RetrogeneDB ID: retro_chof_1961

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_43429:442..913(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RRP15
• Ensembl ID: ENSCHOG00000000174
• Aliases: None
• Description: ribosomal RNA processing 15 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24255]

Sequence

>retro_chof_1961
GAGAACGCTGCAGAATCTGGAGTTGGAACTAATACGGGCTGGGCAGATGCCATGGCTAAGATCCTTAACAAAAAAACTCC
TAAAGGTAAACCCACCATTTTGGTCAAAAACAAAGAGCTGGAAAAGGAAAAAGAAAAGTTAAAGCAAGAGAGATTAGGGA
AAAGAAAACAGCTTGATAAGAAGCGGGAGTGGGAAATGATATGCAGAATAAAGCCAGATGTTGTCAAAGATGAAGAATCA
GAAAGAAATCTTCAGAGAATTGCAACAAGGGGTATGGTGCAATTATTTAATGCTGTTCAGAAGCATCAGAAGAATGTTGA
TGAAAAGGTTAAAGAAGCCTGAAGCTCTATTGGAAAGCGTGCTAAGTTGATACCAACAGTTTCTAAGAAAGATTTCATCA
GTGTTCTTAGAGGAATGGATGGAAGTACAAATGAGAAAAGTTCTACTGGAAGGGACCCAAAAGCCAAACAG

Alignment

ORF - retro_chof_1961 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.62 %
• Parental protein coverage: 66.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ENAAESGVGTNTGWADAMAKILNKKTPKSKPTILVKNKELEKEKEKLKQERLEKRKQLDKKREWEMICRV
          ENAAESGVGTNTGWADAMAKILNKKTPK.KPTILVK....................QLDKKREWEMICR.
Retrocopy ENAAESGVGTNTGWADAMAKILNKKTPKGKPTILVKXXXXXXXXXXXXXXXXXXXXQLDKKREWEMICRI

Parental  KPDVVKDKETERNLQRIATRGVVQLFNAVQKHQKNVDEKVKESGSSIRKRAKLISTVSKKDFISVLRGQD
          KPDVVKD.E.ERNLQRIATRG.VQLFNAVQKHQKNVDEKVKE..SSI.KRAKLI.TVSKKDFISVLRG.D
Retrocopy KPDVVKDEESERNLQRIATRGMVQLFNAVQKHQKNVDEKVKEA*SSIGKRAKLIPTVSKKDFISVLRGMD

Parental  GSTHEKSSTGRNPKAKQ
          GST.EKSSTGR.PKAKQ
Retrocopy GSTNEKSSTGRDPKAKQ

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_1961 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000174	1 retrocopy	retro_chof_1961 ,
Callithrix jacchus	ENSCJAG00000012916	2 retrocopies	retro_cjac_3789, retro_cjac_455,
Mus musculus	ENSMUSG00000001305	1 retrocopy	retro_mmus_3531,
Oryctolagus cuniculus	ENSOCUG00000017863	4 retrocopies	retro_ocun_1738, retro_ocun_820, retro_ocun_962, retro_ocun_992,
Ictidomys tridecemlineatus	ENSSTOG00000001244	1 retrocopy	retro_itri_1554,
Tarsius syrichta	ENSTSYG00000012715	1 retrocopy	retro_tsyr_2006,