RetrogeneDB ID: retro_chof_1224

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_230715:136..721(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MXD1
• Ensembl ID: ENSCHOG00000003047
• Aliases: None
• Description: MAX dimerization protein 1 [Source:HGNC Symbol;Acc:6761]

Sequence

>retro_chof_1224
GCTGAACATGCCTACGCCTCCATGTTACCATACAATAACACGGACAGAGATGCCTTAAAACGGAGGAACACATCCAAGAA
GAATTACAGCAGTAGCAGGTCAACGCACAATGAAATGGAGAACAGACTGGCTCACCTTCGCTTGTGCCTGGAGAAGTTGA
AGGGACCGGTATCATTTGGGCCCGAATCAAATTGACACACTACGTTGAGTTTATTAACAAAAACCAAATTGCATGTAAAG
AAACTTGAAGACTGTGAAGGAAAAGCCATTCACCAAATAGACCAGCTTCAGCGAGAGCAGCGGCACCTGAAAAGGCAGCT
GGAGAAGCTGGGCATGGAGAGGATATGCATGGACAGCATCGGCCCCACGGTCTCCTCGGAGCGCTCGGACTCGGGCAGGG
AAGAAACTGACATTGACGTTGAAAGCACAGACTATCTCACGGGCGATCTGGACTGGAGCGGCAGCAGCGTGAGTGATTCT
GACGAGCGGGGAAGCACGCAGAGCGTCGGAAGTGATGAGGGCTACTCCAGCTCCAGCATCAAGAGAATAAAGCTCCAGGA
CAATCACAAGACTTGTCTTGGTCTA

Alignment

ORF - retro_chof_1224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AEHGYASMLPYNNKDRDALKRRNKSKKNNSSSRSTHNEMEKNRRAHLRLCLEKLKGLVPLGPESNRHTTL
          AEH.YASMLPYNN.DRDALKRRN.SKKN.SSSRSTHNEME.NR.AHLRLCLEKLKG.V..GPESN.HTTL
Retrocopy AEHAYASMLPYNNTDRDALKRRNTSKKNYSSSRSTHNEME-NRLAHLRLCLEKLKGPVSFGPESN*HTTL

Parental  SLLTKAKLHIKKLEDCDRKAIHQIDQLQREQRHLKRQLEKLGIERIRMDSIGSTVSSERSDSDREEIDVD
          SLLTK.KLH.KKLEDC..KAIHQIDQLQREQRHLKRQLEKLG.ERI.MDSIG.TVSSERSDS.REE.D.D
Retrocopy SLLTKTKLHVKKLEDCEGKAIHQIDQLQREQRHLKRQLEKLGMERICMDSIGPTVSSERSDSGREETDID

Parental  VESTDYLTGDLDWSSSSVSDSDERGSMQSLGSDEGYSSSSIKRIKLQDNHKTCLGL
          VESTDYLTGDLDWS.SSVSDSDERGS.QS.GSDEGYSSSSIKRIKLQDNHKTCLGL
Retrocopy VESTDYLTGDLDWSGSSVSDSDERGSTQSVGSDEGYSSSSIKRIKLQDNHKTCLGL

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_1224 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003047	1 retrocopy	retro_chof_1224 ,
Choloepus hoffmanni	ENSCHOG00000006556	2 retrocopies	retro_chof_1350, retro_chof_1817,
Pteropus vampyrus	ENSPVAG00000001244	2 retrocopies	retro_pvam_1415, retro_pvam_1430,