RetrogeneDB ID: retro_chof_154

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_3508:5702..6235(+)
• Located in intron of: ENSCHOG00000006729

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000007736
• Aliases: None
• Description: None

Sequence

>retro_chof_154
GTGCAACCATGGGAGTTAATGACCTTCAAAATTTAGCAGTAGACTTCACTCAGGATAAAGCATTGCTAGATAAACCCCAA
GGAAAGCTATTCAGAGAAGTGATGCTGGAGAATACCAATCATCTGGTTTCAGTGGGATGTCTCATGTGCATATCAGATGT
GCCTTCCCAGTTGGTACAAGGAGAGGAAGTGTGGAAAGAAGGAATAGAATTTCTCCAAAACCAGAATCTGGGCAGGAAAG
TTCCTATAAAAAGCAAGAAAATATATTTATGCAACTTACCTGCAGGAAGGGGAATTCTAACATTGTTTTGCTGCAGATAT
CTCACATTCAAAAGAATTCCTTTCAATGTAATTATTTGCAGGAAGATTCCACTCTCAGATCCACAGTGATTCCACATGCA
TTACTTTCCTATGAGAAAGTAACCATATTTAAGACAATTACTTGAAAAACTCCTCAGTGACCGGTCATCTTTTACTCAAC
CTAAGCAGATTCACACTAGTACATTATATAAATGTCATCAAAGTGCTCAAGCC

Alignment

ORF - retro_chof_154 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.02 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MQPQELISFK-DVSVDFTQEEWALLDTSQRQLFREVMLENINHLFSVGCEVCKSNMFSQLAQGEVVWREG
          .QP.EL..FK....VDFTQ...ALLD..Q..LFREVMLEN.NHL.SVGC..C.S...SQL.QGE.VW.EG
Retrocopy VQPWELMTFK<NLAVDFTQDK-ALLDKPQGKLFREVMLENTNHLVSVGCLMCISDVPSQLVQGEEVWKEG

Parental  KECLQNQSPDMKI-ACEKQEMMLMQLIYRNEHSEEVSLQISHTQKNTFQCNYLQEDSTCRSKVTQHALI-
          .E.LQNQ....K.....KQE...MQL..R...S..V.LQISH.QKN.FQCNYLQEDST.RS.V..HAL..
Retrocopy IEFLQNQNLGRKV<SYKKQENIFMQLTCRKGNSNIVLLQISHIQKNSFQCNYLQEDSTLRSTVIPHALL>

Parental  PIRKKPYLRKPLGKFLSDQSSFNKHEQIHTRIKSYERHQDAKA
          P.RK.PYLR..L.K.LSD.SSF....QIHT....Y..HQ.A.A
Retrocopy PMRK*PYLRQLLEKLLSDRSSFTQPKQIHTS-TLYKCHQSAQA

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_154 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,