RetrogeneDB ID: retro_chof_1625

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_345219:139..822(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCD7
• Ensembl ID: ENSCHOG00000007218
• Aliases: None
• Description: programmed cell death 7 [Source:HGNC Symbol;Acc:8767]

Sequence

>retro_chof_1625
GCGCGGGGCCCTGCGCCTGGTGCAGGGCTGCACGCCGAGCTGGGCGAAAGGCTACAGTCGCTTTCCCAGGCCGCCTTTGT
GGGCGAAGCGTGGCGGAGACTGGAGAGGGTACGGCGCCGCCAGCTGCGGCTGCCCGAGCGGGCCCGGGAACGCGAGGCCG
AGCGGGAGGTGGAGGCCCCATGGGCCACGGAGCGCAAGTAGGCGATTGGACCGCTGGAGGGTCAAGTGCGTGCAGGAGGT
GGAGGAGAAGAAGCGCGAGCAGGAACTCAAAGTTGCTGCTGATGGTGTCTTGTCTGAAGTGAGGAAAAACAAGCAGACAC
CAAAAGAATGGTGGACATTCTTCGGGCCTTGGAGAAATTAAGGAAGCCGAGGAAAGAGACTGCAGCGAGGCAAAAGGTCT
GTCCTCCAGTCTCAGCAGATGAGACTTTTCAGCATCATCTGCAGCGACTGAGAAAGCTGATTTAAAAACGTTCTGAACTG
CATGAAGCTGAAGAGAGAGCCCTTAGAGTATATTGGAAGAAGAGCAAAGGGAAGAGGGGAAAAGATAGTTGGAAAAGAAA
CAGAAAAGAAAAAAGAAAATTTTACTTCAGAAACATGAAATTGAATCCAAATTATTTAGAGATCCAGATGAGTTCCCACT
TGCTCACCTCCTGCAGCCTTTCCGACAGTGTTACCTCCAAGCT

Alignment

ORF - retro_chof_1625 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.72 %
• Parental protein coverage: 67.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ARLHAEAAPLRAELAERLQSLTQAAFVGEARRRLERVRRRRLRLRERAREREAEREAEAARAAERE-QEI
          AR..A..A.L.AEL.ERLQSL.QAAFVGEA.RRLERVRRR.LRL.ERAREREAERE.EA..A.ER.....
Retrocopy ARGPAPGAGLHAELGERLQSLSQAAFVGEAWRRLERVRRRQLRLPERAREREAEREVEAPWATERK>RRL

Parental  DRWRVKCVQEVEEKKREQELKVAADGVLSEVRK-KQADTKRMVDILRALEKLRKLRKEAAARKGVCPPAS
          DRWRVKCVQEVEEKKREQELKVAADGVLSEVRK.KQADTKRMVDILRALEKLRK.RKE.AAR..VCPP.S
Retrocopy DRWRVKCVQEVEEKKREQELKVAADGVLSEVRK<KQADTKRMVDILRALEKLRKPRKETAARQKVCPPVS

Parental  ADETFEHHLQRLRKLIKKRSELYEAEERALRV-MLEGEQEEERKREFEKKQRKEKEKILLQKREIESKLF
          ADETF.HHLQRLRKLI.KRSEL.EAEERALRV..LE.E...E................LLQK.EIESKLF
Retrocopy ADETFQHHLQRLRKLI*KRSELHEAEERALRV<ILE-EEQREEXXXXXXXXXXXXXXXLLQKHEIESKLF

Parental  GDPDEFPLAHLLQPFRQYYLQA
          .DPDEFPLAHLLQPFRQ.YLQA
Retrocopy RDPDEFPLAHLLQPFRQCYLQA

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_1625 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032076	1 retrocopy	retro_cfam_2181,
Choloepus hoffmanni	ENSCHOG00000007218	1 retrocopy	retro_chof_1625 ,
Rattus norvegicus	ENSRNOG00000014340	1 retrocopy	retro_rnor_443,