RetrogeneDB ID: retro_chof_1613

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_340191:74..810(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: E2F6
• Ensembl ID: ENSCHOG00000005114
• Aliases: None
• Description: E2F transcription factor 6 [Source:HGNC Symbol;Acc:3120]

Sequence

>retro_chof_1613
CCATCGAAAAGTATTAATTTAGAAGATAATGTTCAATGTGTGTCCATGAGAAAAGGTCTAAAAGTGAAGAGCCCTCGTTG
CGATGTATCACTGGTTAATTTAACTCGAAAATTTATGGCTCTTGTCAGATCTGCTCCTGGTGGGATTGTTGACTTAAACA
AGGTTGCAACAAAACTCGGAGTGAGAAAACGAAGGATATATGACATCACCAATGTCTTATCTGGGATCCATCTGATTGAA
AAAAAGTCTAAGAATCATATTCGATGGATAGGATCTGATCGCAGTGACTCTGGAGCAATATCCCAGCAAAAGAAGCTACA
GGAGGAACTTTTAGACTTATCAGCAATGGAAAATGCTTTGGATGAGTTAATTAAGGATTGCGCTCAGCAGTTGTTTGAAT
TAACAGATGACAAAGGAAATGAAAGACTAGCATATGTGATGTATCAAGATATTCATAGCATTCAAGCCTTCCATGAACAG
ACTGTTATTGTAGTTAAAGCTCCAGCAGAAACCAGACTGGATGTTCCAGCTCCCAGAGAAGATTCTATAAAAGTACATAA
AAGGAGCACCAAAGGACCTACTGACTTTTATTTATGTGAAGTGGAGGAGGATTAACACAAGTAACAAAATACCTGAAGGT
GGAGGGGCCCCTTCATCTGAAAGCAAGCCTCCAGAACATCCTAATGAGGAAGAAAATCCTCCTCAGCAAAGTGAAGAATT
ACTTGAAGTAAGCAAC

Alignment

ORF - retro_chof_1613 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.78 %
• Parental protein coverage: 87.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PSKIRINLEDNVQYVSMRKALKVYRPRFDVSLVYLTRKFMDLVRSAPGGILDLNKVATKLGVRKRRVYDI
          PSK..INLEDNVQ.VSMRK.LKV..PR.DVSLV.LTRKFM.LVRSAPGGI.DLNKVATKLGVRKRR.YDI
Retrocopy PSK-SINLEDNVQCVSMRKGLKVKSPRCDVSLVNLTRKFMALVRSAPGGIVDLNKVATKLGVRKRRIYDI

Parental  TNVLDGIDLVEKKSKNHIRWIGSDLSEFGAVPQQKKLREELSDLSAMEDALDELIKDCAQQLFELTDDKE
          TNVL.GI.L.EKKSKNHIRWIGSD.S..GA..QQKKL.EEL.DLSAME.ALDELIKDCAQQLFELTDDK.
Retrocopy TNVLSGIHLIEKKSKNHIRWIGSDRSDSGAISQQKKLQEELLDLSAMENALDELIKDCAQQLFELTDDKG

Parental  NERLAYVKLQCGGILQAFHEQIVIAVKAPAETRLDVPAPRKDSITVHIRSTKGPIDVYLCEVEQD-NTSN
          NERLAYV..Q.....QAFHEQ.VI.VKAPAETRLDVPAPR.DSI.VH.RSTKGP.D.YLCEVE.D.NTSN
Retrocopy NERLAYVMYQDIHSIQAFHEQTVIVVKAPAETRLDVPAPREDSIKVHKRSTKGPTDFYLCEVEED>NTSN

Parental  NVPEDGGTPSSENRPPEHPNEEENPPQQSEELLEVSN
          ..PE.GG.PSSE..PPEHPNEEENPPQQSEELLEVSN
Retrocopy KIPEGGGAPSSESKPPEHPNEEENPPQQSEELLEVSN

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_1613 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	ENSCHOG00000005114	5 retrocopies	retro_chof_1613 , retro_chof_2316, retro_chof_2487, retro_chof_2627, retro_chof_537,
Choloepus hoffmanni	ENSCHOG00000008679	2 retrocopies	retro_chof_416, retro_chof_871,
Dipodomys ordii	ENSDORG00000013213	1 retrocopy	retro_dord_369,
Macropus eugenii	ENSMEUG00000007957	4 retrocopies	retro_meug_1169, retro_meug_860, retro_meug_882, retro_meug_893,
Myotis lucifugus	ENSMLUG00000003384	1 retrocopy	retro_mluc_864,
Otolemur garnettii	ENSOGAG00000013601	2 retrocopies	retro_ogar_2337, retro_ogar_3080,