RetrogeneDB ID: retro_chof_845

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_155016:266..688(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCTEX1D2
• Ensembl ID: ENSCHOG00000012543
• Aliases: None
• Description: Tctex1 domain containing 2 [Source:HGNC Symbol;Acc:28482]

Sequence

>retro_chof_845
ATGGCCACGTCAGCCAGCGTGTCCTTCTCTGAGGGTGACGGGGTGCCCGGAACTGCAAAGAACATAGGGGAGCCCAAGGG
CACCATGTATTACAGCCAGTTTTCCAGCAAAGGTCCAGACCCTCCCTGGTTACAGCTGCGCCCACGCCGTACGCTAGGAG
GGCCTGGCTGAGCTGAAAACTCTGCAGAAGAAATGCCTCAGCTCACAACAGTTTATCAGAGAACATTGAAGATAAATGAA
AAGAAATTGGATTTGACCAATATAAAATGGTGGTGCAAGCAGCAATTGAAGAACAAAGAGGAGAAGGAGTATTCGTGTCT
GCCCGCCGTTCCTGGGGTGCTGACGCAGATATCCACACTCGTGACATTTTCACCAATGACAGTTTATTCTGTGTTGTTGC
CAGATTTGGCGGTTTCAACTAC

Alignment

ORF - retro_chof_845 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSASAGVSSSVGDGVPETEKNVGEPENT-YILRPVFQQRFKPSLVK-DCIHAVLKEELAN-AEYSPEETP
          M..SA.VS.S.GDGVP.T.KN.GEP..T...L.PVFQQR..PSLV...C.HAV..E.LA..AE.S.EE.P
Retrocopy MATSASVSFSEGDGVPGTAKNIGEPKGT<HVLQPVFQQRSRPSLVT<SCAHAVR*EGLAE<AENSAEEMP

Parental  QLT-KHLSENIKDKLKEMGFDRYKMVVQVIIGEQRGEGVFMAARCFWDADTDNYTHDVFMNDSLFCIVAA
          QLT...LSENI.DK.KE.GFD.YKMVVQ..I.EQRGEGVF..AR..W.AD.D..T.D.F.NDSLFC.VA.
Retrocopy QLT<NSLSENIEDK*KEIGFDQYKMVVQAAIEEQRGEGVFVSARRSWGADADIHTRDIFTNDSLFCVVAR

Parental  FGSFYY
          FG.F.Y
Retrocopy FGGFNY

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_845 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	ENSCHOG00000012543	1 retrocopy	retro_chof_845 ,
Mus musculus	ENSMUSG00000014075	2 retrocopies	retro_mmus_2987, retro_mmus_3299,