RetrogeneDB ID: retro_chof_1124

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_20558:2654..3017(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOB1B
• Ensembl ID: ENSCHOG00000012418
• Aliases: None
• Description: MOB kinase activator 1B [Source:HGNC Symbol;Acc:29801]

Sequence

>retro_chof_1124
TATAATTGGGCAAATGGTACTAATATTAAAAAGCCAATCAAATGTTCTGCTCCAAAATACATTGACTATTTGATGACTTG
GGTTCAGGATCAGCTTGCTGATGAAACTTTTTCTTTCTAAGATTGGTGTCCCATTTCCCAAAAACTTTATGTCTGTGGCA
AAGACTATTCTAAAGCATCTCTTCAGGGTTTATGCCCATATTTATCATCAGCACTTTGATTCTGTGATGTAGCTGCAAGA
GGAGGCCCACCTCAACACCTCCTTTAAGCACTTTATTTTCTTTGTCAGGATTTTAATCTGATTGATGCCTGTGATGTGGC
ACCTCTTCAGGAATTAGATGAGAAGCTTGGATGGAAAGAAAGA

Alignment

ORF - retro_chof_1124 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.4 %
• Parental protein coverage: 57.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YHWADGTNIKKPIKCSAPKYIDYLMTWVQDQLDDET-LFPSKIGVPFP-KNFMSVAKTILKRLFRVYAHI
          Y.WA.GTNIKKPIKCSAPKYIDYLMTWVQDQL.DET..F.......FP.KNFMSVAKTILK.LFRVYAHI
Retrocopy YNWANGTNIKKPIKCSAPKYIDYLMTWVQDQLADET<FFFLRLVSHFP<KNFMSVAKTILKHLFRVYAHI

Parental  YHQHFDPVIQLQEEAHLNTSFKHFIFFV-QEFNLIDRRELAPLQELIEKLTSKDR
          YHQHFD.V..LQEEAHLNTSFKHFIFFV.Q.FNLID....APLQEL.EKL..K.R
Retrocopy YHQHFDSVM*LQEEAHLNTSFKHFIFFV<QDFNLIDACDVAPLQELDEKLGWKER

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_1124 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007277	1 retrocopy	retro_chof_502,
Choloepus hoffmanni	ENSCHOG00000012418	3 retrocopies	retro_chof_1124 , retro_chof_1337, retro_chof_660,
Macropus eugenii	ENSMEUG00000014210	1 retrocopy	retro_meug_384,
Microcebus murinus	ENSMICG00000006469	2 retrocopies	retro_mmur_1622, retro_mmur_653,
Myotis lucifugus	ENSMLUG00000005838	1 retrocopy	retro_mluc_1067,
Ochotona princeps	ENSOPRG00000009133	1 retrocopy	retro_opri_386,
Sus scrofa	ENSSSCG00000008941	2 retrocopies	retro_sscr_377, retro_sscr_586,
Vicugna pacos	ENSVPAG00000011892	1 retrocopy	retro_vpac_35,