RetrogeneDB ID:

retro_chof_509

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_115926:3466..4074(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TWF1
Ensembl ID:ENSCHOG00000008386
Aliases:None
Description:twinfilin actin-binding protein 1 [Source:HGNC Symbol;Acc:9620]


Retrocopy-Parental alignment summary:






>retro_chof_509
GAGGACAAACAACCGTGCTATGTATTATTCAGATGAGATTCTCAGAATGCCCAGGGATATGAATGGATATTCATTGCATG
GTCTCCAGATCATTCTCATGTTCGTCAGAAAATGTATGCAGCAACGAAAGCAACTCTAAAAAAGGAGTTTGGAGGTGGCC
ACATTAAAGATGAAGTATTTGGAACAGTAAAGGAAGATGTAGCATTACATGGATATAAAAAAATATTTGCTATCACAATC
TTCCCCTGCCCCGGTGACTGCAGTGGAGGAAGAATTACGACAAATTAAAATTAATGAGGAACAAACTGATGTGAGTGTGA
CACTAAGCATCAACACTACAAGGGGGTAGCATTTCCTATTTCTCAGGAAGCTTTTCAGGCTTTGGAAAAACTGAATAACA
GCTCAACTACAAGCAGTTGGAAATAGATATAAAAAATGAAATTATAATTTTGGCCAACAGAACAAATACAGAACTAAAAG
ATTTGCCAAAGAGGTTTCCCAAAGATTCAGCACGTTATCACTTCTTTCTGTATAAACATTCCCATGAAGGAGAGTATTTG
GAGTCCATAGTTTTTATTTATTCAATGCCTTGATATACATATGCAGTA

ORF - retro_chof_509 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.21 %
Parental protein coverage: 53.39 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalEDKQPCYILFRLDSQNAQGYEWIFIAWSPDHSHVRQKMLYAATRATLKKEFGGGHIKDEVFGTVKEDVSL
EDKQPCY.LFR.DSQNAQGYEWIFIAWSPDHSHVRQKM.YAAT.ATLKKEFGGGHIKDEVFGTVKEDV.L
RetrocopyEDKQPCYVLFR*DSQNAQGYEWIFIAWSPDHSHVRQKM-YAATKATLKKEFGGGHIKDEVFGTVKEDVAL
ParentalHGYKK-YLLSQSSPAPLTAAEEELRQIKINEVQTDVSV-DTKHQ-TLQGVAFPISQEAFQALEKLNNRQL
HGYKK.YLLSQSSPAP.TA.EEELRQIKINE.QTDVSV.DTKHQ.TLQG.........F....K....QL
RetrocopyHGYKK>YLLSQSSPAPVTAVEEELRQIKINEEQTDVSV<DTKHQ<TLQGGSISYFSGSFSGFGK-TE*QL
ParentalNYVQLEIDIKNEIIILANTTNTELKDLPKRIPRDSARYHFFLYKHSHEGDYLESIVFIYSMPGYTCSI
NY.QLEIDIKNEIIILAN.TNTELKDLPKR.P.DSARYHFFLYKHSHEG.YLESIVFIYSMP.YT...
RetrocopyNYKQLEIDIKNEIIILANRTNTELKDLPKRFPKDSARYHFFLYKHSHEGEYLESIVFIYSMP*YTYAV

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_509 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 10 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000173321 retrocopy
Choloepus hoffmanni ENSCHOG00000008386 5 retrocopies
Homo sapiens ENSG000001512392 retrocopies
Monodelphis domestica ENSMODG000000185351 retrocopy
Mustela putorius furoENSMPUG000000003641 retrocopy
Mus musculus ENSMUSG000000224511 retrocopy
Nomascus leucogenys ENSNLEG000000179311 retrocopy
Otolemur garnettii ENSOGAG000000075251 retrocopy
Pan troglodytes ENSPTRG000000048461 retrocopy
Rattus norvegicus ENSRNOG000000225071 retrocopy



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