RetrogeneDB ID: retro_chof_1137

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_209372:1553..2101(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN13
• Ensembl ID: ENSCHOG00000013574
• Aliases: None
• Description: tetraspanin 13 [Source:HGNC Symbol;Acc:21643]

Sequence

>retro_chof_1137
CTGCTCTGCATGTTACTAATTGGCATTGCTGAATGAAGCATTGGCTTAGGGTGATTTTCAGTCTCCGAGTATTTGGCGGT
AGTCACTGTAGTGGCATCCTCTTGCTCCTGATTGCATTGGTGGGGCTGATTGGAGCTGTAAAACACCATCAGATGTTGCT
ATTTTTTTATATGATTATTCTCTTACTTGTATTTATTGTTTAGTTTTCTGTATCCTGTGCTTGTTTAGCCCTGAAGGAGG
AGCAACAGGGTCAGCTTGTTGAAATTAGGTGGAACAATACAGCAAGTGTTCGTAATGACATCCATAAAAATTTAAACTGC
CTTGGGTTCCAAAGTTTTAACCCAAATGACACCTTTCTGGCTAGCTGTGCTAAAAGTGGTCACCCATGTTTACCATGTGC
TCTGGTAACAGGAGAATATGCTGGAGAGGTTTTGAGATTTGTTGGCGGCATTGGCCTTTTCTTCAGTTTTATGGAGACCC
TGGGCATTTGGTTGGCCTATAGATACAGGAACAAGAAAGATCCTTGCACAAATCATAGTGCATTTCTT

Alignment

ORF - retro_chof_1137 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.63 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LVSLLLIGIATWGIGFG-LISSLRVVGVVIAVGIFLFLIALVGLIGAVKHHQVLLFFYMIILLLVFIVQF
          L...LLIGIA...IG.G..I.SLRV.G.....GI.L.LIALVGLIGAVKHHQ.LLFFYMIILLLVFIV.F
Retrocopy LLCMLLIGIAE*SIGLG<VIFSLRVFGGSHCSGILLLLIALVGLIGAVKHHQMLLFFYMIILLLVFIV*F

Parental  SVSCACLALNQEQQGQLLEVGWNNTASARNDIQRNLNCCGFRSFNPNDTCLASCAKSGHPCLLCAPIIGE
          SVSCACLAL..EQQGQL.E..WNNTAS.RNDI..NLNC.GF.SFNPNDT.LASCAKSGHPCL.CA...GE
Retrocopy SVSCACLALKEEQQGQLVEIRWNNTASVRNDIHKNLNCLGFQSFNPNDTFLASCAKSGHPCLPCALVTGE

Parental  YAGEVLRFVGGIGLFFSFTEILGVWLTYRYRNQKDPRANPSAFL
          YAGEVLRFVGGIGLFFSF.E.LG.WL.YRYRN.KDP..N.SAFL
Retrocopy YAGEVLRFVGGIGLFFSFMETLGIWLAYRYRNKKDPCTNHSAFL

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_1137 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013574	2 retrocopies	retro_chof_1137 , retro_chof_861,
Ictidomys tridecemlineatus	ENSSTOG00000008833	1 retrocopy	retro_itri_1367,