RetrogeneDB ID: retro_chof_30

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_358315:436..1246(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000008498
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000013959
• Aliases: None
• Description: None

Sequence

>retro_chof_30
ATGAACGGGCAGCTCAACGGCTTCCACGAGGCGTTCATCGAGGAGGGCACGTTCCTTTTCACCTCAGAGTCCGTGGGGGA
AGGCCACCCAGATAAGATTTGTGACCAGATCAGTGATGCTGTCCTTGATGCCCACCTTCAACAGGACCCTGATGCCAAAG
TCGCTTGTGAAACTGTTGCTAAAACTGGAATGATCCTTCTTGCTGGGGAAATTACGTCCAGAGCTGCTGTTGACTACCAG
AAAGTTGTTCGTGAAACCATTAAACATGTTGGCTATGATGATTCTTCCAAAGGGTTTGACTATAAGACTTGTAATGTGCT
GGTGGCTTTGGAGCAGCAGTCACCCGATATTGCTCAAGGTGTTCATCTTGATCGGAATGAAGAAGACATTGGTGCAGGAG
ATCAGGGTTTGATGTTTGGTTATGCCACTGATGAAACTGAAGAGTGTATGCCTTTAACCATTGTCTTGGCACACAAGCTC
AATGCCAAACTGGCTGAACTACGCCGCACTGGCATTTTGCCTTGGCTACGCCCAGATTCTAAAACTCAAGTTACGGTGCA
GTATATGCAGGATCGAGGTGCCGTGCTTCCCATCAGAGTCCACACAATTGTCATATCCGTTCAGCATGATGAAGAAGTTT
GTCTTGATGAGATGAGGGATGCCCTAAAGGAGAAAGTCATCAAAGCTGTTGTACCTGCAAAATATCTTGATGAGGATACA
ATCTACCACCTGCAGCCAAGTGGCAGATTTGTTATTGGTGGGCCTCAGGGTGATGCTGGTTTGACTGGCCGGAAGATCAT
TGTAGACACT

Alignment

ORF - retro_chof_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.15 %
• Parental protein coverage: 68.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNGQLNGFHEAFIEEGTFLFTSDSVRECHPYKICDQISDAVLDAPLQQDPDAKVACETVAKTGMILLAGE
          MNGQLNGFHEAFIEEGTFLFTS.SV.E.HP.KICDQISDAVLDA.LQQDPDAKVACETVAKTGMILLAGE
Retrocopy MNGQLNGFHEAFIEEGTFLFTSESVGEGHPDKICDQISDAVLDAHLQQDPDAKVACETVAKTGMILLAGE

Parental  ITSRAAVDYQKVVRETIKHVGYDDSSKGFDYKTCNVLVALEQQSPDIAQGVHLDRNEEDIGAGDQGLMFG
          ITSRAAVDYQKVVRETIKHVGYDDSSKGFDYKTCNVLVALEQQSPDIAQGVHLDRNEEDIGAGDQGLMFG
Retrocopy ITSRAAVDYQKVVRETIKHVGYDDSSKGFDYKTCNVLVALEQQSPDIAQGVHLDRNEEDIGAGDQGLMFG

Parental  YATDETEECMPLTIVLAHKLNAKLAELRRTGILPWLRPDSKTQVTVQYMQDRGAVLPIRVHTIVISVQHD
          YATDETEECMPLTIVLAHKLNAKLAELRRTGILPWLRPDSKTQVTVQYMQDRGAVLPIRVHTIVISVQHD
Retrocopy YATDETEECMPLTIVLAHKLNAKLAELRRTGILPWLRPDSKTQVTVQYMQDRGAVLPIRVHTIVISVQHD

Parental  EEVCLDEMRDALKEKVIKAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGLTGRKIIVDT
          EEVCLDEMRDALKEKVIKAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGLTGRKIIVDT
Retrocopy EEVCLDEMRDALKEKVIKAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGLTGRKIIVDT

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_30 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 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013959	1 retrocopy	retro_chof_30 ,
Echinops telfairi	ENSETEG00000007634	2 retrocopies	retro_etel_1308, retro_etel_1532,
Echinops telfairi	ENSETEG00000015680	4 retrocopies	retro_etel_1669, retro_etel_1813, retro_etel_597, retro_etel_977,
Ornithorhynchus anatinus	ENSOANG00000003060	1 retrocopy	retro_oana_84,
Otolemur garnettii	ENSOGAG00000026925	1 retrocopy	retro_ogar_1580,
Rattus norvegicus	ENSRNOG00000013520	2 retrocopies	retro_rnor_2032, retro_rnor_955,