RetrogeneDB ID:

retro_chof_864

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_158020:6623..6988(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:LIN7C
Ensembl ID:ENSCHOG00000000111
Aliases:None
Description:lin-7 homolog C (C. elegans) [Source:HGNC Symbol;Acc:17789]


Retrocopy-Parental alignment summary:






>retro_chof_864
ATTCAGGCTTTACAAAGAGTCCTTTAAAGTGAGTTCTGTGATGCTGTAAGAGAGGGATATGAACACATCTATGAAACTGT
GGACATCAGTAGCAGTCCTGAAGTGAGAGCTAATGCAAATGCAAAGGCTACAGTCGCTGCGTTTGCTGCCAGTGAAGGAC
ATTCTCATCCTCGAGTGGTTGAGCTACCAAAAACAGAAGAGGGCCTTGGATTTAATATTATGTGAGGGAAAGAACAAAAC
TCTCCAATCTATATATCTCGAATAATTCCAGGCGGTATTGCTGATAGACATGGGGGCGTCAAATGAGACCACCTCTTTCT
GTTAATGGAGTGAGCGCTGAAGGAGAACATCATGAAAAAGCTGTA

ORF - retro_chof_864 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.71 %
Parental protein coverage: 62.44 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalLQALQRVLQSEFCNAVREVYEHVYETVDISSSPEVRANATAKATVAAFAASEGHSHPRVVELPKTEEGLG
.QALQRVL.SEFC.AVRE.YEH.YETVDISSSPEVRANA.AKATVAAFAASEGHSHPRVVELPKTEEGLG
RetrocopyIQALQRVL*SEFCDAVREGYEHIYETVDISSSPEVRANANAKATVAAFAASEGHSHPRVVELPKTEEGLG
ParentalFNIMGGKEQNSPIYISRIIPGGIADRHGGLKRGDQL-LSVNGVSVEGEHHEKAV
FNIM.GKEQNSPIYISRIIPGGIADRHGG....D.L.LSVNGVS.EGEHHEKAV
RetrocopyFNIM*GKEQNSPIYISRIIPGGIADRHGGV-K*DHL<LSVNGVSAEGEHHEKAV

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Choloepus hoffmanni was not studied using RNA-Seq expression data.
Choloepus hoffmanni was not studied using ChIP-Seq data.
Choloepus hoffmanni was not studied using EST data.
Choloepus hoffmanni was not studied using FANTOM5 data.
retro_chof_864 was not experimentally validated.

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.

Parental genes homology:
Parental genes homology involve 2 parental genes, and 9 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG00000000111 7 retrocopies
Microcebus murinus ENSMICG000000051652 retrocopies



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