RetrogeneDB ID: retro_chof_2409

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_72677:1875..2491(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TBX19
• Ensembl ID: ENSCHOG00000010387
• Aliases: None
• Description: T-box 19 [Source:HGNC Symbol;Acc:11596]

Sequence

>retro_chof_2409
GTGGACCATCTGCTGAGCATCGTGGAGACTAAACTGCAGGTGGGCAGCGAGAAGGGGTATCCCCACAGAGTGTGAGCTGC
ATGTCAGCCTGGCAGAGAGTGATCTGTGACCGTGCTTCAAAGGAGCTCACTAGTGAGATGATCGTCACCAAGAAAGGCTG
GAAGATGCGCCCAGTGCTGAAGGTGAATGTGTCTGGCTTGGACCCCAACACCGTGTATTCCTTCCTCCTGGACTTCGTGG
CGGCTGACAGCTGCCGCAGGAAGTTCATAAATGGGGTGGGGTGCTGGGGGACAATCCCGAGCCACAGGTGCCCAGCTATG
TCTACGTTACTCCGACTCGCCTAACTTCACACTGGATGAAGGCCCCTGTCTCCTTCAGCAAAGTTGAACTCACCAACAGT
CTCGACGGTGGGGGCCAGATCATGTTGACCTCCTTGCCTAAATATGAACCCCACATTCATATAGTGAGGGTTGGGGGTCC
ACAGCAGATGATCACCAGCCATTGCTTTCCCAAGACCCGGTTCATAGCAATGATAGCTTACAAGAACGAGGAGATCACAG
CTCTTGAAATTAAATATAGTCCATTTGCAAACGCTTCCCTTGATGCAAAGGAAAGA

Alignment

ORF - retro_chof_2409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.14 %
• Parental protein coverage: 50.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VSRLLHVVESELQAGREKGDP-TEKQLQIILEDAPLWQRFK-EVTNEMIVTKNGRRMFPVLKISVTGLDP
          V..LL..VE..LQ.G.EKG.P.TE..L...L....L...FK.E.T.EMIVTK.G..M.PVLK..V.GLDP
Retrocopy VDHLLSIVETKLQVGSEKGYP>TECELHVSLAESDL*PCFK>ELTSEMIVTKKGWKMRPVLKVNVSGLDP

Parental  NAMYSLLLDFVPTDSHRWKYVNGEW-VPAGKPEVSNHSCVYIHPDSPNFGAHWMKAPISFSKVKLTNKLN
          N..YS.LLDFV..DS.R.K..NG...V....PE....S.VY..P.......HWMKAP.SFSKV.LTN.L.
Retrocopy NTVYSFLLDFVAADSCRRKFINGVG<VLGDNPEPQVPSYVYVTPT--RLTSHWMKAPVSFSKVELTNSLD

Parental  GGGQ---NSLHKYEPQVHIVRVGGAHRMVMNCSFPETQFIAVTAYQNEEITALKIKYNPFAKAFLDAKER
          GGGQ....SL.KYEP..HIVRVGG...M.....FP.T.FIA..AY.NEEITAL.IKY.PFA.A.LDAKER
Retrocopy GGGQIMLTSLPKYEPHIHIVRVGGPQQMITSHCFPKTRFIAMIAYKNEEITALEIKYSPFANASLDAKER

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_2409 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006236	1 retrocopy	retro_chof_209,
Choloepus hoffmanni	ENSCHOG00000010387	1 retrocopy	retro_chof_2409 ,