RetrogeneDB ID: retro_chof_1055

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_190990:21..551(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TGIF1
• Ensembl ID: ENSCHOG00000000162
• Aliases: None
• Description: TGFB-induced factor homeobox 1 [Source:HGNC Symbol;Acc:11776]

Sequence

>retro_chof_1055
ATCCCCCTGGATCTCTACTCTTCAGCTGGCTCAGACAAGAGAAGGAAAAGGGGCAATCTGACCAGGGAATCTGTTCAGCT
TCTCCAGGGCTGACTGTATGAACACAAATACAATGTGTATCCCTCAGAGCAAAAGGAAGCATTATTATCCTAACAAACAC
ATCTATCCACACTACAGGTCTGTAACTGGTTCATCAATGCCCATTGCAGGCTCCTTCCTGACATGCTGAGAAAGGATGCC
AAAGATCCACATCAGTTCACATTTTCCCTCCATGGGGCCAAGATTTCTGAAGCTATCTCTGTGGAGTCAGCAGTAGACAT
CAGAAACGTCATGCCAGCTCTAGAGGAGAGCCCATTTCCTACCTGTACAGCCAGACCCAGCCCATTCCTAAGGAGGTCAC
TGTCTCCCAAGCCATCATCCCCAAGATCCATTTTGGCTCATCCTTCTGTGATCTGCCGTACCACTGTGATTACTTTGAAA
GATATGCCTTCCCCAATCTGCCAATCAATTGGTGAGGACAAAACACGAAT

Alignment

ORF - retro_chof_1055 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.6 %
• Parental protein coverage: 66.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IPLDLSSSAGSGKRRRRGNLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRR
          IPLDL.SSAGS.KRR.RGNL..ESVQ.L...LYEH.YN.YPSEQ..ALLS.QTHLSTLQVCNWFINA..R
Retrocopy IPLDLYSSAGSDKRRKRGNLTRESVQLLQG*LYEHKYNVYPSEQKEALLS*QTHLSTLQVCNWFINAHCR

Parental  LLPDMLRKDGKDPNQFTISRRGAKISEASSVEPAMGIKNFMPALEESPFHSCSVGPNPTLGRPLSPKPSS
          LLPDMLRKD.KDP.QFT.S..GAKISEA.SVE.A..I.N.MPALEESPF..C...P.P.L.R.LSPKPSS
Retrocopy LLPDMLRKDAKDPHQFTFSLHGAKISEAISVESAVDIRNVMPALEESPFPTCTARPSPFLRRSLSPKPSS

Parental  PGSILARPSVICHTTVTTLKDVPFPLCQSVGV-GQNTD
          P.SILA.PSVIC.TTV.TLKD.P.P.CQS.G..GQNT.
Retrocopy PRSILAHPSVICRTTVITLKDMPSPICQSIGE<GQNTN

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_1055 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	ENSCHOG00000000162	1 retrocopy	retro_chof_1055 ,
Echinops telfairi	ENSETEG00000011891	1 retrocopy	retro_etel_1597,