RetrogeneDB ID: retro_chof_28

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_321909:315..1386(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000009202
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000011399
• Aliases: None
• Description: None

Sequence

>retro_chof_28
ATGGCCCCCATGGGCATCCGCCTGTCCCCGCTGGGGGTGGCCGTGTTCTGCCTACTGGGCCTCGGGGTGCTCTACCACCT
CTACTCGGGCTCCCTGGCTGGGCGCTTCAGCATCTTCGGCCTGGGCGGCGAGCCGGACGGCGCGGCGGGGCCCGCGGCCG
ACGGAACCACGGTGGACCTGCGCGAGCTGCTGGCCGTGTCGGTGCTGGCGGCCGTGCGCGGTGGCGAAGAGGTGCGGCGC
GTCCGCGAGAGCAATGCCCTGCACGAGAAGTCCAAGGGGAAGACGCGGGAGGGTGCCGACGACAAGATGACCAGCGGCGA
CGTGCTGTCCAACCGGAAGATGTTCTACCTGCTCGAGACCGCCTTCCCCAGCGTGCAGATAAATACTGAGGAACATGTGG
ATGCAGCTGATCAGGAAGTTATCTTATGGGATCATAATATTCCTGAGGATATCCTGAAGGAAATAACTACCCCTAAAGAG
GTGCCAGCAGAAAGTGTCACTGTCTGGATTGACCCACTTGATGCAACACAGGAATATACAGAGGACCTTCGCCAGTATGT
CACTACCATGGTGTGTGTGGCTGTGAACGGCAAACCTGTACTAGGAGTAATACATAAGCCATTTTCTGAGTATACAGCAT
GGGCAATGGTGGACGGTGGTTCAAATGTGAAAGCCCGCACTTCTTACAACGAGAAAACCCCAAGGATCGTTGTGTCTCGC
TCCCATTCAGGGATGGTCAAGCAGGTTGCTCTTCAGACGTTTGGAAACCAGACTACAATTCTCCCAGCTGGTGGTGCTGG
TTATAAAGTTTTAGCGCTCTTGGATGTGCCTGATAAGAGTCAAGAAAAAGCTGATTTGTATATCCATGTGACGTACATCA
ACAAGTGGGATATTTGTGCTGGCAACGCCATCTTAAAAGCCCTTGGAGGCCATATGACCACCCTGAGTGGTGAAGAAATC
AGCTACACCGGTTCCGACGGTGTCGACGGGGGACTCCTTGCTAGCATCAGAATGAACCACCAGGCTCTGGTCAAAAAACT
CCCTGATCTAGAGAAGACCGGACATAAATAA

Alignment

ORF - retro_chof_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVQINTEEHVDAADQEVILWDHNIPEDILKEITTPKEVPAESVTVWIDPLDATQEYTEDLRQYVTTMVCV
          SVQINTEEHVDAADQEVILWDHNIPEDILKEITTPKEVPAESVTVWIDPLDATQEYTEDLRQYVTTMVCV
Retrocopy SVQINTEEHVDAADQEVILWDHNIPEDILKEITTPKEVPAESVTVWIDPLDATQEYTEDLRQYVTTMVCV

Parental  AVNGKPVLGVIHKPFSEYTAWAMVDGGSNVKARTSYNEKTPRFVVSRSHSGMVKXXXXXXXXXXXXXXXX
          AVNGKPVLGVIHKPFSEYTAWAMVDGGSNVKARTSYNEKTPR.VVSRSHSGMVK................
Retrocopy AVNGKPVLGVIHKPFSEYTAWAMVDGGSNVKARTSYNEKTPRIVVSRSHSGMVKQVALQTFGNQTTILPA

Parental  XXXXYKVLALLDVPDKSQEKADLYIHVTYIKKWDICAGNAILKALGGHMTTLSGEEISYTGSDGVDGGLL
          ....YKVLALLDVPDKSQEKADLYIHVTYI.KWDICAGNAILKALGGHMTTLSGEEISYTGSDGVDGGLL
Retrocopy GGAGYKVLALLDVPDKSQEKADLYIHVTYINKWDICAGNAILKALGGHMTTLSGEEISYTGSDGVDGGLL

Parental  ASIRMNHQALVKKLPDLEKTGHK
          ASIRMNHQALVKKLPDLEKTGHK
Retrocopy ASIRMNHQALVKKLPDLEKTGHK

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_28 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011399	1 retrocopy	retro_chof_28 ,