RetrogeneDB ID:

retro_chof_407

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_104696:3060..3743(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:YAP1
Ensembl ID:ENSCHOG00000001095
Aliases:None
Description:Yes-associated protein 1 [Source:HGNC Symbol;Acc:16262]


Retrocopy-Parental alignment summary:






>retro_chof_407
CACATTGATCAGACAAGACATGGAAGGACCCCAGGAAGGCCATGCTCTTTCAGGTGAAGGTGACTGCCCCCACCAGTCCT
CCAGGGCAGCAGAATTTGATGAACACCGCCTCCCGTCCTCTTCCTGATGGATGGGAGCAAGCCATGATTCAGGATGGAGA
AATTTACTATATAAACCATAAAAACAAGACCATCTCTTGGCTAGACCCAAAGCTTGACCCTTATTTGGTCATGAACCAGA
CAGTCAGGGTGCTCCGGTGAAACAGCCAGCACCCCTGGTTCCCCGGAGCCCCAGGGAGGAGTTATGGGTGCAGAAACTCC
AATCAGCAGCAGCAGATGAGGCTTCAGCAACTGCAGATGGAGAAAGAGAGACTGTGACAGAAGCAGGAAGATCTGCTTCA
GCAGGCAATAAGGAATATCAATCCCAGCAGAGCAAATTCTCCAAAATGTCAGGAATTAGCTCATGATAGCCAGTTACTGA
CACTGGAGCAGGATGAAGGGACTCAAAACCCAGTATCTTCTCTGGAGGTGTCTCAGATACTGAGAGCAATGACAACTAAT
AGCTCAGACCTCTTTCTTAACAGTGGCACCTAGAACCCTTGAGATGAGAATACAGACAGTGGATGAAGCCTGAGCAGCTA
CAGTGTCTCTCAAAGTTCAGATGTCTTCCTGAATGGTGTTGAT

ORF - retro_chof_407 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.36 %
Parental protein coverage: 73.48 %
Number of stop codons detected: 4
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalHIDQTT-TWQDPRKAMLSQLNVTAPTSPPVQQNMMNAASGPLPDGWEQAMTQDGEIYYINHKNKTTSWLD
HIDQT..TW.DPRKAML.Q..VTAPTSPP.QQN.MN.AS.PLPDGWEQAM.QDGEIYYINHKNKT.SWLD
RetrocopyHIDQTR<TWKDPRKAMLFQVKVTAPTSPPGQQNLMNTASRPLPDGWEQAMIQDGEIYYINHKNKTISWLD
ParentalPRLD-PRFAINQRISQSAPVKQPPPLAPQSP-QGTVMGGG-NSNQQQQMRLQQLQMEKERLRLKQQELLR
P.LD.P.F......SQ.APVKQP.PL.P.SP.QG.VMG...NSNQQQQMRLQQLQMEKERL..KQ..LL.
RetrocopyPKLD<PLFG-HEPDSQGAPVKQPAPLVPRSP<QGGVMGAE<NSNQQQQMRLQQLQMEKERL*QKQEDLLQ
ParentalQAMRNINPSTANSPKCQELALRSQLPTLEQDGGTQNPVSSPGMSQELRTMTTNSSDPFLNSGTYHSRDES
QA.RNINPS.ANSPKCQELA..SQL.TLEQD.GTQNPVSS...SQ.LR.MTTNSSD.FLNSGT....DE.
RetrocopyQAIRNINPSRANSPKCQELAHDSQLLTLEQDEGTQNPVSSLEVSQILRAMTTNSSDLFLNSGT*NP*DEN
ParentalTDSGLSMSSYSVPRTPDDFLNSVD
TDSG.S.SSYSV....D.FLN.VD
RetrocopyTDSG*SLSSYSVSQSSDVFLNGVD

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_407 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 3 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG00000001095 2 retrocopies
retro_chof_1687, retro_chof_407 ,
Callithrix jacchus ENSCJAG000000006271 retrocopy



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