RetrogeneDB ID: retro_chof_2589

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_88402:5349..5778(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRNP27
• Ensembl ID: ENSCHOG00000003042
• Aliases: None
• Description: small nuclear ribonucleoprotein 27kDa (U4/U6.U5) [Source:HGNC Symbol;Acc:30240]

Sequence

>retro_chof_2589
CGTTGGCGGTCCGTGCCCACATTCCTGGAGAGAGAACCAGGCTTCACGAAAGGTCCCCGGTTCCAGGAGAGAAATGGAAG
AAGGAGCCTATCTCGATCCCCGCACAGAAGATGCTCCAGATCACCCAGACGACACAGAGCTACATCTCCCTCCCCTTCTC
TACCTGAAGAAAGAAGAGAGGAGGAAAAAAAAAAAGACAAAAGGAAGGAAGAGCAAAGAATGTCAGTTACTGAGGAAGCC
TTAGAGGGCAAAACACAGAAAGAAATAAAAATTTTGAAGTTAATGGGATTCGCCTCCTTTGACTCCACAAAAGGGAAAAA
GGTGGATGGCTCTGTAAATGCCTATGCCATAAACTTGTCTCAGAGGAGGAAGTACAAGCAGTACATGTATCAAAAAGGTG
GTTTCAACAGATCTCTGGATTTCATAGCA

Alignment

ORF - retro_chof_2589 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.73 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRRSRSTSRERERRRRERSRSRERDRRRSRSRSPHRRRSRSPRRHRSTSPSPSRLKERRDEEKKETKETK
          R.RS..T..ERE.......R..ER..RRS.SRSPHRR.SRSPRRHR.TSPSPS...ERR.E.....K...
Retrocopy RWRSVPTFLEREPGFTKGPRFQERNGRRSLSRSPHRRCSRSPRRHRATSPSPSLPEERREEXXXXDKRKE

Parental  SKERQITEEDLEGKTEEEIEMMKLMGFASFDSTKGKKVDGSVNAYAINVSQKRKYRQYMNRKGGFNRPLD
          ......TEE.LEGKT..EI...KLMGFASFDSTKGKKVDGSVNAYAIN.SQ.RKY.QYM..KGGFNR.LD
Retrocopy EQRMSVTEEALEGKTQKEIKILKLMGFASFDSTKGKKVDGSVNAYAINLSQRRKYKQYMYQKGGFNRSLD

Parental  FIA
          FIA
Retrocopy FIA

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_2589 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000037746	4 retrocopies	retro_btau_1352, retro_btau_375, retro_btau_514, retro_btau_515,
Choloepus hoffmanni	ENSCHOG00000003042	1 retrocopy	retro_chof_2589 ,
Echinops telfairi	ENSETEG00000017344	1 retrocopy	retro_etel_655,
Homo sapiens	ENSG00000124380	1 retrocopy	retro_hsap_3387,
Mus musculus	ENSMUSG00000001158	2 retrocopies	retro_mmus_1977, retro_mmus_2105,
Oryctolagus cuniculus	ENSOCUG00000022967	1 retrocopy	retro_ocun_1281,
Pongo abelii	ENSPPYG00000012332	2 retrocopies	retro_pabe_1990, retro_pabe_2782,
Pan troglodytes	ENSPTRG00000012022	1 retrocopy	retro_ptro_2300,
Sus scrofa	ENSSSCG00000025674	1 retrocopy	retro_sscr_285,