RetrogeneDB ID: retro_chof_316

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_7289:7343..7866(+)
• Located in intron of: ENSCHOG00000012898

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC46A1
• Ensembl ID: ENSCHOG00000013565
• Aliases: None
• Description: solute carrier family 46 (folate transporter), member 1 [Source:HGNC Symbol;Acc:30521]

Sequence

>retro_chof_316
CAGGAAATCCTGGCCCTCTATGAACTGAAAACACCATTCTACCGGGACTCCAAGCTAGCTGGCTATGGCTCTGTGGCTCA
GTGCTTCCCATACCTCACAAGCCTGCTGGGCCTGTGGCTTCTATAGTACTGTCTGGCTGACACCTGGATGACTGGGATCG
GCCTGGCCTCAACTGCATGGGGAAGGTGGTATTTGCATTTGCTACCATCATACCCCTCAGGTTCATAGGGTATGGGCTCC
TCTTCCTGCTATTAGTCATCATACCCATCATCTTGGCCAAGTTCTCCAGACTGGTGAGCAAGTCGGAGCAAGGTGCTCTC
TTCTCTGCTGTGGCTGTGTGAATGGCTTAGCCATGCTGACAGCCACTGGCATCTTCAACTCGCTCCACCAACCACCATGA
ACTTCAGGAAGGGGTTCCGCTTCCTCCCAGGAGCCAGCCTCCTCTTCACCCCAGCCATTCTCATTGGGATGCTGGAAAAA
GGCTAATCCTCACACGGAATTCCAGCAGTTTCCCCAGAGCCCC

Alignment

ORF - retro_chof_316 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.83 %
• Parental protein coverage: 53.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QDILTLYELSAPLCWDSQLIGYGSMAQQLPYLTSLLGLRLLQYCLADTWVAEIGLA-FNILGMVVFAFAT
          Q.IL.LYEL..P...DS.L.GYGS.AQ..PYLTSLLGL.LL.YCLADTW...IGLA..N..G.VVFAFAT
Retrocopy QEILALYELKTPFYRDSKLAGYGSVAQCFPYLTSLLGLWLL*YCLADTWMTGIGLA<LNCMGKVVFAFAT

Parental  ITALMFTGYGLLFLSLAITPVIRAKLSRLVSESEQGALFSSVA-CVNSLAMLTATGIFNSLY-PATLNFM
          I..L.F.GYGLLFL.L.I.P.I.AK.SRLVS.SEQGALFS.VA.CVN.LAMLTATGIFNSL..P.T.NF.
Retrocopy IIPLRFIGYGLLFLLLVIIPIILAKFSRLVSKSEQGALFSAVA<CVNGLAMLTATGIFNSLH<PTTMNFR

Parental  KGFPFLLGAGLLLIPGI---VLEK-ADPHPEFQQFPQSP
          KGF.FL.GA.LL..P.I....LEK.A.PH.EFQQFPQSP
Retrocopy KGFRFLPGASLLFTPAILIGMLEK>ANPHTEFQQFPQSP

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_316 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003156	1 retrocopy	retro_chof_231,
Choloepus hoffmanni	ENSCHOG00000013565	1 retrocopy	retro_chof_316 ,