RetrogeneDB ID: retro_chof_2186

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_56833:5106..6120(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BVES
• Ensembl ID: ENSCHOG00000008742
• Aliases: None
• Description: blood vessel epicardial substance [Source:HGNC Symbol;Acc:1152]

Sequence

>retro_chof_2186
ACCATTACACCCTGCCTTCCAATGAGACCACGTGTGAAAACTGGAGAGAGATTCATCATCTAGCTTTTCATATAGAAAAT
ATTTGTTTTGCAAATGGGCCAGTTATTCCAACTTCTCTTCACCTTCATATGATTCTTCTTAAGGGGATGTTAACTATAGG
ATGTCCCTCTGTATCTTCTGGGCCACTCTCTACTGATGTGTCTTGGTTATAATGATCTGGAACTCTCTGTTCTTGGGTGT
TAACCTTTTGCATCTTTCATGTCTTTTGTACAAGAAAGACCAGCAATAAAGGATTGAAAAGGAACTCAACAGCATCTACC
AGTGATTGTCTGAACCACTCTATGTGCCTCTAGATTTGTTCAGAAGATTAACTGGACAGATTGGGATCATCCAACTTTAA
AAAAGGGTCAGACTTATGCTGCAGAGGATGAGACCTCAGTTGACGACTGCCTGGGTATCCTCTTGAAGGGAAAAATGAAG
GTCTCCTATAGAGGACATTTACTGCAAAACATTTACCCCTGTGCCTTTACAGATTCTCTTGAATTTAGATCAACTCAGGT
GCACAAAGGCAAAAAATCCCAGGTCACCATTACTGCAGATGACAACCACAGATACTTATATTGGTCAAGAGAATGATTAA
CTTACTTTCTGGAATCAGAACCTTTCCTATGTGAAATATTTAGGTATCTTACAGGAAAAGATCTTGCACACAAGCTCTAC
TCATTGAACCATCCTACTTTAAATGACAAAAAGGCCAAATTATGGATCACCATCTCAGCCTTTAAACACAGATTTCCATG
CTGGAAATGAAAATAACAGAGCCAGCTCCAGTGACAGTGAAGATGGGTGACACCAGTTTCTTCAGGGGGACCGCCAGTGT
TTGTTCTCTCTGTGTGTCATCCCAACACTGGTGAGCCTGTGCCAAAATGACGCTAATAGAAGAAGGGGTAGTAGATGGAT
GATGATGAGGTTCTTGAACCCATGTCGCTAGATGATGAAGTGCATCAGTTGCCT

Alignment

ORF - retro_chof_2186 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.33 %
• Parental protein coverage: 93.87 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  SITP-VPSNETTCENWREIHHLVFHVANICFAIGLVIPTSLHFHMILLRGMFSIGC-TLYIVWATLYRCA
          .ITP..PSNETTCENWREIHHL.FH..NICFA.G.VIPTSLH.HMILL.GM..IGC..L.I.WATLY.C.
Retrocopy TITP<LPSNETTCENWREIHHLAFHIENICFANGPVIPTSLHLHMILLKGMLTIGC<SLCIFWATLY*CV

Parental  LDIMIWNSVFLGVNLLHLSYLLYKK-RPVKIEKELNGIYRRLFEPLRVHPDLFRRLTGQFCMIQ-SLKKG
          L.IMIWNS.FLGVNLLHLS.LLYKK.....IEKELN.IY..L.EPL.V..DLFRRLTGQ...IQ..LKKG
Retrocopy LVIMIWNSLFLGVNLLHLSCLLYKKDQQ*RIEKELNSIYQ*LSEPLYVPLDLFRRLTGQIGIIQ<TLKKG

Parental  QTYAVEDKTSVDDRLSILLKGKMKVSYRGHFLHNIYPCAFIDSPEFRSTLMHKGEKFQVTIIADDNCRFL
          QTYA.ED.TSVDD.L.ILLKGKMKVSYRGH.L.NIYPCAF.DS.EFRST..HKG.K.QVTI.ADDN.R.L
Retrocopy QTYAAEDETSVDDCLGILLKGKMKVSYRGHLLQNIYPCAFTDSLEFRSTQVHKGKKSQVTITADDNHRYL

Parental  CWSRERLTYFLESEPFLYEIFRYLIGKDITNKLYSLNDPTLNDKKAK-TLDHQLSLSTQISILEMR-NSI
          .WSRE.LTYFLESEPFL.EIFRYL.GKD...KLYSLN.PTLNDKKAK...DH.LSL.TQIS.LEM..N..
Retrocopy YWSRE*LTYFLESEPFLCEIFRYLTGKDLAHKLYSLNHPTLNDKKAK<IMDHHLSL*TQISMLEMK<NNR

Parental  ASSSDSEDGLH-YLR-GTASISSLHVSSPHQRASAKMKPIEEGVED-DD-EVFEPVPPNTLKVHQLP
          ASSSDSEDG.H..L..GTAS..SL.VSS.H..A.AKM..IEEGV.D.DD.EV.EP.......VHQLP
Retrocopy ASSSDSEDG*HQFLQ>GTASVCSLCVSSQHW*ACAKMTLIEEGVVD>DDDEVLEPMSLDD-EVHQLP

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_2186 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008742	1 retrocopy	retro_chof_2186 ,