RetrogeneDB ID: retro_chof_737

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_142227:887..1318(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCL2
• Ensembl ID: ENSCHOG00000012692
• Aliases: None
• Description: phosducin-like 2 [Source:HGNC Symbol;Acc:29524]

Sequence

>retro_chof_737
AAAACCTACGAAGATATGACTTTGGAAGAGCTAGAGGATCATAAAGATGAATTCAGTGAGGAGGATGAGCGTGCTATGGA
GATGTACAGGCAACAAAGACTGGCTGAGTTGAAAGCCAATAACTGAAGAATAAACTTGGAGAAGTTTTGGAGATCTCGGG
AAAGGATTATGTCCAAGAAGTTACCAAAACTGGTGAGGGCTTGTGGGTAATCTTGCACCTTTACAAGCAAGGAATTCCCC
TGTGTGCCCTGATAAATCAACACTTCAGTGAACTTGCAAGGAAGTTTCCTGATGTCAAATTTATCAAAGCCATTTCGACC
ACCTGCATACCCAATTATCCTGATAGAAATCTGCCCACAATATTTATTTACCTTGAAGGTGATATCAAGGCTCAATTTAT
TGGACCTCTAGTGTTTGGCAGCATGAACCTG

Alignment

ORF - retro_chof_737 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.1 %
• Parental protein coverage: 97.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KPYEKMSLAQLKEAEDEFDEEDMRAIEVYREKRLQEWKALKER-QKFGELREISGNQYVKEVTNAEKDVW
          K.YE.M.L..L....DEF.EED.RA.E.YR..RL.E.KA...R..K.GE..EISG..YV.EVT......W
Retrocopy KTYEDMTLEELEDHKDEFSEEDERAMEMYRQQRLAELKANN*R<NKLGEVLEISGKDYVQEVTKTGEGLW

Parental  VIILLYRSSIPMCLLVNQHLSLLARKFPETKFVKAIVNSCIQHYHDNCLPTIFVYKNGQIEGKFIGIIEC
          VI..LY...IP.C.L.NQH.S.LARKFP..KF.KAI...CI..Y.D..LPTIF.Y..G.I...FIG....
Retrocopy VILHLYKQGIPLCALINQHFSELARKFPDVKFIKAISTTCIPNYPDRNLPTIFIYLEGDIKAQFIGPLVF

Parental  GGINL
          G..NL
Retrocopy GSMNL

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_737 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 5 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012692	3 retrocopies	retro_chof_1554, retro_chof_562, retro_chof_737 ,
Echinops telfairi	ENSETEG00000000666	1 retrocopy	retro_etel_1568,
Gorilla gorilla	ENSGGOG00000007908	1 retrocopy	retro_ggor_2890,
Monodelphis domestica	ENSMODG00000020680	2 retrocopies	retro_mdom_1048, retro_mdom_993,
Pan troglodytes	ENSPTRG00000016073	7 retrocopies	retro_ptro_148, retro_ptro_1810, retro_ptro_1865, retro_ptro_2402, retro_ptro_2690, retro_ptro_2784, retro_ptro_675,