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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcactcattttaattgatttacttttgtcaaaagtttctatttaaattgtctcgtgtttgtgctatttcttattttattagctttgctgataaattgtttattgatttctgcagATTATGATTGGCATTCTGTTTTTTCTCTTTGAGTTTTATGATGATCAGCTACTTGCTTTCATGGTCTTGATTCTTGTCTGGTTGTGTGAACTTTTTACTC

Basic information

species Glycine max
transcript GLYMA08G19970.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os03g45770.1 (Oryza sativa), 3'ss of exon 10
gtaagcactcattttaattgatttacttttgtcaaaagtttctatttaaattgtctcgtgtttgtgctatttcttattttattagctttgctgataaattgtttattgatttctgcagATTATGATTGGCATTCTGTTTTTTCTCTTTGAGTTTTATGATGATCAGCTACTTGCTTTCATGGTCTTGATTCTTGTCTGGTTGTGTGAACTTTTTACTC
||| |   |  ||||   | | | |  |         ||  || |||| ||              | | | || ||| ||| ||  ||   || |           ||||   ||||||| |||||||| || || |||||||| |||||||| |||||||||||| | ||||| ||  | || |||| |||||| ||||||||||| || |||||  
gtatgatattttttttccttaatgagctgaaaattttgtggctgtttagatgtatctactcaacagatttctcatatcttactaatttctttgttg----------tgatcattgcagATAATGATTGGGATCCTCTTTTTTCTATTTGAGTTCTATGATGATCAGTTGCTTGCATTTCTAGTTTTGACTCTTGTATGGTTGTGTGAGCTATTTACGA

upper sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM5G814310_T01 (Zea mays), 3'ss of exon 1
gtaagcactcattttaattgatttactt--ttgtcaaaagtttctatttaaattgtctcgtgtttgtgctatttcttattttattagctttgctgataaattgtt---tattgatttctgcagATTATGATTGGCATTCTGTTTTTTCTCTTTGAGTTTTATGATGATCAGCTACTTGCTTTCATGGTCTTGATTCTTGTCTGGTTGTGTGAACTTTTTACTC
||||      || ||  |||   |  |    | |    ||||| |  | ||| |   |  |   ||    |||    |   |  ||  || ||| |   ||| ||   |  |||| | || ||||||||||||| ||||| |||||||| |||||||| |||||||||||  | ||||| ||  | || |||| |||||| ||||| || || || || ||  
gtaatgggaaatattctttggcgttttggagtatttgtagtttgtgatgaaaatacat--tcgctgcagaattcaccaaacttctatattagctcactcattattttgttctgatctttgtagATTATGATTGGGATTCTCTTTTTTCTATTTGAGTTCTATGATGATCAATTGCTTGCGTTTCTTGTTTTGACTCTTGTATGGTTATGCGAGCTATTCACGA

upper sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G60995.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaagcactcattttaattgatttacttttgtcaaaagtttctatttaaat-tgtctcgtgtttgtgctatt-tcttattttattagctttgctgataaattgt--ttattgatttctgcagATTATGATTGGCATTCTGTTTTTTCTCTTTGAGTTTTATGATGATCAGCTACTTGCTTTCATGGTCTTGATTCTTGTCTGGTTGTGTGAACTTTTTACTC
                                      |   ||  |||   ||  || | ||| | | |   | | |    |||  |||    || |   | |   ||||      |||||||||||||||| ||| |||| || || ||||||||||| || ||||||||| | ||||| |||||  |  ||||||||||| | || ||| | || || |
-----------------------------------gtatgcatacataaccctggttcttttttattccaagatttcagaggattctcttaagcgacatgatataactatttgaaattgcagATTATGATTGGGATTTTGTTCTTCCTGTTTGAGTTTTACGACGATCAGCTATTGGCTTTTATGGTTCTAGTTCTTGTCTGGCTTTGCGAATTATTCACCC

upper sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv12s0034g02140.t01 (Vitis vinifera), 3'ss of exon 10
gtaagcactcattttaattgatttacttttgtcaaaagtttctatttaaattgtctcgtgtttgtgctatttcttatt-ttattagctttg-ctgataaa-ttgtttattgatttctgcagATTATGATTGGCATTCTGTTTTTTCTCTTTGAGTTTTATGATGATCAGCTACTTGCTTTCATGGTCTTGATTCTTGTCTGGTTGTGTGAACTTTTTACTC
               ||||| | | | ||| |     |||| | |||   || ||     | | |  |||     ||  |||| |   |||  ||||||| |||| | |||  |||||||||| |||||||| ||  | |||||||||||||| |||||||||||||| ||| | || ||||||||||| ||||||||||||||||| || || ||||| |
-------------cgaattgttgtgcctttct-----gttttttttttgtttctcct---tgtatattatcctccatgattatcactgttgattgataaaattgtgtgttgcattctgcagATAATGATTGGTATCTTATTTTTTCTCTTTGAATTTTATGATGATCAACTATTGGCATTCATGGTCTTAATTCTTGTCTGGTTGTGCGAGCTATTTACAC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|7589379|gb|AW705154.1|AW705154
EST:     ATTGAATCACTAGTTTTTGTTCCT                         ATTATGATTGGCATTCTGTTTTTTCTCTTTGAGTTTTATGATGATCAGCTA
genomic: ATTGAATCACTAGTTTTTGTTCCTgtaagcactc ... atttctgcagATTATGATTGGCATTCTGTTTTTTCTCTTTGAGTTTTATGATGATCAGCTA
EST: gi|5606329|gb|AI900427.1|AI900427
EST:     CATTTCAGCTGATCTTTGTACATGTGATTGAATCACTAGTTTTTGTTCCT                         ATTATGATTGGCATTCTGTTTTTTCTCTTTGAGTTTTATGATGATCAGCTA
genomic: CATTTCAGCTGATCTTTGTACATGTGATTGAATCACTAGTTTTTGTTCCTgtaagcactc ... atttctgcagATTATGATTGGCATTCTGTTTTTTCTCTTTGAGTTTTATGATGATCAGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgctatttcttattttattagctttgctgataaattgtttattgatttctgcagATTATGATTGGCATTCTGTTTTTTCTCTTTGAGTTTTATGATGATCAGCTACTTGCTTTCATGGTCTTGATTCTTGTCTGGTTGTGTGAACTTTTTACTC
                                        tattgat  putative branch site (score: 3)
                                              tttctgc  CT-rich tract
     atttcttattttatta  TA-rich tract