RetrogeneDB ID: retro_chof_451

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_110751:3585..4463(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCAT1
• Ensembl ID: ENSCHOG00000011431
• Aliases: None
• Description: branched chain amino-acid transaminase 1, cytosolic [Source:HGNC Symbol;Acc:976]

Sequence

>retro_chof_451
TGCAATCATGGATGCTTGGCAAAATGTATTGGAGAAGGAAGATCAAGAGATTCAGTGGAGACCTTTAAGGCAAAAGATCT
AATAATAACACCAGCCACCAATTTAAAAGAGAAACCTGGCCCAAATACTTTGAGTTTTGGAACATCATGGATCACATGTT
GACAGTGGAATGGTCCTCAGAGTTTGGATGGGAGAAACCTCACATCAACCCTCTTCAAAACCTGTCATTGCACCCTGGCT
CATCAACTTTTCACTATGCAGTGGAATTATTTGAAGGTTTGAAGGCATCTAGAGGAGTAGATAATAAAATTCAACTATTT
TGGCCAAACCTAAACATGGATAGAATGCATCAATCTGTAGTGAGGACAACTTTGCCAATATTTGATAAAGAAGAGCTTTT
ATAATGTATTCAGCAGCTTGTGAAATTGGATCAAGAATGGGTCTTGTTTTCAACATCTTCTAGTATATGTATTCATCCTA
CATTCATTGGAACTGAGCCTTCTCTTAGAGTCAAAAAGCCAACCAAAGCTTGGCTCTTTGTAATCTTGAGTCTGGTGGGA
CCTTATTTTTCCAGTGGGAGCTTTAATCCAGAGTTCTTGTGGGTCAACCTGAAGTGTATAAGAGCCTGGAAAGGTGGAAT
CAGGGACTGCAAAATGGGAAGAATTTATGGCTCATTTCTCTTTGCCCAATGTGAAACATTGGAGAATGGGTGACAGCAGG
TTCGGTGGCTCTATGTAGAGAATACCAAAATAACTGAAGTTGGAACTATGAACCTTTTTCTTTAGTGGATAAATGAAGAT
AAAGAAGAACTGGTACCTCCTATGTTAGATGGTATCATTCTGCCAGGAGTGATGTGGCAGAACATTTTAGTCCTGGCA

Alignment

ORF - retro_chof_451 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.99 %
• Parental protein coverage: 76.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CNHGCSAEC-GEGRXXXXXXXXXAKDLMITPATILKEKPD-PNNLIFGTVFTDHMLTVEWSSEFGWGKPH
          CNHGC.A.C.GEGR.........AKDL.ITPAT.LKEKP..P....F.....DHMLTVEWSSEFGW.KPH
Retrocopy CNHGCLAKCIGEGRSRDSVETFKAKDLIITPATNLKEKPG<PKYFEFWNIM-DHMLTVEWSSEFGWEKPH

Parental  IKPFQNLSLHPGSSALHYAVELFEGLKAFRGVDNKIRLFRPNLNMDRMYRSAVRATLPAFDKEELLECIQ
          I.P.QNLSLHPGSS..HYAVELFEGLKA.RGVDNKI.LF.PNLNMDRM..S.VR.TLP.FDKEELL.CIQ
Retrocopy INPLQNLSLHPGSSTFHYAVELFEGLKASRGVDNKIQLFWPNLNMDRMHQSVVRTTLPIFDKEELL*CIQ

Parental  QLVKLDQEWVPYSTSASLYIRPTFIGTEASLGVKKPTKALLFVILSPVGPYFSSGSFNPVSLWANPKYVR
          QLVKLDQEWV..STS.S..I.PTFIGTE.SL.VKKPTKA.LFVILS.VGPYFSSGSFNP..LW.N.K..R
Retrocopy QLVKLDQEWVLFSTSSSICIHPTFIGTEPSLRVKKPTKAWLFVILSLVGPYFSSGSFNPEFLWVNLKCIR

Parental  AWKGGIGDCKMGGNYGSSLFAQCEAVENGCQQVLWLYGEDNQITEVGTMNFFLYWINEDGEEELATPLLD
          AWKGGI.DCKMG..YGS.LFAQCE..ENG.QQV.WLY.E...ITEVGTMN.FL.WINED..EEL..P.LD
Retrocopy AWKGGIRDCKMGRIYGSFLFAQCETLENG*QQVRWLYVENTKITEVGTMNLFL*WINED-KEELVPPMLD

Parental  GIILPGVMRQSILDLA
          GIILPGVM.Q.IL.LA
Retrocopy GIILPGVMWQNILVLA

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_451 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011431	1 retrocopy	retro_chof_451 ,
Ictidomys tridecemlineatus	ENSSTOG00000004938	1 retrocopy	retro_itri_20,