTACTTTCTGCCCTCAGATATGTACTTTACTCTTCCATGGGTGC
CCCGGATAACAGAG

Alignment

ORF - retro_chof_1459 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.18 %
• Parental protein coverage: 89.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSMQGQITDSNI-SEILHPQVQTLDLRSCDISDAALLHLRNCRKLKKLNLNSSKENRMSITSEGIKAVAS
          MSMQGQI.D.NI.SEILHPQVQTLDLRSCDISDAALLHL.NCRKLKKLN.NSSKENRMSITS.GIKAVAS
Retrocopy MSMQGQIKDLNI>SEILHPQVQTLDLRSCDISDAALLHLCNCRKLKKLNSNSSKENRMSITSKGIKAVAS

Parental  SCLYLHEASLKRCCNLTDEGVLALALNCR-LLKIIDLGGCLGITDVSLHALGENCPFLQCVDF-SATQVS
          S..YLHEASLK...NLTDEGVL.L.LNCR..LK...LG.CL.ITDV.LHALGENCP.LQCVDF.SATQVS
Retrocopy SYFYLHEASLKTYFNLTDEGVLVLTLNCR<ALKTTGLGSCLDITDVPLHALGENCPVLQCVDF<SATQVS

Parental  DNGVVALVNGPCAKKLEEIHMGHCVNLTDESVEAVLTFCPQIRILLFHGC-PRITD
          DNGVV.LV.GPCAKKLEEIH..HCVNLTDESVEAVLTFCPQI..LLFHGC.PRIT.
Retrocopy DNGVVMLVRGPCAKKLEEIHIRHCVNLTDESVEAVLTFCPQICTLLFHGC<PRITE

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_1459 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014156	1 retrocopy	retro_btau_1488,
Canis familiaris	ENSCAFG00000010668	1 retrocopy	retro_cfam_1650,
Choloepus hoffmanni	ENSCHOG00000008485	2 retrocopies	retro_chof_1418, retro_chof_1459 ,