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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAATATGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttctttcacttttgcttggttctcttttatctcttatagtttttatgcctagtgtctcctctcgcctgccttgtgatcctctcaaagatgatg...

Basic information

species Glycine max
transcript GLYMA14G38600.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G38600.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv06s0004g08180.t01 (Vitis vinifera), 5'ss of exon 9
ATGAATATGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaatt----ttctttcacttt-----tgcttggttctctttt----atctcttatagtttttatgcctagtgtctcctctcgcctgccttgtgatcctctcaaagatgatg
|||| ||||| || |||||||||||||| |||||||| || || |||||||||||||||||||||||||||||| | || ||| |||| | ||    | | |  ||  |     |||   |||   || |    ||||| ||   | |||||    ||    | || ||   ||   ||  ||   ||           
ATGAGTATGTAATATGCCTTGGGTGCAAAAGTCCGGACACAATTCTTTCAAAGGAGAATCGTCTCTTCTTTCTCAGATGCGAGCAGgtaatttatggtccctataccctctggttgcactgtttctttctctccatctcctaggttatttatattaaggaatttctttc---tgtactggtatttgctt----------

upper sequence: GLYMA14G38600.1 (Glycine max), 5'ss of exon 9
lower sequence: PP1S386_20V6.1 (Physcomitrella patens), 5'ss of exon 7
ATGAATATGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttc-----tttcacttttgcttggttctcttttatctcttatagtttttatgcctagtgtctcctctcgcc---------tgccttgtgatcctctcaaagatgatg---------------------------------
||||||| ||||| |||  ||| |||||||||||||| ||||| ||| | |||||||||||  | |||||||| || |||||| |||||| |  ||     |    || ||   |   | |  |||    ||  |  |  | |  |   |||  || |||||           || | |  |   |  |  |  || |||                                 
ATGAATACGTTATGTGCAATGGTTGCAAGAGTCCGGACACTATCCTTACGAAGGAGAATCGGTTGTTCTTTCTTCGTTGTGAGCAGgtgagtaatcactggtcctgctattctgtcagtgttgttttaggctactcctcatcactctctgtgcttcatctcgagaaaagaggatgacatcagtcgcatttcacaatcatggtgtaatgattcttctacctcgtttcttttcag

upper sequence: GLYMA14G38600.1 (Glycine max), 5'ss of exon 9
lower sequence: PP1S81_161V6.1 (Physcomitrella patens), 5'ss of exon 5
ATGAATATGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtga---attttct-ttcacttttgcttggttctcttt-tatctcttatagtttttatgcctagtgtctcctctcgcctgccttgt--gatcctctcaaagat-gatg---------------------------------------------------------------------------------------
|||| |||||||| |||  ||| ||||||||||| || ||||| ||||| ||||||||||| || |||||||| || |||||  |||| |   ||| ||| ||  | | ||  ||||||| ||  | ||  ||  |||  || |  ||  | |  |   |  || || | |   || | | | | | || | |                                                                                        
ATGAGTATGTTATGTGCAATGGTTGCAAGAGTCCAGACACTATCCTTTCCAAGGAGAATCGGCTGTTCTTTCTTCGTTGTGAACAGgttagcaattatctatttgcgtctgtgtggttcttttggtttcagtttcagtggttct--ctgctcttgcagttgaccagcttggcaggacctttttacaaattggttatttgcatcttcgaagaacgacgtcagtcttgtttcatggtggttgtgttgtgctgacgtagtctcttggtttttgtacgttgacag

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|193702000|gb|FK635974.1|FK635974
EST:     ATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCC
genomic: ATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttc ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCC
EST: gi|151398862|gb|EV268733.1|EV268733
EST:     ATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttc ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|298182522|gb|HO031257.1|HO031257
EST:     ATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCA
genomic: ATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttc ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCA
EST: gi|9983218|gb|BE657326.1|BE657326
EST:     ATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttc ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|192309791|gb|FG999920.1|FG999920
EST:     ATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTTTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCGAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttc ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|192296247|gb|FG992263.1|FG992263
EST:     ATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTTTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttc ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|193720942|gb|FK661206.1|FK661206
EST:     ATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATC
genomic: ATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttc ... ttgctttcagTGTGGATCAGGAAGATC
EST: gi|10235771|gb|BE804659.1|BE804659
EST:     ATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTCGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttc ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|192299974|gb|FG991820.1|FG991820
EST:     ATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttc ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
EST: gi|193383251|gb|FK348604.1|FK348604
EST:     ATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG                         TGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT
genomic: ATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttc ... ttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGAATATGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAGgtgaattttctttcacttttgcttggttctcttttatctcttatagtttttatgcctagtgtctcctctcgcctgccttgtgatcctctcaaagatgatg

- - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcctctc