RetrogeneDB ID: retro_chof_2686

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_97147:7862..8275(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35C2
• Ensembl ID: ENSCHOG00000011583
• Aliases: None
• Description: solute carrier family 35 (GDP-fucose transporter), member C2 [Source:HGNC Symbol;Acc:17117]

Sequence

>retro_chof_2686
ACCATGTTCTACCTGCAGCCACTGATGTTACTGGGGCTCTTGCCTCTCTTTTCCATATTTGAAGATCTCTGTTTGTCCAC
ATCTGAGAAACGACTCTGTTTCCAAGACCCAGTGCTTCTTCTGTGGGTACTTGGAAGCCTCTTCCTGGGTGGGATCCTCG
TCTTTGGTTTGGGCTTCTCCAAATTCCTCCTGGTCTCCAGAACCTCCAGCCTCTCTACATTGCTGGCATTTTTAAAGAAG
TCTGCACTCTGCTGTTGGCAGCTCATCTGCTGGGTGACCAGATCAGCCTCCTCAGCTGGCTGGGCTTCACCCTCTGCCTC
TCGGGGATATCCCTGCATGTTGCCCTCAAAGCTCTGCACTCCAGAGATGATGGTGACCCTAAACCGCTGAAGGAGCTGGG
CTCCAGCCCTGAC

Alignment

ORF - retro_chof_2686 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.0 %
• Parental protein coverage: 64.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TMFHLQPLMFLGLFPLFAIFEGLHLSTSEKIFRFQDPGLLLRVLGSLFLGGILAFGLGFSEFLLVSRTSS
          TMF.LQPLM.LGL.PLF.IFE.L.LSTSEK...FQDP.LLL.VLGSLFLGGIL.FGLGFS.FLLVSRTSS
Retrocopy TMFYLQPLMLLGLLPLFSIFEDLCLSTSEKRLCFQDPVLLLWVLGSLFLGGILVFGLGFSKFLLVSRTSS

Parental  LTLSIAGIFKEV-CTLLLAAHLLGDQISLLNWLGFALCLS-ISLHV-LKALXXXXDDDPN-LKELQEEDD
          L....A...K.....LL.A.HLLGDQISLL.WLGF.LCLS.ISLHV.LKAL....D.DP..LKEL....D
Retrocopy LSTLLAFLKKSA<TLLLAA-HLLGDQISLLSWLGFTLCLSGISLHVALKALHSRDDGDPKPLKELGSSPD

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_2686 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011583	2 retrocopies	retro_chof_2686 , retro_chof_952,
Callithrix jacchus	ENSCJAG00000017091	1 retrocopy	retro_cjac_4140,
Homo sapiens	ENSG00000080189	1 retrocopy	retro_hsap_4789,
Gorilla gorilla	ENSGGOG00000014052	1 retrocopy	retro_ggor_2982,
Nomascus leucogenys	ENSNLEG00000006880	1 retrocopy	retro_nleu_1104,
Pongo abelii	ENSPPYG00000011091	1 retrocopy	retro_pabe_3726,
Pan troglodytes	ENSPTRG00000013582	1 retrocopy	retro_ptro_3186,
Tupaia belangeri	ENSTBEG00000005486	1 retrocopy	retro_tbel_531,