RetrogeneDB ID: retro_chof_861

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_157068:1273..1680(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000000038
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_chof_861
AAACGCCATCAGGTGTTGCTATTTTTTACATGATTATTCTCTTACTTGTATTTATTGTTCAGTTTTCTGTATCCTGTGCT
TGTTTAGCCCTGAACCAGGAGCAACTGGGTCAGCTTCTTGAAGTTGGGTGGAACAATACAGCAAGTGCTCGAAATGACAT
CCAGAGAAATTTAAACTGCAGTGGGTTCCGAAGTTTTAATCCAGATGACACCTGTCTGGCTAGCTGTGCTAAAAGTGGTC
ACCCGTGCTTACTGTGTGCTCCGATAATAGGAGAATATTCTGGAGACGTTTTGAGATTTGTTGGCAGCATTGGCCTTTTC
TTCAGTTTTACGGAGATCTGGAGCGTTTGGTTGACCTACAGATACTGGAACCAGAAAGATCCTCGTGCTAAGCCTAGTGC
ATTTCTT

Alignment

ORF - retro_chof_861 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.24 %
• Parental protein coverage: 74.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KHHQVLLF-FYMIILLLVFIVQFSVSCACLALNQEQQGQLLEVGWNNTASARNDIQRNLNCCGFRSFNPN
          K.HQVLLF.FYMIILLLVFIVQFSVSCACLALNQEQ.GQLLEVGWNNTASARNDIQRNLNC.GFRSFNP.
Retrocopy KRHQVLLF<FYMIILLLVFIVQFSVSCACLALNQEQLGQLLEVGWNNTASARNDIQRNLNCSGFRSFNPD

Parental  DTCLASCAKSGHPCLLCAPIIGEYAGEVLRFVGGIGLFFSFTEILGVWLTYRYRNQKDPRANPSAFL
          DTCLASCAKSGHPCLLCAPIIGEY.G.VLRFVG.IGLFFSFTEI..VWLTYRY.NQKDPRA.PSAFL
Retrocopy DTCLASCAKSGHPCLLCAPIIGEYSGDVLRFVGSIGLFFSFTEIWSVWLTYRYWNQKDPRAKPSAFL

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_861 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,