RetrogeneDB ID:

retro_itri_1679

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393630.1:1009978..1010565(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GAPDH
Ensembl ID:ENSSTOG00000007538
Aliases:None
Description:glyceraldehyde-3-phosphate dehydrogenase [Source:HGNC Symbol;Acc:4141]


Retrocopy-Parental alignment summary:






>retro_itri_1679
TTCAACTCTGGAAAAGTGGTTATTATTGACATCAATGACTCCTTCATTGACTTTAACTGTATGATGTAAATGTTCCAGTT
CAATTCCATCCATGACAAGTTCAAAGCTGAAAACACAAACCTTGTCATCAACAGGAAGCCCATATCTATGCTCCAAAGGG
CAAAACCCCAGTCCGTCAGTGGGGCTAAGCTGGTGATGGATACATTGTGGAGTCCACAGGTGTCTTCACTACCATGGAGA
AGGCTGGGGTTCACTTGAAGGGTGAAACCAAAAAAGTTATCATCTCTGCCTTTTCTGCTGACACTCCATGTTTGCGATGG
GTATAAACTCTGAGAAGTATTCCAACTTCCTCAATTTGGTCAGCAATACTTCCTGTACCATGAATTGCTTAGTTCTAGCT
GAAGTCATCCATGACAAATTTGGTATCATGAATGGACTCATAACTACAATTTCAAGCAACCATGGCTAACCAAATGACTG
CGTGTGGCCCCTCTGGGAAATTGTGGTGTGATGACCATTGGGATGCCTATAACATTATCCCTGCATGCACTGGCATTGCC
AAGGCTATGGGAGAGAGTGTCTCTGAA

ORF - retro_itri_1679 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.27 %
Parental protein coverage: 60.36 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalFNSGKVEIVAINDPFIDLNYMVYMFQYDSTHGKFHGTVKAENGKLVINGKSISIFQERDPANI-KWGDAG
FNSGKV.I..IND.FID.N.M..MFQ..S.H.KF....KAEN..LVIN.K.IS..Q...P.....WG.AG
RetrocopyFNSGKVVIIDINDSFIDFNCMM*MFQFNSIHDKF----KAENTNLVINRKPISMLQRAKPQSV<QWG*AG
ParentalAEYVVESTGVFTTMEKAGAHLKGGAKRVIISAPSADAP-MFVMGVNHEKYDNSLKIVSNASCTTNCLAPL
..Y.VESTGVFTTMEKAG.HLKG..K.VIISA.SAD.P.MF.MG.N.EKY.N.L..VSN.SCT.NCL..L
RetrocopyDGYIVESTGVFTTMEKAGVHLKGETKKVIISAFSADTP<MFAMGINSEKYSNFLNLVSNTSCTMNCLV-L
ParentalAKVIHDNFGIVEGLMTTV-HAITATQKTVDGPSGKLWRDGRGAAQNIIPASTGAAKAVGKVIPE
A.VIHD.FGI..GL.TT...A..A.Q.T..GPSGKLW.D....A.NIIPA.TG.AKA.G....E
RetrocopyAEVIHDKFGIMNGLITTI>QATMANQMTACGPSGKLWCDDHWDAYNIIPACTGIAKAMGESVSE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide