RetrogeneDB ID: retro_chof_1318

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_26105:7809..8346(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSER1
• Ensembl ID: ENSCHOG00000008281
• Aliases: None
• Description: oxidative stress responsive serine-rich 1 [Source:HGNC Symbol;Acc:16105]

Sequence

>retro_chof_1318
GTGAAATTCAAAGCCAAGGATGGAGAGGAAGAGAGTCCACAAACTTCTTTCAAGAAATTAAGAGTGGATGCATCAGGGTT
GATGGCATCTCTGTCTGTTGGAGACAGCACAAGTGTTAGAGCATCAGTCAGAACAGCTGCAGAGAATCCATGTGCATCTA
AGGATCGTTGACATGGGTCTACAAGGAAGTCTTCACGAGGAGCAGTGAGAACCCAGCTTCATTGATGTTCTAAGTCTTCC
GTTCTTCATTCTCCAAAGTTTAAACTTTGCAGTACAATAACTTCTTCCAGCAACCAGCTCAAGTACAAAAGCCAGACTGA
CTCCACTGATGGCAGCAGTGGGCTGGGATTTTCACCCCTAAAGAGTTCAGTGCAGGAGAATGCTTTGCTTCTCCTCTTGA
TGCTAATTACACAGGGGCAGTTGTTAAGCCTTTAAGAACTTCGGTTTCAAGGCTCCCATCAAAGAGTAAGAAGGAAGATT
CCTGAGGCTACCTAAGTTTCCCAAACAAGTCTCAAGACCAACGATCTCTCTGACTTT

Alignment

ORF - retro_chof_1318 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.26 %
• Parental protein coverage: 63.36 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKSEAKDGEEESLQTAFKKLRVDASGSIVSLSVGDSTSVRASVRTAADDTKPKTTCASKDSWHGSTRKSS
          .K..AKDGEEES.QT.FKKLRVDASG...SLSVGDST....SVR.A...T.....CASKD..HGSTRKSS
Retrocopy VKFKAKDGEEESPQTSFKKLRVDASGLMASLSVGDST----SVR-ASVRTAAENPCASKDR*HGSTRKSS

Parental  RGAVRTQRRRRSKSPVLHPPKFIHCSTITSSSNQLKHKSQTDSPDGSSGLGIS-SSKEFSAGECCTSPLD
          RGAVRTQ....SKS.VLH.PKF..CSTITSSSNQLK.KSQTDS.DGSSGLG.S...KEFSAGEC..SPLD
Retrocopy RGAVRTQLH*CSKSSVLHSPKFKLCSTITSSSNQLKYKSQTDSTDGSSGLGFS<TPKEFSAGECFASPLD

Parental  ANHTGAVVEPLRTSVPRLPSKSKKEDYS-EATRVSQASLKANDLSDF
          AN.TGAVV.PLRTSV.RLPSKS.K...S.EAT.VSQ.SLK.NDLSDF
Retrocopy ANYTGAVVKPLRTSVSRLPSKS-KKEDS>EAT*VSQTSLKTNDLSDF

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_1318 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008281	1 retrocopy	retro_chof_1318 ,
Echinops telfairi	ENSETEG00000013561	1 retrocopy	retro_etel_1755,
Mus musculus	ENSMUSG00000035399	1 retrocopy	retro_mmus_713,