RetrogeneDB ID: retro_chof_1951

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_431302:19..375(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFXAP
• Ensembl ID: ENSCHOG00000012518
• Aliases: None
• Description: regulatory factor X-associated protein [Source:HGNC Symbol;Acc:9988]

Sequence

>retro_chof_1951
AGCCAGGTGGCCAAGCAGTAGAAGCTGTGGATGTGCAAGAAGCACCTCAACAAGATGTACAAGGACAAGTACAAGAAGAA
GAAGAGTGACCAGGCCCCAAGCAGTAGTGCTGCAGGCAGCAGGGTGGCATCAAGTTGGAGGAAAGTGCAAATAGAATCCT
CACCATTTTCAACAGACAACAGGATCTTTCAGTGATTGTCCTGCAAGACCAACTCTTTTAGAACAAGTGTTAAATCAAAA
AAAGACTGTCCTTGCTAAGAAGTCCTGAAGTAGTGCAGTTTTTACAGAAACAGCAGCAACTATTAAACCAGCAAGTTTTG
GAGCAAAGACAGCAACAGTTGCCAGGAGCACCAATG

Alignment

ORF - retro_chof_1951 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.13 %
• Parental protein coverage: 55.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SQVAKQRKP-VCKTHCNKMYKAKYKKN-SDQAPRGGAASSSTSAD-SIESADSILAIV-KQRAGSFGDRP
          SQVAKQ.K...CK.H.NKMYK.KYKK..SDQAP...AA.S........ESA..IL.I...Q..GSF.D.P
Retrocopy SQVAKQ*KLWMCKKHLNKMYKDKYKKKKSDQAPSSSAAGSRVASS<LEESANRILTIF<QQTTGSFSDCP

Parental  ARPTLLEQVLNQ-KRLSLLRSPEVVQFLQKQQQLLNQQVLEQRQQQFPGAPV
          ARPTLLEQVLNQ.KRLSLLRSPEVVQFLQKQQQLLNQQVLEQRQQQ.PGAP.
Retrocopy ARPTLLEQVLNQ>KRLSLLRSPEVVQFLQKQQQLLNQQVLEQRQQQLPGAPM

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_1951 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012518	1 retrocopy	retro_chof_1951 ,
Tursiops truncatus	ENSTTRG00000007901	2 retrocopies	retro_ttru_220, retro_ttru_55,