RetrogeneDB ID: retro_chof_231

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_5093:38572..39388(+)
• Located in intron of: ENSCHOG00000002341

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC46A3
• Ensembl ID: ENSCHOG00000003156
• Aliases: None
• Description: solute carrier family 46, member 3 [Source:HGNC Symbol;Acc:27501]

Sequence

>retro_chof_231
TCTGGCTATTTTATTCGAGAACTAAGTTTCTTGTGGTCGTATTTAATTATTATTCTGGTTATTGCAGTTAACTTGATCTA
TATTTTATTTTTTCTTGGCAATCCAAAGAAAGAATCTTCATCTCAGAATGTTCCTGTATCATGTAGTGAAAGCTTTAAAA
ACATATTTTACAGAACTCACATGCTATTCAAAAATACTTCCAGGAAGCAGCAGGTTTTGCTCTTTTTGTTACTTTTTACA
ATGGTCACTTATTTTTTCGTGGTAATTGGCATCTCCCCAGTTTTTATCCTTTATGAATTGGATTCCCCACTCTGCTGGAA
TGAAGTTTTTATAGGTTATGGGTCAGCTTTGGGCAGCATCTCCTTTTTGAGTAGTTTCCTGGGAATCTGGTTTTTTTCGA
ACTGTCTGGATGATATCCACATAGCCTTCATTGGAATTTTAACCACCACGTCCAGGATGGCAGTGACTGCTTTTGCCAGA
ACAACCCTGATGATGCTTTTAGTGAGGTTGCCGTTCCTTTTTACTATTGTTCTGCTTTCTGTTCTACAGTCCATGTTGTC
AAAAGTGGTCTGTTCTACTGAACAAGGCACTCTGTTAGCTTGTATTGCTTTCTTAGAGACACTTGGAGTCACCGCAGTGT
CTACTTTTAATGGAATTTATTCAGCCACTGTTGTGTGGTACCCTGTCTTCACTTTTCTGCTGTCTGCTGATCTATTACTA
ATTCCAGCCATCAGTCTATGTGTTGTCAAGTGCACCAAGTGGAATGAGGAAAGCTATGCACTTCTTACACAAGAAGATTC
CAGGGAAGACACTGCA

Alignment

ORF - retro_chof_231 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.28 %
• Parental protein coverage: 58.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGYFIRELGFVWSYFIITLVMAVNLIYILFFLGNPKKESSSQNVPVSCSESFKNLFYRTYMLFKNTSRKR
          SGYFIREL.F.WSY.II.LV.AVNLIYILFFLGNPKKESSSQNVPVSCSESFKN.FYRT.MLFKNTSRK.
Retrocopy SGYFIRELSFLWSYLIIILVIAVNLIYILFFLGNPKKESSSQNVPVSCSESFKNIFYRTHMLFKNTSRKQ

Parental  RVLLCLLLFTMVTYFFVVIGVSPIFILYELDSPLCWNEVLIGYGSALGSISFLSSFLGIWIFSCCLDDIH
          .VLL.LLLFTMVTYFFVVIG.SP.FILYELDSPLCWNEV.IGYGSALGSISFLSSFLGIW.FS.CLDDIH
Retrocopy QVLLFLLLFTMVTYFFVVIGISPVFILYELDSPLCWNEVFIGYGSALGSISFLSSFLGIWFFSNCLDDIH

Parental  IAFIGILTTMSGMAVTAFARTTLMMLLVRLPFLFTIVPFSVLRSMLSKVVRSTEQGTQFACTAFLETLGG
          IAFIGILTT.S.MAVTAFARTTLMMLLVRLPFLFTIV..SVL.SMLSKVV.STEQGT..AC.AFLETL.G
Retrocopy IAFIGILTTTSRMAVTAFARTTLMMLLVRLPFLFTIVLLSVLQSMLSKVVCSTEQGTLLACIAFLETL-G

Parental  VTAVSTFNGIYSATVAWHPGFTFLLSAGLLLIPAISL-VVKCTKWIEESYALLTLEDSREDTA
          VTAVSTFNGIYSATV.W.P.FTFLLSA.LLLIPAISL.VVKCTKW.EESYALLT.EDSREDTA
Retrocopy VTAVSTFNGIYSATVVWYPVFTFLLSADLLLIPAISLCVVKCTKWNEESYALLTQEDSREDTA

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_231 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,