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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcattcttcctctattatattatctgtgctctagtacatacattaccctatcgctattattttctttatttctatttgcttatttatggatacagATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGTTGTGAACAGGCTGACAACAGCTGTTGAACTACCATCTCAATTCATTCAC

Basic information

species Glycine max
transcript GLYMA02G00750.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G00750.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os11g13694.1 (Oryza sativa), 3'ss of exon 9
gtatgcattcttcctctattatattatctgt-gctctagtacatacattaccctatcgctattattttct--ttat----ttctatttgcttatttatggat---acagATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGTTGTGAACAGGCTGACAACAGCTGTTGAACTACCATCTCAATTCATTCAC
||||| |   |  |  | |  | |  ||| | | | |  ||  || |||||    |  ||||  || |||  | |     |  || |  | |   | |   |   |||| ||||||    | |||||  | ||||| ||||| |||||||||||||||||||| |||||||| || ||||| || || |||||| |   ||||||||| 
gtatgtagattagccttgtcgtttattctattgttttcttattta-attactaatttactatgtttctctactcacaacgtcttactcacatgcctttttctttgacagTTACTTTGATATTCTTGTGCACATGGAAATGAGCCTACATTCAATGGAAGTTGTAAACAGGCTCACTACAGCAGTAGATCTACCACCAGGATTCATTCAT

upper sequence: GLYMA02G00750.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os12g09610.1 (Oryza sativa), 3'ss of exon 8
gtatgcattcttcctctattatattatctgtgctctagtacatacattaccctatcgctattattttctttatttctatt-tgcttatttatggatacagATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGTTGTGAACAGGCTGACAACAGCTGTTGAACTACCATCTCAATTCATTCAC
          |   ||| || | || ||| ||||  |||  |||   | | | | | || || |||  | |||||  ||| ||    |||     | ||| |||||    || |||||  ||||||| ||||| || ||||| ||||||||||| |||||||| || || ||||| ||||| ||  |  | ||  | || 
---------gtatgtctgtt-tcttttctttgct--agtcaatatgat-caccaacacttttttttaatatattttaattgtgacccttttctttttcagTTACTTAGATGTTCTTGTGCATATGGAGATGAGCCTGCATTCTATGGAAGTTGTAAACAGGCTTACTACTGCTGTAGAACTCCCGACAGAGTTTGTCCAT

upper sequence: GLYMA02G00750.2 (Glycine max), 3'ss of exon 9
lower sequence: AT5G18420.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgcattcttcctctattatattatctgtgctctagtacatacattaccctatcgctattattttctttatttctatttgcttatttatggatacagATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGTTGTGAACAGGCTGACAACAGCTGTTGAACTACCATCTCAATTCATTCAC
           |     || |  ||||  ||  || |  |  ||| ||   | |    ||| | |||     |    || |    ||   |   | ||| || | |  ||  || |  |||||||||||||| || || ||||||||||||||||| ||||| ||||| || |||||||| ||     | ||||| |  
----------gtaagtcatcaccttattggt--tccaccatttactttcgaccaaaattataacttttaaagtgggaatctaagaatgcttc--ttcagCTATTATGAAGCTCTAGGAAATATGGACATGAGCCTGCACTCAATGGAAGTTGTGAATAGGCTCACAACTGCAGTTGAACTTCCCAAGGACTTCATACGG

upper sequence: GLYMA02G00750.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0130g00310.t01 (Vitis vinifera), 3'ss of exon 9
-------------------gtatgcatt-cttcctctattat----attatctgtgctctagtacat--acattaccctatcgctattattttctttatttctatttgcttatttatggatacagATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGTTGTGAACAGGCTGACAACAGCTGTTGAACTACCATCTCAATTCATTCAC
                    | | | || ||| || |||||     || ||  |    | || || |  |  ||   || |   | || | |  |||   | |  || ||| ||| |  ||  || ||||| | ||| ||||||| |||||||||||| ||||||||||||||||| || |||||||| || ||||| |||||||| ||  |  ||||  | |||
gtatgtttttgtcatgttgatttacctttcttgctttattactgaaatgataagcatcccagcactttaatctttttcttttttttttctgtatttttgctttcctttcttttttgtcaatttagGTACTTCAGAGTTCTTGTCAGTATGGACATGAGCCTACATTCAATGGAAGTCGTTAACAGGCTTACTACAGCGGTTGAACTTCCCACCGAATTTGTACAC

upper sequence: GLYMA02G00750.2 (Glycine max), 3'ss of exon 9
lower sequence: PP1S166_16V6.2 (Physcomitrella patens), 3'ss of exon 9
gtatgcattcttcctctattatattatctgtgctctagtacatacattaccctatcgctattattttctt----tatttctatttgcttatttatggatacagATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGTTGTGAACAGGCTGACAACAGCTGTTGAACTACCATCTCAATTCATTCAC
 |||  | | ||  ||| | | ||||           ||  ||    | |  | |  |  ||||||| ||    |  ||||| | |  |     ||  | ||| || |||| | | || ||||||||||| || ||||| |||||||||||||| |||||| | || |||||| |||| || || ||  || | ||  |||| 
-tattgacttttt-tctgt-agattaagcagatagatgtgaatggtctcctttcttacctttattttgttatggttattctaatagaattgggttgcttgcagTTATTTTAAAATGCTGGTCAATATGGATATTAGTCTTCATTCAATGGAAGTAGTGAACCGCCTAACAACAACTGTGGATCTTCCCACTGAGTTTGTTCAT

upper sequence: GLYMA02G00750.2 (Glycine max), 3'ss of exon 9
lower sequence: PP1S82_30V6.1 (Physcomitrella patens), 3'ss of exon 9
gtatgcattcttcctctattatattatctgtgc--tctagtacatacattaccctatcgctatt-attttctttatttctatttgcttatttatggatacagATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGTTGTGAACAGGCTGACAACAGCTGTTGAACTACCATCTCAATTCATTCAC
   |    | ||     |  || |    ||     | |  |    | |||  ||| || || |  || |    |  ||||  | |       |    | ||| || |||| | | |||||||||||||| || |||||||| || ||||||||||||||  | || ||||||||||| || || ||  || | ||  | || 
--ttatgatgttgaatgaacatttgcgttgcatcgtttcttgtggatattgtcctctccctttccatgtatgatcattctgatagaagtgagacttttgcagCTATTTTAAAATGCTTGTCAATATGGATATTAGTCTACACTCGATGGAAGTTGTGAATCGCCTTACAACAGCTGTGGATCTTCCTACTGAGTTTGTGCAT

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|193718862|gb|FK655240.1|FK655240
EST:     TTGATAAATTCTCCAGAAANAGCAGA                         ATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGT
genomic: TTGATAAATTCTCCAGAAATAGCAGAgtatgcattc ... atggatacagATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGT
EST: gi|13562521|gb|BG550741.1|BG550741
EST:     ATTGCAGTTGACGTTCTCACTAAGTTGATAAATTCTCCAGAAATAGCAGA                         ATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGT
genomic: ATTGCAGTTGACGTTCTCACTAAGTTGATAAATTCTCCAGAAATAGCAGAgtatgcattc ... atggatacagATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGT
EST: gi|209723773|gb|BW665682.1|BW665682
EST:     ATTGCAGTTGACGTTCTCACTAAGTTGATAAATTCTCCAGAAATAGCAGA                         ATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGT
genomic: ATTGCAGTTGACGTTCTCACTAAGTTGATAAATTCTCCAGAAATAGCAGAgtatgcattc ... atggatacagATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGT
EST: gi|193568019|gb|FK524356.1|FK524356
EST:     ATTGCAGTTGACGTTCTCACTAAGTTGATAAATTCTCCAGAAATAGCAGA                         ATACTTTACAGTACTTGTCAATACGGACATGAGTCTACATTCAATGGAAGT
genomic: ATTGCAGTTGACGTTCTCACTAAGTTGATAAATTCTCCAGAAATAGCAGAgtatgcattc ... atggatacagATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattaccctatcgctattattttctttatttctatttgcttatttatggatacagATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGTTGTGAACAGGCTGACAACAGCTGTTGAACTACCATCTCAATTCATTCAC
              tattattttctttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcattcttcctctattatattatctgtgctctagtacatacattaccctatcgctattattttctttatttctatttgcttatttatggatacagATACTTTACAGTACTTGTCAATATGGACATGAGTCTACATTCAATGGAAGTTGTGAACAGGCTGACAACAGCTGTTGAACTACCATCTCAATTCATTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT