RetrogeneDB ID:

retro_chof_1377

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_27631:3406..4130(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS3A
Ensembl ID:ENSCHOG00000007238
Aliases:None
Description:ribosomal protein S3A [Source:HGNC Symbol;Acc:10421]


Retrocopy-Parental alignment summary:






>retro_chof_1377
GTTGATCCATTTTCTAAGAAAGACTGGTATAGTGTGAAACCACCAGCAGTGCTTAATATAAAAAATATTGGAAAACCATC
AGTCAGAAGGACATAAGGAACCAAAATTGCATTTGATGGCTTTAAGGCTCATAATTTTGAAGTGAGTCTTGCTGATCTAC
AGAATAATGATGTTGCGTTTAGAAAATTCCAGATAATTACTGAGGATGTTCAGAGCAAAAGCTACCAAACCAACTTCCAT
GGCATGGATCTTACCCAAGACAAAATGTGCTCATGATCAAAAATGGCAGCTCATGACTGAAGCTTGTGTTGACATCAAAA
CTACCAGTGATTACTTGCTTTATCTGTACTGCATTGGTTTTACTAAAAAACACAGTTAGATTCAGAAGACCTCTTATGCT
TAGCACCAAGAGGTCTGTCAAAACCATAAGAAAATAATGGATATCATGACCCAAGAGGTGCAGACAACTGACTTGAAAGA
AGTTGTCAATAAATTGATTCCAGAAAGTGTTGGTAAAGACATAGAAAAGTTTTGCCAATCTATCTATCCTTTCCATGCTG
TGCTTGTTAGAACAGTAAAAATGCTGTAGAAGCCCAAGTTTGAACTGGGAAAACTCATATTGTTTCATGGTGTAAGTAGT
GGTTTTAGAAAAGCTCCTGGGGATGGGATGAATACTGAAGTTGAAAGAGCTGATGGATACGAGCCACCAACCCAAGAATT
TGTT

ORF - retro_chof_1377 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.2 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVSLADLQNDEVAFRKFKLITEDV
VDPFSKKDWY.VK.PA..NI.NIGK..V.RT.GTKIA.DG.K...FEVSLADLQN..VAFRKF..ITEDV
RetrocopyVDPFSKKDWYSVKPPAVLNIKNIGKPSVRRT*GTKIAFDGFKAHNFEVSLADLQNNDVAFRKFQIITEDV
ParentalQGKNCLTNFHGMDLTRDKMCS-MVK-KWQTMIEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQ
Q.K...TNFHGMDLT.DKMCS.M.K.KWQ.M.EA.VD.KTT..YLL.L.C.GFTKK....I.KTSYA.HQ
RetrocopyQSKSYQTNFHGMDLTQDKMCS<MIK<KWQLMTEACVDIKTTSDYLLYLYCIGFTKK-HS*IQKTSYA*HQ
ParentalQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLM
.V.Q..KK.M.IMT.EVQT.DLKEVVNKLIP.S.GKDIEK.CQSIYP.H.V.VR.VKML.KPKFELGKL.
RetrocopyEVCQNHKKIMDIMTQEVQTTDLKEVVNKLIPESVGKDIEKFCQSIYPFHAVLVRTVKML*KPKFELGKLI
ParentalELHGEGSSSGKATGDETGAKVERADGYEPPVQESV
..HG..S...KA.GD.....VERADGYEPP.QE.V
RetrocopyLFHGVSSGFRKAPGDGMNTEVERADGYEPPTQEFV

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_1377 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 7 parental genes, and 56 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG00000007238 34 retrocopies
Macaca mulatta ENSMMUG000000218211 retrocopy
Monodelphis domestica ENSMODG000000009696 retrocopies
Mus musculus ENSMUSG000000280812 retrocopies
Rattus norvegicus ENSRNOG000000118931 retrocopy
Sarcophilus harrisii ENSSHAG000000150882 retrocopies
Tursiops truncatus ENSTTRG0000001309410 retrocopies



Copyright © RetrogeneDB 2014-2017