RetrogeneDB ID: retro_chof_1819

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_392464:167..1092(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAP3K7
• Ensembl ID: ENSCHOG00000001962
• Aliases: None
• Description: mitogen-activated protein kinase kinase kinase 7 [Source:HGNC Symbol;Acc:6859]

Sequence

>retro_chof_1819
CAATATCCTTGTCTTTATAAAAAATGAAGGACAGAGCAACTCTGCCACCAGTACAGGCTCCTACATAGACATCACTTCTA
CAAATACCAGTAATAAAAGTGACACTAATATGGAGCAAGTTCCTGCCACAAATGACACTATTAAACGCTTAAAATCAAAA
TTGTTGAAAAATCAGGCAAAGCAACAGAATGAATCTGGACGTTTGAGCTTGGGTACCTCCCGTGGGAGCAGCATGGAGAG
CTTGCCCCCAACCTCTGAGGGCAAGAGGATGAGTGCTGACATGTCTGAAATAGAAGCAAGGATACCTGCAACCACAGCCT
ATTCCAAGCCTAAAAGGGGCCACCGTAAAACCGCTTCATTTGGCAACATTCTGGATGTCCCTGAGATCGTCATATCAGGC
AACGGACAACCAAGACGGAGGTCCATCCAAGACTTGACTGTTACTGGAACAGAACCTGGTCAGGTGAGCAGTAGGTCATC
TAGTCCTAGCATCAGAATGATCACTACCTCAGGACCAACCTCAGAAAAGCCAACTCGAAGTCATCCATGGACCCCTGATG
ATTCCACAGATACCAATGGATCAGATAACTCTATCCCAATGGCTTATCTCACACTGGATCACCAATTACAGCCTCTAGCA
CCATGTCCAAACTCCAAAGAATCTATGGCAGTGTTTGAACAGCATTGTAAGATGGCACAAGAATATATGAAAGTTCAAAC
AGAAATTGCATTATTATTGCAGAGAAAGCAAGAACTAGTTGCAGAACTGGACCAGGATGAAAAGGACCAGCAAAATACAT
CTCGTCTGGTACAGGAACATAAAAAGCTTTTAGACGAAAACAAAAGCCTTTCTACTTATTACCAGCAATGCAAAAAACAA
CTAGAAGTCATCAGAAGTCAGCAACAAAAACGACAAGGCACTTCA

Alignment

ORF - retro_chof_1819 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.76 %
• Parental protein coverage: 50.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QYPCQYS-DEGQSNSATSTGSFIDITSTNTSNKSDTNMEQVPATNDTIKRLESKLLKNQAKQQNESGRLS
          QYPC.Y...EGQSNSATSTGS.IDITSTNTSNKSDTNMEQVPATNDTIKRL.SKLLKNQAKQQNESGRLS
Retrocopy QYPCLYK>NEGQSNSATSTGSYIDITSTNTSNKSDTNMEQVPATNDTIKRLKSKLLKNQAKQQNESGRLS

Parental  LGTSRGSSMESLPPTSEGKRMSADMSEIEARIAATXXYSKPKRGHRKTASFGNILDVPEIVISGNGQPRR
          LGTSRGSSMESLPPTSEGKRMSADMSEIEARI.AT..YSKPKRGHRKTASFGNILDVPEIVISGNGQPRR
Retrocopy LGTSRGSSMESLPPTSEGKRMSADMSEIEARIPATTAYSKPKRGHRKTASFGNILDVPEIVISGNGQPRR

Parental  RSIQDLTVTGTEPGQVSSRSSSPSIRMITTSGPTS-KPTRSHPWTPDDSTDTNGSDNSIPMAYLTLDHQL
          RSIQDLTVTGTEPGQVSSRSSSPSIRMITTSGPTS.KPTRSHPWTPDDSTDTNGSDNSIPMAYLTLDHQL
Retrocopy RSIQDLTVTGTEPGQVSSRSSSPSIRMITTSGPTSEKPTRSHPWTPDDSTDTNGSDNSIPMAYLTLDHQL

Parental  QPLAPCPNSKESMAVFEQHCKMAQEYMKVQTEIALLLQRKQELVAELDQDEKDQQNTSRLVQEHKKLLDE
          QPLAPCPNSKESMAVFEQHCKMAQEYMKVQTEIALLLQRKQELVAELDQDEKDQQNTSRLVQEHKKLLDE
Retrocopy QPLAPCPNSKESMAVFEQHCKMAQEYMKVQTEIALLLQRKQELVAELDQDEKDQQNTSRLVQEHKKLLDE

Parental  NKSLSTYYQQCKKQLEVIRSQQQKRQGTS
          NKSLSTYYQQCKKQLEVIRSQQQKRQGTS
Retrocopy NKSLSTYYQQCKKQLEVIRSQQQKRQGTS

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_1819 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001962	1 retrocopy	retro_chof_1819 ,
Myotis lucifugus	ENSMLUG00000003344	1 retrocopy	retro_mluc_1173,
Mus musculus	ENSMUSG00000028284	1 retrocopy	retro_mmus_579,