RetrogeneDB ID: retro_chof_2174

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_55448:801..1452(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HIAT1
• Ensembl ID: ENSCHOG00000010468
• Aliases: None
• Description: hippocampus abundant transcript 1 [Source:HGNC Symbol;Acc:23363]

Sequence

>retro_chof_2174
ATAATGAAATTTTCACCAGAAAGTGTTGCAGCATTTATAGCAGTCCTTGGCATTCTTTCCATTATTGCACAGACTGTAGT
CTTGAGTTTACTTATGAGATCAATTGGAAATAAGAACACCATTTTGTTGGGTCTGGGATTTCAGATATTACAGCTAGCAT
GGTATGGCTTCGGTTCAGAACCTTGGATGATGTGGGCTGCTGGGGCAGTAGCAGCCATGTCTAGCATTACCTTTCCAGCT
GTCAGTGCACTTGTTTCACGAACTGCTGATGCTGATCAACAGGGTGTCGTTCAAGGAATGATAACAGGAATTCGAGGGTT
GTGCAATGGCCTGGGACCAGCCCTTTATGGATTCATATTCTACATATTCCATGTGGAACTTAAGGAATTGCCAATAACAG
GAACAGACTTGGGAACAAACGCAAGCCCTCAGCACCACTTTGAACAGAATTCCATCATCCCTGGCCCCCCCTTCCTCTTT
GGAGCCTGTTCGGTACTGCTGGCTCTGCTTGTTGCCTTGTTTATTCCGGAACATACCAACTTAAGCTTAAGGTCTAGCAG
TTGGAAGAAACACTGTGGCAGTCACAGCCATCCTCATAGTACACAAGCCCCAGGAGAGGCCAAAGAACCTTTACTCCAAG
ACACAAATGTG

Alignment

ORF - retro_chof_2174 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.54 %
• Parental protein coverage: 50.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IMKFSPESVAAFIAVLGILSIIAQTVVLSLLMRSIGNKNTILLGLGFQILQLAWYGFGSEPWMMWAAGAV
          IMKFSPESVAAFIAVLGILSIIAQTVVLSLLMRSIGNKNTILLGLGFQILQLAWYGFGSEPWMMWAAGAV
Retrocopy IMKFSPESVAAFIAVLGILSIIAQTVVLSLLMRSIGNKNTILLGLGFQILQLAWYGFGSEPWMMWAAGAV

Parental  AAMSSITFPAVSALVSRTADADQQGVVQGMITGIRGLCNGLGPALYGFIFYIFHVELKELPITGTDLGTN
          AAMSSITFPAVSALVSRTADADQQGVVQGMITGIRGLCNGLGPALYGFIFYIFHVELKELPITGTDLGTN
Retrocopy AAMSSITFPAVSALVSRTADADQQGVVQGMITGIRGLCNGLGPALYGFIFYIFHVELKELPITGTDLGTN

Parental  TSPQHHFEQNSIIPGPPFLFGACSVLLALLVALFIPEHTNLSLRSSSWKKHCGSHSHPHSTQAPGEAKEP
          .SPQHHFEQNSIIPGPPFLFGACSVLLALLVALFIPEHTNLSLRSSSWKKHCGSHSHPHSTQAPGEAKEP
Retrocopy ASPQHHFEQNSIIPGPPFLFGACSVLLALLVALFIPEHTNLSLRSSSWKKHCGSHSHPHSTQAPGEAKEP

Parental  LLQDTNV
          LLQDTNV
Retrocopy LLQDTNV

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_2174 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010468	1 retrocopy	retro_chof_2174 ,
Echinops telfairi	ENSETEG00000005809	1 retrocopy	retro_etel_2047,
Myotis lucifugus	ENSMLUG00000002112	1 retrocopy	retro_mluc_718,
Oryctolagus cuniculus	ENSOCUG00000007819	1 retrocopy	retro_ocun_1386,
Drosophila melanogaster	FBgn0035400	1 retrocopy	retro_dmel_13,