RetrogeneDB ID:

retro_chof_1559

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_324541:116..947(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PLEKHA3
Ensembl ID:ENSCHOG00000013997
Aliases:None
Description:pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3 [Source:HGNC Symbol;Acc:14338]


Retrocopy-Parental alignment summary:






>retro_chof_1559
ATGGAGGGGGTTCTGTACAAGTGGACCAACTATCTCACAGGTTGGCAGCCTCGTTGGTTTGTTTTAGATAATGGAATCCT
GTCCTACTATGATTCACAGGATGATGTTTGCAAAGGGAGCAAAGGAAGTATAAAGATGGCAGTTTGTGAAATTAAAGTCC
ATTCAGCAGACAACACAAGAATGGAATTAATCATTCCAGGAGAGCAGCATTTCTACATGAAAGCAGTGAATGCGGCTGAA
AGACAGAGGTGGCTGGTTGCTCTGGGGAGCTCCAAAGCCTGTTTGACTGATACTAGGACTAAAAAAGAAAAAGAAATAAG
TGAAACCAGTGTATCTCTGAAAACCAAAATGTCTGAACTCCGCCTCTACTGTGACCTCCTAATGCAACAAGTTCATACAA
TCCAAGAGTTTGTTCACCATGATGAGAGGCATTCATCTTCCAGCGTGGAGAACATGAATGAAGCCTCTTCTTTGCTTAGT
GCCACCTGTAATACCTTCATCACAATACTTGAGGAATGTGTGAAGATAGCAAATGCCAAGTTTAAACCTGATATGTTTCA
GCTGTCCCATCCAGATCCCTTAGTTTCTCCTGTGTCACCTTCTCCTGTTCAAATGATGAAGCCACCTGGTTCTTGCAGTT
CAGAGAGGGGGTAGCCACTCTATAAAAAGAACCCAGGATCTACACATCACCGATTATCCCAGCGACGCCGAAGAACCTAC
TCAGATACAGACTCTTGTAATGATATTCCACTTTGAAGACCCAGATAGACCTGTTCACTTGTTCAAGAAAATACACTTTA
ATGGAGATTTTGACATCTTGTTAACATTCCC

ORF - retro_chof_1559 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.63 %
Parental protein coverage: 92.67 %
Number of stop codons detected: 0
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalMEGVLYKWTNYLTGWQPRWFVLDNGILSYYDSQDDVCKGSKGSIKMAVCEIKVHSADNTRMELIIPGEQH
MEGVLYKWTNYLTGWQPRWFVLDNGILSYYDSQDDVCKGSKGSIKMAVCEIKVHSADNTRMELIIPGEQH
RetrocopyMEGVLYKWTNYLTGWQPRWFVLDNGILSYYDSQDDVCKGSKGSIKMAVCEIKVHSADNTRMELIIPGEQH
ParentalFYMKAVNAAERQRWLVALGSSKACLTDTRTKKEKEISETSESLKTKMSELRLYCDLLMQQVHTIQEFVHH
FYMKAVNAAERQRWLVALGSSKACLTDTRTKKEKEISETS.SLKTKMSELRLYCDLLMQQVHTIQEFVHH
RetrocopyFYMKAVNAAERQRWLVALGSSKACLTDTRTKKEKEISETSVSLKTKMSELRLYCDLLMQQVHTIQEFVHH
ParentalDERHSSSSVENMNEASSLLSATCNTFITTLEECVKIANAKFKPEMFQLSHPDPLVSPVSPSPVQMMKRSV
DERHSSSSVENMNEASSLLSATCNTFIT.LEECVKIANAKFKP.MFQLSHPDPLVSPVSPSPVQM.....
RetrocopyDERHSSSSVENMNEASSLLSATCNTFITILEECVKIANAKFKPDMFQLSHPDPLVSPVSPSPVQM----M
ParentalSHPGSCSSERG-SHSI-KEP-GSTHHRLSQRRRRTYSDTDSCNDIPL-EDPDRPVH-CSRN-TLNGDLTS
..PGSCSSERG.SHSI.KEP.GSTHHRLSQRRRRTYSDTDSCNDIPL.EDPDRPVH.CSR..TL...LTS
RetrocopyKPPGSCSSERG>SHSI>KEP>GSTHHRLSQRRRRTYSDTDSCNDIPL>EDPDRPVH>CSRKYTLMEILTS
Parental-VNIP
.VNIP
Retrocopy>VNIP

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_1559 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 14 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG00000013997 5 retrocopies
Cavia porcellus ENSCPOG000000039061 retrocopy
Dasypus novemcinctus ENSDNOG000000027171 retrocopy
Erinaceus europaeus ENSEEUG000000041691 retrocopy
Homo sapiens ENSG000001160951 retrocopy
Macropus eugenii ENSMEUG000000153172 retrocopies
Microcebus murinus ENSMICG000000098981 retrocopy
Myotis lucifugus ENSMLUG000000058232 retrocopies
Oryctolagus cuniculus ENSOCUG000000054951 retrocopy
Otolemur garnettii ENSOGAG000000027241 retrocopy
Tupaia belangeri ENSTBEG000000075503 retrocopies
Tarsius syrichta ENSTSYG000000053411 retrocopy
Tursiops truncatus ENSTTRG000000097292 retrocopies
Vicugna pacos ENSVPAG000000034903 retrocopies



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