RetrogeneDB ID: retro_chof_1868

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_40929:160..898(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: B3GALNT2
• Ensembl ID: ENSCHOG00000007385
• Aliases: None
• Description: beta-1,3-N-acetylgalactosaminyltransferase 2 [Source:HGNC Symbol;Acc:28596]

Sequence

>retro_chof_1868
GCTGCAGAGGGTGCATTGCCTCATGAATTCATGGAAGGTGTGGAGGGAATTGCAGGAGGTTTTATTTATACTATTCAGGA
AGGTGATGCTCTCTTAAAAAACCTTCATTCTCGCCCTCAAAGACTTATTGATCATATAAGTAATCTCCACGAGGAAGATG
CCTTACTGAAGGAGGAAAGCAGCACCTATGATGACATTGTTTTTGTGGATGTTGTTGACACTTACCGAAATGTTCCTGCA
AAACTACTGAACTTCTATAGATGGACTGTGGAAACAACCAACTTCGATTTATTGCTAAAGACAGATGACGACTGTTACAT
AGACTTAGAAGCTGTATTTAATAGCATTGCCCACAAAAATCTAGAAGGGCCTAATTTTTGGTGGGGAAATTTCAGATTGA
ATTGGGCAGTTGACCGAACTGGAAAGTGGCAAGAGTTAGAGTACCCCAGTCCTGCTTATCCTGCCTTTGCATGTGGGTCA
GGTTATGTTATCTCCAAAGACATTGTCCACTGGCTGGCAAGCAACTCAGAGAGACTGAAGACCTATCAGGGTGAAGATGT
AAGCGTGGGCATTTGGATGGCAGCGATAGGACCTAAAAGATACCAGGAGAGTCTCTGGTTGTGCGAGAAGACTTGTGAAA
CTGGAATGTTGTCTTCCCCTCAGTATTCTCCACAGGAACTAACAGAACTATGGAAACTGAAGGAATTGTGTGGTGATCCT
TGTAAATGTGAAGCAAGA

Alignment

ORF - retro_chof_1868 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.19 %
• Parental protein coverage: 53.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAEGALPHEFMEGVEGIAGGFIYTIQEGDALLKNLHSRPQRLIDHISNLHEEDALLKEESSTYDDIVFVD
          AAEGALPHEFMEGVEGIAGGFIYTIQEGDALLKNLHSRPQRLIDHISNLHEEDALLKEESSTYDDIVFVD
Retrocopy AAEGALPHEFMEGVEGIAGGFIYTIQEGDALLKNLHSRPQRLIDHISNLHEEDALLKEESSTYDDIVFVD

Parental  VVDTYRNVPAKLLNFYRWTVETTNFDLLLKTDDDCYIDLEAVFNSIAHKNLEGPNFWWGNFRLNWAVDRT
          VVDTYRNVPAKLLNFYRWTVETTNFDLLLKTDDDCYIDLEAVFNSIAHKNLEGPNFWWGNFRLNWAVDRT
Retrocopy VVDTYRNVPAKLLNFYRWTVETTNFDLLLKTDDDCYIDLEAVFNSIAHKNLEGPNFWWGNFRLNWAVDRT

Parental  GKWQELEYPSPAYPAFACGSGYVISKDIVHWLASNSERLKTYQGEDVSMGIWMAAIGPKRYQESLWLCEK
          GKWQELEYPSPAYPAFACGSGYVISKDIVHWLASNSERLKTYQGEDVS.GIWMAAIGPKRYQESLWLCEK
Retrocopy GKWQELEYPSPAYPAFACGSGYVISKDIVHWLASNSERLKTYQGEDVSVGIWMAAIGPKRYQESLWLCEK

Parental  TCETGMLSSPQYSPQELTELWKLKELCGDPCKCVAR
          TCETGMLSSPQYSPQELTELWKLKELCGDPCKC.AR
Retrocopy TCETGMLSSPQYSPQELTELWKLKELCGDPCKCEAR

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_1868 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	ENSCHOG00000007385	1 retrocopy	retro_chof_1868 ,