RetrogeneDB ID: retro_chof_514

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_116643:436..711(+)
• 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_514
ATGGCATCAGGCAGCTGAACAAAAAACTTGGACTTTTGCTGAAAGTAGGACAAAGATGAATACAATATGCTCACTGAGAA
GAGTCTCATGGAAGAGAGAGAAAAGGACAGAAAACCAGTACAGTCAGTCAAGCAGCACAGGGAATACAGGGTGACCTAGA
ATCCAAGCTTGGGAAGACAATTTTCATTACCAAGACCACCCCGCAATCTGAGATGGGAGGATACTACCACAATGTCTGTG
ACTGTATGGTGAAGGCCTTTCTGGAAATGATGGAA

Alignment

ORF - retro_chof_514 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.39 %
• Parental protein coverage: 63.4 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASGSGTKNLDFRRKWDKDEYEKLAEKRLTEEREKKDGKPVQPVKRELLRHRDYKV-DLESKLGKTIVIT
          MASGS.TKNLDF..K.DKDEY..L.EK.L.EEREK.D.KPVQ.VK.....HR.Y.V.DLESKLGKTI.IT
Retrocopy MASGS*TKNLDFC*K*DKDEYNMLTEKSLMEEREK-DRKPVQSVKQ----HREYRV<DLESKLGKTIFIT

Parental  KTTPQSEMGGYYCNVCDCVVKDSINFLD
          KTTPQSEMGGYY.NVCDC.VK.......
Retrocopy KTTPQSEMGGYYHNVCDCMVKAFLEMME

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_514 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,