RetrogeneDB ID: retro_chof_209

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_453:114094..114677(+)
• Located in intron of: ENSCHOG00000012973

Retrocopy information

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

Parental gene information

• Parental gene symbol: T
• Ensembl ID: ENSCHOG00000006236
• Aliases: None
• Description: T, brachyury homolog (mouse) [Source:HGNC Symbol;Acc:11515]

Sequence

>retro_chof_209
TATTCTCAGTTGGGGAGATGCTTATTCCTGGAACCAGTCCATTGGTTCCACCTTCCAGCCCCTACCCTTGTTTGGAGGTT
CTGCCTCCCTCTCCTCCCTGCATGACTGTGAAAGATAGCTCAACCTGCGAAACTACATCTCAACCCTGTACCCCAGTCCA
TACACTCATCAAAACAGCTCTCCAACCTTTCTGACAATTCATCTGCATGTTTAGGCATGCTCCAATTTCATGACAGTTGG
TCCAGCCTTGGGGTGCCTGCCCAAACCAGCATGCTACTCCTGAGCCATAGCACAGATCCACCCCCTGGTTCTAGTCAGTA
CCTCAACCGGTGGTCTGTGAGTTAACAGCACCATCACTCCTGGCTCCCAGAAGCCAGGGATGTCCAGTGGGCTGGGAGTT
CAGTTCTCTCTAGGCTCCACAGTGCACTGTGCACCCCTTGCCCACATGGTCTCTGCTTCCTCTTCCTCAGGGCCCCTGCT
GTGTGAAGGGGGCACATGCCACAGACATTCCTGTAGCCAGTACAATGCCTTGGCACAAACCTGCCTCACAGCCTCACGGA
CGCCCTTGTTGCCATGTTCCATG

Alignment

ORF - retro_chof_209 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64. %
• Parental protein coverage: 53.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  YSQ-WG-WLIPSTSPLCPPASPHP-QFGGSLPLSSPHGCERYPALRSHRSTPYPSPYAHRNNSPTY-SDS
          YSQ.WG..LIP.TSPL.PP.SP.P..FGGS..LSS.H.CER...LR...ST.YPSPY.H.N.SPT..SD.
Retrocopy YSQ>WG>MLIPGTSPLVPPSSPYP<LFGGSASLSSLHDCER*LNLRNYISTLYPSPYTHQNSSPTF<SDN

Parental  SSACLSMLQSHDNWSSLGMPAHPSMLPMSHNPSPPTGSSQYPNLWPVS-NGTITPGSQTPGMSNGLGTQF
          SSACL.MLQ.HD.WSSLG.PA..SML..SH...PP.GSSQY.N.W.VS.N.TITPGSQ.PGMS.GLG.QF
Retrocopy SSACLGMLQFHDSWSSLGVPAQTSMLLLSHSTDPPPGSSQYLNRWSVS>NSTITPGSQKPGMSSGLGVQF

Parental  FRGSTAHYAPLTHTVPASSSSGSPLYEGGATATDIPDSQYDASAQARLIASWTPVSPPSM
          ..GST.H.APL.H.V.ASSSSG..L.EGG.T......SQY.A.AQ..L.AS.TP..P.SM
Retrocopy SLGSTVHCAPLAHMVSASSSSGPLLCEGG-TCHRHSCSQYNALAQTCLTASRTPLLPCSM

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_209 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006236	1 retrocopy	retro_chof_209 ,
Choloepus hoffmanni	ENSCHOG00000010387	1 retrocopy	retro_chof_2409,
Equus caballus	ENSECAG00000007994	1 retrocopy	retro_ecab_568,
Microcebus murinus	ENSMICG00000016122	1 retrocopy	retro_mmur_1130,
Nomascus leucogenys	ENSNLEG00000011552	1 retrocopy	retro_nleu_1501,