RetrogeneDB ID: retro_chof_1923

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_42405:5234..5647(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000011097
• Aliases: None
• Description: None

Sequence

>retro_chof_1923
AATGTGCTTTCCCAGTTGGCTCAAGGAGAGGAAGTATGGAGAGAAGGGATGAGGTTTCTCCAAAACCAGAATCCAGGCAG
GAAAAGGGCCTGTAAAAAGCAAGAAATGATATTCATGCAACTTACCTACAGGAAAGACAATTCTGACATCATGTCATTGC
ACATATCTCACACTCAAAAGAATTCCTTTCAATGTAATTATTTGCATGAAGATTCCACTGTCAGATCCACAGTGACTCAG
CATGCATTAATTCCCATGAGAAAGAAACCATATTTAAGCAAATCACTTGGAAAACTTCTCAGTGACCAGTCATTTTTAAT
TAACATAAGCAGATTAACACTAGGAGTAATACATATGAATTCCATGGATGTACTAAATCTTTTATTAAAAGCTTTGGCCA
CAAACAATACAAT

Alignment

ORF - retro_chof_1923 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.75 %
• Parental protein coverage: 72.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DVFSLLAQKQVMWREGMEFLRNQSPGMEIACKKQEMIFMQLIYRNDNSEDASLRISYTQKNSFKFNYLQE
          .V.S.LAQ....WREGM.FL.NQ.PG...ACKKQEMIFMQL.YR.DNS...SL.IS.TQKNSF..NYL.E
Retrocopy NVLSQLAQGEEVWREGMRFLQNQNPGRKRACKKQEMIFMQLTYRKDNSDIMSLHISHTQKNSFQCNYLHE

Parental  DSTLRSAVTQHALIPMRKRPYLRKPFGKVLSEQS-SFNKHEQFHTGSKSYECHRNVKAFIKNAGHKEYD
          DST.RS.VTQHALIPMRK.PYL.K..GK.LS.QS..FN.H.Q..T.S..YE.H...K.FIK..GHK.Y.
Retrocopy DSTVRSTVTQHALIPMRKKPYLSKSLGKLLSDQS<IFN*HKQINTRSNTYEFHGCTKSFIKSFGHKQYN

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_1923 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007736	2 retrocopies	retro_chof_154, retro_chof_2671,
Choloepus hoffmanni	ENSCHOG00000011097	2 retrocopies	retro_chof_1923 , retro_chof_228,
Choloepus hoffmanni	ENSCHOG00000011899	1 retrocopy	retro_chof_379,
Homo sapiens	ENSG00000196946	1 retrocopy	retro_hsap_2965,