RetrogeneDB ID: retro_chof_1766

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_379778:248..759(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM33
• Ensembl ID: ENSCHOG00000007675
• Aliases: None
• Description: transmembrane protein 33 [Source:HGNC Symbol;Acc:25541]

Sequence

>retro_chof_1766
CCCAAAGGCCCACATGGGGTGGGTGCAGTGCAATGTATGATGATCAATAAACTGGATACAGCAATGTGGCTTTCTCGCTT
GTTCACAGTTGACTGCTCTGCTCTGTTTGTTCTGCTTCTTCTTGGGTTGCATGAAGCAGCAAGCTTTACCAACATGCTTT
GCTGGCAAATGCTCTTACCAGTGCTTTGAGGCTGCACCAATGATAACCACACTTCAGTTAAGCACAGTGCTCCTGGCCCG
GGCATTGTTAGAGGACAGCTGCCACTGTCTCTTGTATTCTCTCATCTTTGTCAACTCCTGCCCAGTCACAAACAGTATTT
TCCCAGTCCTGTTATTCTCTTTGCTTCATGCTGCCACATATACTAAAAAGGTCCTTGATGCAAAGGGTTCAAATAGTTTA
CCTTGGCTGAGATCTGTCTTGGATAAATTAAGTGCTAATGAACAGAATATTCCGAAATTCATTGCTTGTAATGAAATATT
CTTGATGCCTGCTACAGTTTTTATGCTTTTT

Alignment

ORF - retro_chof_1766 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.28 %
• Parental protein coverage: 69.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PNGPQGAGAVQFMMTNKLDTAMWLSRLFTVYCSALFVLPLLGLHEAASF-YQRALLANALTSALRLHQRL
          P.GP.G.GAVQ.MM.NKLDTAMWLSRLFTV.CSALFVL.LLGLHEAASF.YQ.ALLANALTSALRLHQ..
Retrocopy PKGPHGVGAVQCMMINKLDTAMWLSRLFTVDCSALFVLLLLGLHEAASF<YQHALLANALTSALRLHQ**

Parental  PHF-QLSRAFLAQALLEDSCHYLLYSLIFVNSYPVTMSIFPVLLFSLLHAATYTKKVLDAKGSNSLPLLR
          PHF.QLS...LA.ALLEDSCH.LLYSLIFVNS.PVT.SIFPVLLFSLLHAATYTKKVLDAKGSNSLP.LR
Retrocopy PHF<QLSTVLLARALLEDSCHCLLYSLIFVNSCPVTNSIFPVLLFSLLHAATYTKKVLDAKGSNSLPWLR

Parental  SVLDKLSANQQNILKFIACNEIFLMPATVFMLF
          SVLDKLSAN.QNI.KFIACNEIFLMPATVFMLF
Retrocopy SVLDKLSANEQNIPKFIACNEIFLMPATVFMLF

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_1766 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000043958	1 retrocopy	retro_btau_390,
Choloepus hoffmanni	ENSCHOG00000007675	1 retrocopy	retro_chof_1766 ,
Tursiops truncatus	ENSTTRG00000003870	1 retrocopy	retro_ttru_673,