RetrogeneDB ID: retro_chof_100

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_1947:50737..51186(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDHD2
• Ensembl ID: ENSCHOG00000009397
• Aliases: None
• Description: haloacid dehalogenase-like hydrolase domain containing 2 [Source:HGNC Symbol;Acc:25364]

Sequence

>retro_chof_100
ATGGCAGCACGCCATGCATTAAAAGCTGTTTGGTAGATCTCAGTGCACACTTCACATTGAAGATGCAGCTGTGCCGGGCG
CACAGGAAGCTTTTAAAAGGGTTACGTGGTGCTTCTGTAAAAGTTAGGTTTGTGACTAACACAACTAAAGAGAGCAAGCA
AGATCTATTGGAAAGGTTGAAAAAACTGGAATTTGAGATCTCTGAAGATGAAATATTCACTTCTCTGACTGCAGCCAGAA
ATTTAGTAGAGCAGAAACAGGTCAGACCCATGCTGCTGGTTGATGATCGGGCACTACGTGACTTCAGAGGAATACAAACT
AGTGATCCTAATGCAGTGGTCATAGGATTGGCACCAGAACACTTTCATTATCAAATTCTGAATCAAGCATTCCGGCTACT
CCTGGACGGGGCACCTCTCATAGCGATCCACAAAGCCAGGTACTACAGG

Alignment

ORF - retro_chof_100 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.12 %
• Parental protein coverage: 57.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAARRALKAV-LVDLSG-TLHIEDAAVPGAQEALKR-LRGASVKVRFVTNTTKESKQDLLERLKKLEFEI
          MAAR.ALKAV.LVDLS..TLHIEDAAVPGAQEA.KR.LRGASVKVRFVTNTTKESKQDLLERLKKLEFEI
Retrocopy MAARHALKAV<LVDLSA<TLHIEDAAVPGAQEAFKR>LRGASVKVRFVTNTTKESKQDLLERLKKLEFEI

Parental  SEDEIFTSLTAARNLVEQKQVRPMLLVDDRALPDFRGIQTSDPNAVVIGLAPEHFHYQFLNQAFRLLLDG
          SEDEIFTSLTAARNLVEQKQVRPMLLVDDRAL.DFRGIQTSDPNAVVIGLAPEHFHYQ.LNQAFRLLLDG
Retrocopy SEDEIFTSLTAARNLVEQKQVRPMLLVDDRALRDFRGIQTSDPNAVVIGLAPEHFHYQILNQAFRLLLDG

Parental  APLIAIHKARYYK
          APLIAIHKARYY.
Retrocopy APLIAIHKARYYR

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_100 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011893	1 retrocopy	retro_btau_1336,
Choloepus hoffmanni	ENSCHOG00000009397	1 retrocopy	retro_chof_100 ,
Macaca mulatta	ENSMMUG00000010999	1 retrocopy	retro_mmul_595,
Ictidomys tridecemlineatus	ENSSTOG00000008527	1 retrocopy	retro_itri_55,