RetrogeneDB ID: retro_chof_101

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_1983:57515..57860(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZMAT2
• Ensembl ID: ENSCHOG00000007795
• Aliases: None
• Description: zinc finger, matrin-type 2 [Source:HGNC Symbol;Acc:26433]

Sequence

>retro_chof_101
GAAGCTCGCCAAGAAGAAGCTCATGGAAGAGAGCCAGTCAAGTGGGAACTTCTGTGGCACAGGGACTACGAAGTGGACCT
GGAATCTAAGCTTGGGAAGACAACTGTCATTCCCAAGACCACCCCGCAATCTGAGATGGGTGGATGCTACTGCAGTGTTT
GTGACTGTGTGGTGAAGAACTCCATCAACTTCCTGGATCATATTAATGGAAAGAAACATCAGCAAAACCTGGGTATGTCT
ATGCATGTGGAACGTTCTACCCTGGATCAGGTGAAGAAATGCTCTGAAGTCAACAAAAAGAAGATGGAAGAGAAGCAGAA
AGATTATGATTTTGAGGAAAGGATG

Alignment

ORF - retro_chof_101 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.65 %
• Parental protein coverage: 73.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EREKKDGKPVQPVKRELLRHRDYKVDLESKLGKTIVITKTTPQSEMGGYYCNVCDCVVKDSINFLDHING
          E..........PVK.ELL.HRDY.VDLESKLGKT.VI.KTTPQSEMGG.YC.VCDCVVK.SINFLDHING
Retrocopy EARQEEAHGREPVKWELLWHRDYEVDLESKLGKTTVIPKTTPQSEMGGCYCSVCDCVVKNSINFLDHING

Parental  KKHQRNLGMSMRVERSTLDQVKKRFEV--KEMGE-QTDYDFEERM
          KKHQ.NLGMSM.VERSTLDQVKK..EV..K.M.E.Q.DYDFEERM
Retrocopy KKHQQNLGMSMHVERSTLDQVKKCSEVNKKKMEEKQKDYDFEERM

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_101 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 6 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007795	2 retrocopies	retro_chof_101 , retro_chof_514,
Dipodomys ordii	ENSDORG00000014559	8 retrocopies	retro_dord_123, retro_dord_127, retro_dord_129, retro_dord_131, retro_dord_133, retro_dord_135, retro_dord_136, retro_dord_138,
Echinops telfairi	ENSETEG00000005406	2 retrocopies	retro_etel_156, retro_etel_882,
Ficedula albicollis	ENSFALG00000008988	1 retrocopy	retro_falb_9,
Monodelphis domestica	ENSMODG00000011269	1 retrocopy	retro_mdom_1209,
Ictidomys tridecemlineatus	ENSSTOG00000002025	1 retrocopy	retro_itri_1272,