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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcagaactgttttggaacacaaataccccctgtaattcatgtagtttctcttctagtcttatgtgatatttgttgcttatccattaattttgttatttctgtaattgtctgtttgattttagatcattcattgaaggtcttcacatttattttgcttccttgtattgatagATCAAGAAGTCGATCACTGTGGGTTTGATTGGCTTGCCCAATGTTGGTAAGAGTAGTCTTATTAATAGCTTAAAGAGGTCCCATGTTGTCAATGTTGGTT

Basic information

species Glycine max
transcript GLYMA10G24060.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G24060.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G07050.1 (Arabidopsis thaliana), 3'ss of exon 5
gtagcagaactgttttggaacacaaataccccctgtaattcatgtagtttctcttctagtcttatgtgatatttgttgcttatccattaattttgttatttctgtaattgtctgtttgattttagatcattcattgaaggtcttcacatttattttgcttccttgta--ttgatagATCAAGAAGTCGATCACTGTGGGTTTGATTGGCTTGCCCAATGTTGGTAAGAGTAGTCTTATTAATAGCTTAAAGAGGTCCCATGTTGTCAATGTTGGTT
                                                                             | |  | |  || |||    | ||   | ||  |   || |  |  || |   ||||| |     ||||  |  || || |||  ||||   |||  || | || || || ||||| || ||| | |||||  |||| ||||| || ||||||||||||||||| ||  | |||||  | |||||||||||||||||| 
-----------------------------------------------------------------------------gttggttccatagtttaa--actttaatcatcctaccttagcatcaagttatatcattcag---tttcaattaaatcttcctttgttgttctttggcagTTAAAAAAATCTATCACAGTTGGTATTATTGGACTGCCTAATGTCGGCAAGAGTAGTCTTATTAACAGTCTGAAGAGAGCGCATGTTGTCAATGTTGGTG

upper sequence: GLYMA10G24060.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S144_97V6.1 (Physcomitrella patens), 3'ss of exon 5
gtagcagaactgttttggaacacaaataccccctgtaattcatgtagtttctcttctagtcttatgtgatatttgttgcttatccattaattttgttatttctgtaattgtctgttt-gattttagatcattcattgaaggtcttcacatttattttgcttccttgtattgatagATCAAGAAGTCGATCACTGTGGGTTTGATTGGCTTGCCCAATGTTGGTAAGAGTAGTCTTATTAATAGCTTAAAGAGGTCCCATGTTGTCAATGTTGGTT
                                           ||| | ||| || || | |||| || |  | |    || |   |  |   |    || ||| |||  | |||   || |  |  | ||  |||    ||  | |  ||   | ||  |  ||| ||    |||| || |   | ||||| || ||| |  |||| || || |||||||| ||||||||||||||||| || ||||||||  | |  || | || ||||||  
-------------------------------------------gtactgtctgttgtaattttatctgttcctaggatgttgtt--tcgagcgtaac-ttactgcaatgttgtgtacagactagaagtgatggattttttgtgcttattttgtgtatgacttgttgcatgtgcagATGAAAACAGCTATCACAGTTGGTGTAGTTGGGTTTCCAAATGTTGGGAAGAGTAGTCTTATTAACAGTTTAAAGAGAACACGAGTGGCCAGTGTTGGAG
















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|151399315|gb|EV269186.1|EV269186
EST:     GTGCTGATACTCTCATCAAATTGTTGAAAAATTACTCAAGAAGTCATGAG                         ATCAAGAAGTCGATCACTGTGGGTTTGATTGGCTTGCCCAATGTTGGTAAG
genomic: GTGCTGATACTCTCATCAAATTGTTGAAAAATTACTCAAGAAGTCATGAGgtagcagaac ... gtattgatagATCAAGAAGTCGATCACTGTGGGTTTGATTGGCTTGCCCAATGTTGGTAAG
EST: gi|16104768|gb|BI892508.1|BI892508
EST:     GTGCTGATACTCTCATCAAATTGTTGAAAAATTACTCAAGAAGTCATGAG                         ATCAAGAAGTCGATCACTGTGGGTTTGATTGGCTTGCCCAATGTTGGTAAG
genomic: GTGCTGATACTCTCATCAAATTGTTGAAAAATTACTCAAGAAGTCATGAGgtagcagaac ... gtattgatagATCAAGAAGTCGATCACTGTGGGTTTGATTGGCTTGCCCAATGTTGGTAAG
EST: gi|208282447|gb|GE075127.1|GE075127
EST:     GTGCTGATACTCTCATCAAATTGTTGAAAAATTACTCAAGAAGTCATGAG                         ATCAAGAAGTCGATCACTGTGGGTTTGATTGGCTTGCCCAATGTTGGTAAG
genomic: GTGCTGATACTCTCATCAAATTGTTGAAAAATTACTCAAGAAGTCATGAGgtagcagaac ... gtattgatagATCAAGAAGTCGATCACTGTGGGTTTGATTGGCTTGCCCAATGTTGGTAAG
EST: gi|193707599|gb|FK645897.1|FK645897
EST:     ACTCAAGAAGTCATGAG                         ATCAAGAAGTCGATCACTNTGGGTTTGATTGGCTTGCCCAATGTTGGTAAG
genomic: ACTCAAGAAGTCATGAGgtagcagaac ... gtattgatagATCAAGAAGTCGATCACTGTGGGTTTGATTGGCTTGCCCAATGTTGGTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttagatcattcattgaaggtcttcacatttattttgcttccttgtattgatagATCAAGAAGTCGATCACTGTGGGTTTGATTGGCTTGCCCAATGTTGGTAAGAGTAGTCTTATTAATAGCTTAAAGAGGTCCCATGTTGTCAATGTTGGTT
                                 ttttgcttccttgt  CT-rich tract
                       ttcacatttatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcagaactgttttggaacacaaataccccctgtaattcatgtagtttctcttctagtcttatgtgatatttgttgcttatccattaattttgttatttctgtaattgtctgtttgattttagatcattcattgaaggtcttcacatttattttgcttccttgtattgatagATCAAGAAGTCGATCACTGTGGGTTTGATTGGCTTGCCCAATGTTGGTAAGAGTAGTCTTATTAATAGCTTAAAGAGGTCCCATGTTGTCAATGTTGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG