RetrogeneDB ID: retro_chof_2429

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_7448:12138..12897(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTX2
• Ensembl ID: ENSCHOG00000009655
• Aliases: None
• Description: metaxin 2 [Source:HGNC Symbol;Acc:7506]

Sequence

>retro_chof_2429
GCAGAACCTTGGCCTGAAAATGCTACATTATATCAGCAACTAAAAGGGGAGCATATTTTGCTTTCTGACAATGCAGCTTC
TCTTGCTGTGCAGACCTTCTTGCAAATGTGTGATCTGCCTATCAAAGTGGTTTGTAGGGCAAATCCAGAATATATGTCTC
CATCTGGTAAAGTACCTTCTATTCATGTAGGAAATCAAGTAGTATCAGAACTTGGTCCAGTAGTCCAATTTGTTAAAGCC
AAGGGCCATTCTCCTAGTGATGGGCTGGATGAAGTCCAAAAAGCAGAAATGAAAGCCTGCATGGAATTAGTCAAGAATAT
GCTATTGGCTGCAGAGTTGTATCTTCAGTGGTGTGATGAAGCTACAGTAGGGAAGATCACTCACGCTAGGTATGGATCAC
CTTACCCTTGGCCTCTGGATCATATTTTGGCCTATCAGAAACAGTGGGAAGTCAAGCGAAAGATGAAAGCTATTGGATGG
GGTAACAAGACTCTGGACCAGGTCTTGGAATATGTAGACCAGTGCTGTCAAGCTCTTTCTCAAAGACCGGGAACACAACT
TTATTTCTTCAATAAGCAGCCTACCAAACTAGATGCACTGGTATTAGGGCATCTGTACACCATTCTTACCACACAGCTGA
CCAATGGTGAACTTTCTGAGAAGGGGAAAAACTATAGCAACCTCCTTGCTTTCTGTAGAATAATTGAGCAGCATTATTCT
GAAGATCATGATAAAGGCAACTCACCTATCGGGTTGTCT

Alignment

ORF - retro_chof_2429 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AEPWPENATLYQQLKGEQILLSDNAASLAVQTFLQMCNLPIKVVCRANAEYMSPSGKVPFIHVGNQVVSE
          AEPWPENATLYQQLKGE.ILLSDNAASLAVQTFLQMC.LPIKVVCRAN.EYMSPSGKVP.IHVGNQVVSE
Retrocopy AEPWPENATLYQQLKGEHILLSDNAASLAVQTFLQMCDLPIKVVCRANPEYMSPSGKVPSIHVGNQVVSE

Parental  LGPIVQFVKAKGHSLSDGLDEVQKAEMKAYMELVNNMLLTAELYLQWCDEATVGEITHARYGSPYPWPLN
          LGP.VQFVKAKGHS.SDGLDEVQKAEMKA.MELV.NMLL.AELYLQWCDEATVG.ITHARYGSPYPWPL.
Retrocopy LGPVVQFVKAKGHSPSDGLDEVQKAEMKACMELVKNMLLAAELYLQWCDEATVGKITHARYGSPYPWPLD

Parental  HILAYQKQWEVKRKMKAIGWGNKTLDQVLEDVDQCCQALSQRLGTQLYFFNKQPTELDALVFGHLYTILT
          HILAYQKQWEVKRKMKAIGWGNKTLDQVLE.VDQCCQALSQR.GTQLYFFNKQPT.LDALV.GHLYTILT
Retrocopy HILAYQKQWEVKRKMKAIGWGNKTLDQVLEYVDQCCQALSQRPGTQLYFFNKQPTKLDALVLGHLYTILT

Parental  TQLTNDELSEKVKNYSNLLAFCRRIEQHYFEDCDKGNSPIRLS
          TQLTN.ELSEK.KNYSNLLAFCR.IEQHY.ED.DKGNSPI.LS
Retrocopy TQLTNGELSEKGKNYSNLLAFCRIIEQHYSEDHDKGNSPIGLS

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_2429 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009655	1 retrocopy	retro_chof_2429 ,
Choloepus hoffmanni	ENSCHOG00000010893	1 retrocopy	retro_chof_1828,
Cavia porcellus	ENSCPOG00000011099	1 retrocopy	retro_cpor_218,
Dipodomys ordii	ENSDORG00000003848	2 retrocopies	retro_dord_159, retro_dord_192,
Homo sapiens	ENSG00000128654	1 retrocopy	retro_hsap_3780,
Macaca mulatta	ENSMMUG00000010185	1 retrocopy	retro_mmul_1643,
Nomascus leucogenys	ENSNLEG00000006020	1 retrocopy	retro_nleu_1117,
Pan troglodytes	ENSPTRG00000012674	1 retrocopy	retro_ptro_2561,
Sarcophilus harrisii	ENSSHAG00000016381	1 retrocopy	retro_shar_162,