RetrogeneDB ID: retro_chof_2623

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_91931:565..1950(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: INTS12
• Ensembl ID: ENSCHOG00000011569
• Aliases: None
• Description: integrator complex subunit 12 [Source:HGNC Symbol;Acc:25067]

Sequence

>retro_chof_2623
GTGGCTGCTGCTGTGAATTTGGAACTGGATCCCATTTTTTTAAAAGCACTAGGCTTCTTACATTCAAAGAGTAAGGATTC
TGCTGAAAAACTGAAGGCGCTGCTTGATGAATCTTTGGCTCAGGGTTATTGATTCGAGTTACCGTCCATCTCAAAAGAAT
GTGGAGCCACCCAGAATTTCAAGTACAAAATCTGCTCCCATTAAGCAAGAACCCAAAACTTCACCCAGTCTTCCTTCTGG
TAATAGTAATGGCAAGGGTCTCACAACTGAAAAGGTAAAGAAGGAAGCTGAAAAGAGGCCTGCTGATAAAGTGAAATCAG
ACATCAGTGCAGGAGTTGATGTTCCAAAGAAACCTAGATTGGAGAAATGAGAGACAGGGTCCTCTCCCATTACCATCCAA
ACCCGCAAGGATTTAGCTATGGCTGACCTGTCTAGTTTTGAGGAGACCAGCGCTAACGATTTTGCCACGGAGATGGATTG
GCCTGTGTTGTTTGTAGGCAAATGACAGTGGCATCTAGTAATCAATTAGTAGGATGTCAGGAGTGCCATAATCTCTATCA
CCAAGACTGCCACAAGCCCCAGGTGAGAGACAAGGAAGTGAATGACCCTCTTCTGATGTGGTATTGTGCCCGAAGTACCA
GACAAATGAAAAGAATGGCTCAAAAAACTCAGAAACCACCACAGAAACCAGCCCCAACAGTTGTTTCTGTCACTCCAGCT
GTCAAAGATCCATTGGTTAAGAAACCAGAAACTAAACTCAAACAAGAGACAACTTTTCTAGCATTCAAGAGAACAGAAGT
CAAGACATCTGAGTTATTTGAGGAAATTCTTCTAGTACCAGTGTTTCCTCTTTAGTAACTAGTGGCCTAACTGGTTGGGC
AGGCTTCGCAGCCAAAACCTCCTCTGCTGGTCCATCAACAGCAAAATTGAATTCAACAACACAGAACAATAGTGGAAAAC
CTGCTACCTCATCAGCTAACCAGAAGCCTGTGGGTTTGACTGGTCTGGTAACATCATCCAAAGGTGGAATAGGTTCCAAA
ATAGGTTCTGGTAACAGCACTATGCCCAATGTACCATTGAAACCACCTCCGCCTCTAACCTTGGGCAAAAGTGGCCTTAA
TCGCTCAGTTAGTTGTGACAGTGTTAGCAAAGTAGGTCTTCCTAGTCCAAGTAGTTTAGTTCCGGGAAGCAGCAGCCAAC
TAAGTGGGAATGGAAGTAGTGGGACATCAGGGCTCAGTGGAAGTACCACCAGCAAAACCACTTCAGAATCAAGCAGCTCT
TCCTCAGCATCCCTCAAAGGTCCACCTTCACAAGAATCACAGCTCAATGCCATGAAGTGATTACAGATGGTCAGGAAGAA
AGCTGCCCAAAAGAAACTCAGGAAG

Alignment

ORF - retro_chof_2623 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.11 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAAVNLELDPIFLKALGFLHSKSKDSAEKLKALLDESLARG-IDSSYRPSQKDMEPPKISSTKTIPIKQ
          .AAAVNLELDPIFLKALGFLHSKSKDSAEKLKALLDESLA.G.IDSSYRPSQK..EPP.ISSTK..PIKQ
Retrocopy VAAAVNLELDPIFLKALGFLHSKSKDSAEKLKALLDESLAQG>IDSSYRPSQKNVEPPRISSTKSAPIKQ

Parental  EPKTSPSLPSGNNNGKGLTTEKVKKEAEKRPADKVKSDISEGVDVPKKPRLEKPETGSSPITVQTSKDLA
          EPKTSPSLPSGN.NGKGLTTEKVKKEAEKRPADKVKSDIS.GVDVPKKPRLEK.ETGSSPIT.QT.KDLA
Retrocopy EPKTSPSLPSGNSNGKGLTTEKVKKEAEKRPADKVKSDISAGVDVPKKPRLEK*ETGSSPITIQTRKDLA

Parental  ITDLSSFEETSADDFAMEM-GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWY
          ..DLSSFEETSA.DFA.EM.GLACVVCRQMTVAS.NQLV.CQECHNLYHQDCHKPQV.DKEVNDP.L.WY
Retrocopy MADLSSFEETSANDFATEM<GLACVVCRQMTVASSNQLVGCQECHNLYHQDCHKPQVRDKEVNDPLLMWY

Parental  CARCTRQMKRMAQKTQKPPQKPAPTVVSVAPAVKDPLVKKPETKLKQETTFLAFKRTEVKTSA-VISGNS
          CAR.TRQMKRMAQKTQKPPQKPAPTVVSV.PAVKDPLVKKPETKLKQETTFLAFKRTEVKTS..VI.GNS
Retrocopy CARSTRQMKRMAQKTQKPPQKPAPTVVSVTPAVKDPLVKKPETKLKQETTFLAFKRTEVKTSE<VI*GNS

Parental  SSTSVSSSVSSGLTGWAAFAAKTSSAGPSTAKLNSTTQNNSGKPATSSANQKPVGLTGLATSSKGGIGSK
          SSTSVSS.V.SGLTGWA.FAAKTSSAGPSTAKLNSTTQNNSGKPATSSANQKPVGLTGL.TSSKGGIGSK
Retrocopy SSTSVSSLVTSGLTGWAGFAAKTSSAGPSTAKLNSTTQNNSGKPATSSANQKPVGLTGLVTSSKGGIGSK

Parental  IGSSNSTTPTVPLKPPPPLTLGKTGLSRSVSCDNVSKVGLPSPSSLVPGSSSQLSGNGNSGTAGPSGNTT
          IGS.NST.P.VPLKPPPPLTLGK.GL.RSVSCD.VSKVGLPSPSSLVPGSSSQLSGNG.SGT.G.SG.TT
Retrocopy IGSGNSTMPNVPLKPPPPLTLGKSGLNRSVSCDSVSKVGLPSPSSLVPGSSSQLSGNGSSGTSGLSGSTT

Parental  SKTTSESSSSSSASLKGPTSQESQLNAMKRLQMVKKKAAQKKLKK
          SKTTSESSSSSSASLKGP.SQESQLNAMK.LQMV.KKAAQKKL.K
Retrocopy SKTTSESSSSSSASLKGPPSQESQLNAMK*LQMVRKKAAQKKLRK

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_2623 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011569	1 retrocopy	retro_chof_2623 ,
Myotis lucifugus	ENSMLUG00000011757	1 retrocopy	retro_mluc_62,
Mustela putorius furo	ENSMPUG00000008999	1 retrocopy	retro_mputfur_1546,
Oryctolagus cuniculus	ENSOCUG00000011321	1 retrocopy	retro_ocun_416,