RetrogeneDB ID:

retro_chof_2134

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_52302:3513..4058(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:YWHAQ
Ensembl ID:ENSCHOG00000004661
Aliases:None
Description:tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide [Source:HGNC Symbol;Acc:12854]


Retrocopy-Parental alignment summary:






>retro_chof_2134
AGGGTCTGCTGGAGGCTCATCTCAAGCATCGAGCAGAAACCAGTATCTCTGACAAGTTGCAGCTGATTAAAGACTACCGG
GAGAAAGTGGAGCTGGAACTGAGATCCAACTGCACCACATTGCTGGAATTGTTGGATAAGTATTTCACAGCCAATGCAAC
TAATCCAGAGAGTAGGGATTTCTATCTGAAAATGAAGGGAGTTTACTTCTGGTACCTTGCTGAAGTGGTGAGTGGTGATG
ATTGAAAACAACCGATAGATAATTCCCAAGGAGCTTACCAAGAGGCATTCGATACAAGCAAGAAAGAGCTGCAACCCCCA
CACACAATCTGCCCGGGGCTGGCTCGTAACTCTTCTGTATTTTTACTATGAGATCCTTAATAACCCAGAGCTTCCCTGTA
CTCTGGCTAAAACAGCTTTTGATGAGGCCCTTGCAGAACTTGATACACTGAATGCAACTCACACAAACACAGCACCCTCA
TCGTGCAGTTGCTTAGAGACAGCCTAACATTATGGGTCTCAGACTGCAGAAGAATGCAATGCAAC

ORF - retro_chof_2134 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.58 %
Parental protein coverage: 74.9 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalRSTWRVILSMEQK-TNTSDKKVQLIKDYKEN-ELELRSICTMVLELLDKYLIANATNPESKVFYLKMKGD
R..WR.I.S.EQK.T..SDK..QLIKDY.E..ELELRS.CT..LELLDKY..ANATNPES..FYLKMKG.
RetrocopyRVCWRLISSIEQK<TSISDK-LQLIKDYREKVELELRSNCTTLLELLDKYFTANATNPESRDFYLKMKGV
ParentalYFRYLAEVACGDDRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSV-FYYEILNNPELACTLAK
YF.YLAEV..GDD.KQ.IDNSQGAYQEAFD.SKKE.QP.H.I..GLA.N.SV.FYYEILNNPEL.CTLAK
RetrocopyYFWYLAEVVSGDD*KQPIDNSQGAYQEAFDTSKKELQPPHTICPGLARNSSV>FYYEILNNPELPCTLAK
ParentalTAFDEAIAELDTLNE-DSYKDSTLIMQLLRDNLTLWTSDSAGEECD
TAFDEA.AELDTLN...S.K.STLI.QLLRD.LTLW.SD.....C.
RetrocopyTAFDEALAELDTLNA<NSHKHSTLIVQLLRDSLTLWVSDCRRMQCN

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_2134 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 8 parental genes, and 50 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000027989 retrocopies
Choloepus hoffmanni ENSCHOG00000004661 13 retrocopies
Choloepus hoffmanni ENSCHOG0000000578215 retrocopies
Choloepus hoffmanni ENSCHOG000000108612 retrocopies
Callithrix jacchus ENSCJAG000000063942 retrocopies
Monodelphis domestica ENSMODG000000147401 retrocopy
Nomascus leucogenys ENSNLEG000000135343 retrocopies
Rattus norvegicus ENSRNOG000000081045 retrocopies



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