RetrogeneDB ID: retro_chof_2232

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_59894:1824..2109(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ORMDL2
• Ensembl ID: ENSCHOG00000009601
• Aliases: None
• Description: ORM1-like 2 (S. cerevisiae) [Source:HGNC Symbol;Acc:16037]

Sequence

>retro_chof_2232
CTTCCGGTGGCTCTACTCAGGACCCGCTGCTCCAGCCTTCCTGTTGTCTGGCTCCTGACCAGCGTCATCTGTAACTTGGC
AATGGATGCCCTTCTACATATAGTGAAAGGGACACCCTTTGAGACCCCTGACCAAGAAAAAGCTCAGTGATGGACACACT
GGGAGCAGATGGACAGTGGGCTCCAGTTTTCCTCTTGTGGCAAGTTCCTCTGTGTCTCTCCTATTGGACTCTACCTCCTG
GCCAGCCTCTACACCAAATGAGATGCTGCTCACTCCCTCATTAAC

Alignment

ORF - retro_chof_2232 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.47 %
• Parental protein coverage: 62.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LHVVLLSIPFFSIPVVWTLTNVIHNLAMYVFLHTVKGTPFETPDQGKARLLTHWEQMDYGLQFTSSRKFL
          L.V.LL.....S.PVVW.LT.VI.NLAM...LH.VKGTPFETPDQ.KA...THWEQMD.GLQF.S..KFL
Retrocopy LPVALLRTRCSSLPVVWLLTSVICNLAMDALLHIVKGTPFETPDQEKAQ*WTHWEQMDSGLQFSSCGKFL

Parental  SISPIVLYLLASFYTKYDAAHFLIN
          ..SPI.LYLLAS.YTK.DAAH.LIN
Retrocopy CVSPIGLYLLASLYTK*DAAHSLIN

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_2232 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 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003047	2 retrocopies	retro_amel_140, retro_amel_735,
Canis familiaris	ENSCAFG00000000071	8 retrocopies	retro_cfam_1078, retro_cfam_1248, retro_cfam_1512, retro_cfam_1786, retro_cfam_187, retro_cfam_335, retro_cfam_576, retro_cfam_972,
Choloepus hoffmanni	ENSCHOG00000009601	1 retrocopy	retro_chof_2232 ,
Erinaceus europaeus	ENSEEUG00000015224	1 retrocopy	retro_eeur_16,
Felis catus	ENSFCAG00000013964	1 retrocopy	retro_fcat_895,
Macropus eugenii	ENSMEUG00000014896	1 retrocopy	retro_meug_767,
Microcebus murinus	ENSMICG00000010920	1 retrocopy	retro_mmur_212,
Myotis lucifugus	ENSMLUG00000003575	1 retrocopy	retro_mluc_901,
Macaca mulatta	ENSMMUG00000006292	1 retrocopy	retro_mmul_2358,
Mustela putorius furo	ENSMPUG00000000911	2 retrocopies	retro_mputfur_452, retro_mputfur_738,
Mus musculus	ENSMUSG00000025353	1 retrocopy	retro_mmus_2646,
Otolemur garnettii	ENSOGAG00000001695	2 retrocopies	retro_ogar_3016, retro_ogar_951,