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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGTTTGATATGAAGCCCCATGGTGAAAACATTGAAGAGTATGGTAAATTGTGTCGTGAGAGGACAAACAAATCTATGATTAAAAATCGACAAATACAGgtatttgttcatgtttattatttaattatcccttaatgtttcttgctttctgtctatgattaaataattgattctctgggtcccttgatactattggaag

Basic information

species Glycine max
transcript GLYMA04G03030.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G03030.2 (Glycine max), 5'ss of exon 3
lower sequence: AT1G75510.1 (Arabidopsis thaliana), 5'ss of exon 3
TAAGTTTGATATGAAGCCCCATGGTGAAAACATTGAAGAGTATGGTAAATTGTGTCGTGAGAGGACAAACAAATCTATGATTAAAAATCGACAAATACAGgtatttgttcatgtttattatttaattatcccttaatgtttcttgctttctgtctatgattaaataattgattctctgggtcccttgatactattggaag
|| || ||||||||||| ||||||||| ||||||||| |||| || | ||||||||||| || | |||| | ||| ||||||||||||| || ||||| | | || ||| ||| | | | || ||| | || || | || | || | ||| | || |||
CAAATTCGATATGAAGCCATATGGTGAAACCATTGAAGAATATGCTAGGCTTTGTCGTGAGAGAACGAGCAAAGCCATGGTTAAAAATCGACAGATTCAGgtctgttttatattttcacattcaggtgtttgttttcctttgcttctcctatactggctcttaagtgtaaggacttttcttccttgaatttgcgctaaag

upper sequence: GLYMA04G03030.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv18s0001g13370.t01 (Vitis vinifera), 5'ss of exon 3
TAAGTTTGATATGAAGCCCCATGGTGAAAACATTGAAGAGTATGGTAAATTGTGTCGTGAGAGGACAAACAAATCTATGATTAAAAATCGACAAATACAGgtatttgttc--------atgtttattatttaattatccc-ttaatgtttcttgctttctgtctatgattaaataattgattctctgggtcccttgatactattggaag--
||| ||||| |||||||| || |||||| ||||| |||||||| |||||||| ||||| |||||||| |||||||||||||| ||| ||||||| |||||| | || || ||| | ||| |||| | || ||| || || || |||||||| | | ||| | | | || || |||| ||
TAAATTTGACATGAAGCCTCACAATGAAAATATTGAGGAGTATGGCAAATTGTGCCGTGAAAGGACAAATAAATCTATGATTAAGAATAGACAAATTCAGgtagctcatctcacttgcatttttttccttttgttattacattggcatttttt--ttgttgcatatgattataatggtcatttttttttctctttaat-ttattcaaaaag
















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|207837406|gb|GD806226.1|GD806226
EST:     AAATCTATGATTAAAAATCGACAAATACAG                         GTTATTGATAATGACC-GGGAGTTCTAATGAGGCCAATGCCTGGAATGATT
genomic: AAATCTATGATTAAAAATCGACAAATACAGgtatttgttc ... ctattggaagGTTATTGATAATGACCGGGGAGTTCTAATGAGGCCAATGCCTGGAATGATT
EST: gi|193401525|gb|FK367990.1|FK367990
EST:     TGTGTCGTGAGAGGACAAACAAATCTATGATTAAAAATCGACAAATACAG                         GTTATTGATAATGACCGGGGAGTTCTAATGAGGCCAAATGCCTGGAATGAT
genomic: TGTGTCGTGAGAGGACAAACAAATCTATGATTAAAAATCGACAAATACAGgtatttgttc ... ctattggaagGTTATTGATAATGACCGGGGAGTTCTAATGAGGCC-AATGCCTGGAATGAT
EST: gi|298168092|gb|HO013355.1|HO013355
EST:     TGCGTCGTGAGAGGACAAACAAATCTATGATTAAAAATCGACAAATACAG                         GTTATTGATAATGACCGGGGA
genomic: TGTGTCGTGAGAGGACAAACAAATCTATGATTAAAAATCGACAAATACAGgtatttgttc ... ctattggaagGTTATTGATAATGACCGGGGA
EST: gi|7685262|gb|AW755910.1|AW755910
EST:     TGTGTCGTGAGAGGACAAACAGATCTATGATTAATAATCGACAAATACAG                         GTTATTGATAATGACCGGGGAGTTCTTATGATGCCAATGCCTGGAATGATT
genomic: TGTGTCGTGAGAGGACAAACAAATCTATGATTAAAAATCGACAAATACAGgtatttgttc ... ctattggaagGTTATTGATAATGACCGGGGAGTTCTAATGAGGCCAATGCCTGGAATGATT
EST: gi|298180364|gb|HO025565.1|HO025565
EST:     TGTGTCGTGAGTGGACAAACAAATCTATGATTAAAAATCGACAAATACAG                         GTTATTGATAATGACCGGGGAGTTCTAATGAGGCCAATGCCTGGAATGATT
genomic: TGTGTCGTGAGAGGACAAACAAATCTATGATTAAAAATCGACAAATACAGgtatttgttc ... ctattggaagGTTATTGATAATGACCGGGGAGTTCTAATGAGGCCAATGCCTGGAATGATT
EST: gi|192308908|gb|FK002132.1|FK002132
EST:     TGTGTCGTGAGAGGACAAACAAATCTATGATTAAAAATCGACAAATACAG                         GTTATTGATAATGACCGGGGAGTTCTAATGAGGCCAATGCCTGGAATGATT
genomic: TGTGTCGTGAGAGGACAAACAAATCTATGATTAAAAATCGACAAATACAGgtatttgttc ... ctattggaagGTTATTGATAATGACCGGGGAGTTCTAATGAGGCCAATGCCTGGAATGATT
EST: gi|298192192|gb|HO036274.1|HO036274
EST:     TGTGTCGTGAGAGGACAAACAAATCTATGATTAAAAATCGACAAATACAG                         GTTATTGATAATGACCGGGGA
genomic: TGTGTCGTGAGAGGACAAACAAATCTATGATTAAAAATCGACAAATACAGgtatttgttc ... ctattggaagGTTATTGATAATGACCGGGGA
EST: gi|15202686|gb|BI425532.1|BI425532
EST:     TGTGTCGTGAGAGGACAAACAAATCTATGATTAAAAATCGACAAATACAG                         GTTATTGATAATGACCGGGGAGTTCTAATGAGGCCAATGCCTGGAATGATT
genomic: TGTGTCGTGAGAGGACAAACAAATCTATGATTAAAAATCGACAAATACAGgtatttgttc ... ctattggaagGTTATTGATAATGACCGGGGAGTTCTAATGAGGCCAATGCCTGGAATGATT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAGTTTGATATGAAGCCCCATGGTGAAAACATTGAAGAGTATGGTAAATTGTGTCGTGAGAGGACAAACAAATCTATGATTAAAAATCGACAAATACAGgtatttgttcatgtttattatttaattatcccttaatgtttcttgctttctgtctatgattaaataattgattctctgggtcccttgatactattggaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA