RetrogeneDB ID: retro_chof_2674

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_96397:479..973(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BTG4
• Ensembl ID: ENSCHOG00000000032
• Aliases: None
• Description: B-cell translocation gene 4 [Source:HGNC Symbol;Acc:13862]

Sequence

>retro_chof_2674
ATAAACAATAATCAGAATAAAGATCCCATTCTAGAAAGGGCTTTTGCTGAAAGTAATGTGACTTTTTCTCAGCTGGGACT
TCCAAAGGAGATGACCATCTGGGTAGATCCCTTTGAAATGTGCTGTAAGTATTGTGAGAAAAATCATCCATTTACAATTG
CTTCCTTTAAAGGCACATGGGAGGAATGGGATCTATTTCAACAAATCAGCCATGCTGTTAGTAGGCTCACATTAGACTTA
GACTACCTCTGGCACTTCCTCCGATAAAGAAAGTTGTAGCAAAAACCTCAGAAATTCCTAAAGTCAGCAATCCAAAGAGT
ATTTATCAGGTTGAAAACTTGAATCAGCCCTTTCAATCTTGGTTCCAAATCCCCCATAAAAAGAACACAACAGATGGCCA
TGCCAGTCTCTTGGGAAATGCTTATCATGCATGGCACAAGAACCCTAGAAGTTCCAGGCCTGCTGCTATGCTGGTTGGAC
ACCAGGTAGACCAG

Alignment

ORF - retro_chof_2674 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.37 %
• Parental protein coverage: 72.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  INNNQNRDPILERACVESNVNFSHLRLPKXXXXXXXXXXXXXXYGEKNHPFTIASFKDRWEGWELSQQIS
          INNNQN.DPILERA..ESNV.FS.L.LPK..............Y.EKNHPFTIASFK..WE.W.L.QQIS
Retrocopy INNNQNKDPILERAFAESNVTFSQLGLPKEMTIWVDPFEMCCKYCEKNHPFTIASFKGTWEEWDLFQQIS

Parental  RAVSRLTLDLDDY-SGASSDEESCSK-EPQM-IPKVSNPKSIYQVENLKQPFQSWFQIPRKKNMTDGQAS
          .AVSRLTLDL.DY.SG.SSD.ESCSK..PQ..IPKVSNPKSIYQVENL.QPFQSWFQIP.KKN.TDG.AS
Retrocopy HAVSRLTLDL-DY>SGTSSDKESCSK<KPQK<IPKVSNPKSIYQVENLNQPFQSWFQIPHKKNTTDGHAS

Parental  LLGNAYRAWHKNPKSYRPAAMLVGQRVDR
          LLGNAY.AWHKNP.S.RPAAMLVG..VD.
Retrocopy LLGNAYHAWHKNPRSSRPAAMLVGHQVDQ

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_2674 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014210	2 retrocopies	retro_cfam_1324, retro_cfam_471,
Choloepus hoffmanni	ENSCHOG00000000032	1 retrocopy	retro_chof_2674 ,
Equus caballus	ENSECAG00000012564	1 retrocopy	retro_ecab_299,
Monodelphis domestica	ENSMODG00000014496	1 retrocopy	retro_mdom_1647,
Sus scrofa	ENSSSCG00000015020	1 retrocopy	retro_sscr_680,
Tursiops truncatus	ENSTTRG00000010435	1 retrocopy	retro_ttru_1303,