RetrogeneDB ID: retro_chof_1119

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_204612:1476..1869(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF9
• Ensembl ID: ENSCHOG00000009241
• Aliases: None
• Description: serine/arginine-rich splicing factor 9 [Source:HGNC Symbol;Acc:10791]

Sequence

>retro_chof_1119
GGAGGGCGGGGTGGGTGGCCCCCTGGTGGGAGGAATGGGCCTCCTACCAGAAGATCGGATTTCCGAGTTCTTGCTTCAGG
ACCTCCTCCATCAGGCAGCTGGCAGGACCTGAAGGATCACGTGCGAGAGGCTGGGGATGTCTGTTACGCAGATGTGCAGA
AGGATGCAATGGGGATGGTTGAATGTCTCAGAAAAGAAGACATGGAATATGCCCTGCGTAAACTGGATGACACCAAATTC
CGCTCTCATGAGGGGGAAACTTCCTACATCCGAGTTTATCCTGAGAGAAGCACCAGCTATGGCTGCTCCAGATCTCGATC
TGGGTCAAGGGGCGGTGACTCTCCATACCAAAGCAGGGGTTCCCCACACTAGTTCTTCCCTTTCAGGCCCCAC

Alignment

ORF - retro_chof_1119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.84 %
• Parental protein coverage: 82.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGRGGWPRAGRNGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGMGMVEYLRKEDMEY
          GGRGGWP..GRNGPPTRRSDFRVL.SG.PPSGSWQDLKDH.REAGDVCYADVQKD.MGMVE.LRKEDMEY
Retrocopy GGRGGWPPGGRNGPPTRRSDFRVLASGPPPSGSWQDLKDHVREAGDVCYADVQKDAMGMVECLRKEDMEY

Parental  ALRKLDDTKFRSHEGETSYIRVYPERSTSYGYSRSRSGSRGRDSPYQSRGSPHYFSPFRPY
          ALRKLDDTKFRSHEGETSYIRVYPERSTSYG.SRSRSGSRG.DSPYQSRGSPH.F.PFRP.
Retrocopy ALRKLDDTKFRSHEGETSYIRVYPERSTSYGCSRSRSGSRGGDSPYQSRGSPH*FFPFRPH

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_1119 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 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012792	1 retrocopy	retro_btau_837,
Choloepus hoffmanni	ENSCHOG00000009241	1 retrocopy	retro_chof_1119 ,
Choloepus hoffmanni	ENSCHOG00000013858	1 retrocopy	retro_chof_1058,
Callithrix jacchus	ENSCJAG00000001187	1 retrocopy	retro_cjac_442,
Dasypus novemcinctus	ENSDNOG00000012598	2 retrocopies	retro_dnov_1555, retro_dnov_2648,
Homo sapiens	ENSG00000111786	1 retrocopy	retro_hsap_2530,
Macaca mulatta	ENSMMUG00000016494	1 retrocopy	retro_mmul_2154,
Nomascus leucogenys	ENSNLEG00000015661	1 retrocopy	retro_nleu_1931,
Otolemur garnettii	ENSOGAG00000003852	1 retrocopy	retro_ogar_2328,
Ochotona princeps	ENSOPRG00000004234	1 retrocopy	retro_opri_878,
Pongo abelii	ENSPPYG00000005031	1 retrocopy	retro_pabe_119,
Sarcophilus harrisii	ENSSHAG00000005685	1 retrocopy	retro_shar_598,
Sus scrofa	ENSSSCG00000009906	1 retrocopy	retro_sscr_745,
Tupaia belangeri	ENSTBEG00000008499	1 retrocopy	retro_tbel_2602,
Tarsius syrichta	ENSTSYG00000006848	4 retrocopies	retro_tsyr_1432, retro_tsyr_1648, retro_tsyr_585, retro_tsyr_891,