RetrogeneDB ID: retro_chof_661

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_132708:4769..5384(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAF8
• Ensembl ID: ENSCHOG00000010516
• Aliases: None
• Description: TAF8 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 43kDa [Source:HGNC Symbol;Acc:17300]

Sequence

>retro_chof_661
TTCACTGTGGACACCCTCCCTGCCTATGCCAAACAGTTGAAGAAGATGGCCATCACTGCTCCTCCAGTGACCAGTCAGCC
TGTAACTCCTAAGGCTGTCACTGCAGGGCAGAACTGACCCCACCTGACATAACATCCCCAGTCACTTTCCTGAGTTCCCT
GATCCCCACACCTACATCAAAACTCCTACACACCGTGAGCCTGGGTTGGATTACCAGGTCCTGCAGGAGAAAGTTGCAAC
CCAGAGGTGTGATGTGGAGCGGGCACTCACCCATTTTACAAACTAGACAGGTGAGGCACAGAGTCATTTCAAAGATGATG
TCAGCACATTTCCATTGATTGCTGCCAGGACTTTCACCGTCTCCTACCAGACAGCTCTTCCTCCTCCTGAGCTAGAGATG
GAACAAATGGAAGAGATGGATTCTTCAGAGCAGCATGGGCAGACAGACACAGAGAACCTCCCTCTTCTTATCAGCACGGA
CAGTTCTGGAGCAGAGAAGAGGAACACCTCTGTACTACAACAGAACCCCTCCTTGTCAGAAAACCGGAATGGGGAGAGAA
TATTATCGATAACCCGTATCTGCAATCTGTGAAGGAACCTAAGATCTACAGGAAG

Alignment

ORF - retro_chof_661 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.26 %
• Parental protein coverage: 70.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FNVDTLPAYAKRSQRMVITAPPVTNQPVTPKALTAGQNRPHPP-HIPSHFPEFPDPHTYIKTPTYREPVL
          F.VDTLPAYAK....M.ITAPPVT.QPVTPKA.TAGQN.PH....IPSHFPEFPDPHTYIKTPT.REP.L
Retrocopy FTVDTLPAYAKQLKKMAITAPPVTSQPVTPKAVTAGQN*PHLT>NIPSHFPEFPDPHTYIKTPTHREPGL

Parental  DYQVLREKAASQRRDVERALTRFMAKTGETQSLFKDDVSTFPLIAARPFTIPYLTALLPSELEMQQMEET
          DYQVL.EK.A.QR.DVERALT.F...TGE.QS.FKDDVSTFPLIAAR.FT..Y.TAL.P.ELEM.QMEE.
Retrocopy DYQVLQEKVATQRCDVERALTHFTN*TGEAQSHFKDDVSTFPLIAARTFTVSYQTALPPPELEMEQMEEM

Parental  DSSEQDEQTDTENLPLHISTDDSGAEKENTSVLQQNSSLSGNRNGE-ENIIDNPYLRPVKKPKIRRK
          DSSEQ..QTDTENLPL.ISTD.SGAEK.NTSVLQQN.SLS.NRNGE.ENIIDNPYL..VK.PKI.RK
Retrocopy DSSEQHGQTDTENLPLLISTDSSGAEKRNTSVLQQNPSLSENRNGE<ENIIDNPYLQSVKEPKIYRK

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_661 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 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010516	1 retrocopy	retro_chof_661 ,
Macropus eugenii	ENSMEUG00000006952	1 retrocopy	retro_meug_150,
Microcebus murinus	ENSMICG00000011353	6 retrocopies	retro_mmur_112, retro_mmur_1455, retro_mmur_443, retro_mmur_455, retro_mmur_554, retro_mmur_555,
Monodelphis domestica	ENSMODG00000012785	2 retrocopies	retro_mdom_1206, retro_mdom_1357,
Mus musculus	ENSMUSG00000023980	1 retrocopy	retro_mmus_436,
Otolemur garnettii	ENSOGAG00000016885	1 retrocopy	retro_ogar_759,
Rattus norvegicus	ENSRNOG00000015249	1 retrocopy	retro_rnor_2317,