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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACAAACAAACATCTTTTACCTTAAACAACAATGGCCGATGCCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAGgtatcaatttcccatgggatcataggttttcttttaccgattttgtcgatgactaatcttggcggcaaattaagtctttgtttaagggatctgagtccag...

Basic information

species Glycine max
transcript GLYMA19G32990.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G32990.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv08s0007g06520.t01 (Vitis vinifera), 5'ss of exon 1
CAACAAACAAACATCTTTTACCTTAAACAACAATGGCCGATGCCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAGgtatcaatttcccatgggatcataggttttcttttaccgattttgtcgatgactaatcttggcggcaaattaagtctttgtttaagggatctgagtccag-------
                            |  |||||| ||  | ||||||||||| || || || |||||||||||||||||||||||||||||||  |||       | |||  |  | || ||| |  | || ||    ||| |    |||| |   |   |  |  || |||    |||        |        
--------------------------TAAGGAATGGCAGAAACTGAGGATATTCAGCCTCTTGTCTGCGATAATGGAACCGGAATGGTCAAGgtattgattc-----agaatccaaaatgttgtttga--gtttgtgggattgattggatttggagaatacccagttgcttatttctttgattctttctgaaatttcag

upper sequence: GLYMA19G32990.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S198_154V6.4 (Physcomitrella patens), 5'ss of exon 1
---CAACAAACAAACATCTTT-----TACCTTAAACAACAATGGCCGATGCCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAGgtatcaatttcccatgggatcataggttttcttttaccgattttgtcgatgactaatcttggcggcaaattaagtctttgtttaagggatctgagtccag------
   |        |||  || |      |   |||| ||    ||  || |  |||||| | || ||  | || |||||||||||| ||||||||||||||||||  | |  | |  |  |  ||      ||   ||  |  ||  || |  |   |  | |     |   |  |  |   |   || || ||| ||||       
GCACTGTTTTTGAACTCCTGTAGGATCATTCTAAAAAATGGCGGGGGAAGGTGAGGATGTCCAGCCTTTGGTGTGCGATAATGGATCCGGAATGGTCAAGgtatgcactgtctactgtttttta----ccctcacacgaacattcacgtt--ccccttcttgttatgatacacattgtaactcctggaatttgactccaaattagg

upper sequence: GLYMA19G32990.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S198_154V6.3 (Physcomitrella patens), 5'ss of exon 2
CAACAAACAAACATCTTTTACCTTAAACAACAATGGCCGATGCCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAGgtatcaatttcccatgggatcataggttttcttttaccgattttgtcgatgactaatcttggcggcaaattaagtctttgtttaagggatctgagtccag------
                 | |   |||| ||    ||  || |  |||||| | || ||  | || |||||||||||| ||||||||||||||||||  | |  | |  |  |  ||      ||   ||  |  ||  || |  |   |  | |     |   |  |  |   |   || || ||| ||||       
---------------GATCATTCTAAAAAATGGCGGGGGAAGGTGAGGATGTCCAGCCTTTGGTGTGCGATAATGGATCCGGAATGGTCAAGgtatgcactgtctactgtttttta----ccctcacacgaacattcacgtt--ccccttcttgttatgatacacattgtaactcctggaatttgactccaaattagg

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|151396191|gb|EV266068.1|EV266068
EST:     CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAG                         GCTGGTTTTGCTGGAGATGATGCACCGAGGGCTGTGTTCCCTAGCATTGTG
genomic: CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAGgtatcaattt ... tgtgatatagGCTGGTTTTGCTGGAGATGATGCACCGAGGGCTGTGTTCCCTAGCATTGTG
EST: gi|41146304|gb|CK606515.1|CK606515
EST:     CGAGGATATTCAACCCCTCGTTTGCGATAAT-GAACCGGGAATGGTCAAG                         GCTGGTTTTGCTGGAGATGATGCACCGAGGGCTGTGTTCCCTAGCATTGTG
genomic: CGAGGATATTCAACCCCTCGTTTGCGATAATGGAACC-GGAATGGTCAAGgtatcaattt ... tgtgatatagGCTGGTTTTGCTGGAGATGATGCACCGAGGGCTGTGTTCCCTAGCATTGTG
EST: gi|192329006|gb|FK019705.1|FK019705
EST:     CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAG                         GCTGGTTTTGCTGGAGATGATGCACCGAGGGCCGTGTTCCCTAGCATTGTG
genomic: CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAGgtatcaattt ... tgtgatatagGCTGGTTTTGCTGGAGATGATGCACCGAGGGCTGTGTTCCCTAGCATTGTG
EST: gi|193312823|gb|FK282320.1|FK282320
EST:     CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAG                         GCTGGTTTTGCTGGAGATGATGCACCGAGGGCTGTGTTCCCTAGCATTGTG
genomic: CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAGgtatcaattt ... tgtgatatagGCTGGTTTTGCTGGAGATGATGCACCGAGGGCTGTGTTCCCTAGCATTGTG
EST: gi|193421389|gb|FK389590.1|FK389590
EST:     CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAG                         GCTGGTTTTGCTGGAGATGATGCACCGAGGGCTGTGTTCCCTAGCATTGTG
genomic: CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAGgtatcaattt ... tgtgatatagGCTGGTTTTGCTGGAGATGATGCACCGAGGGCTGTGTTCCCTAGCATTGTG
EST: gi|193663559|gb|FK604585.1|FK604585
EST:     CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAG                         GCTGGTTTTGCTGGAGATGATGCACCGAGGGCTGTGTTCCCTAGCATTGTG
genomic: CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAGgtatcaattt ... tgtgatatagGCTGGTTTTGCTGGAGATGATGCACCGAGGGCTGTGTTCCCTAGCATTGTG
EST: gi|193310736|gb|FK274632.1|FK274632
EST:     CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAG                         GCTGGTTTTGCTGGAGATGATGCACCGAGGGCTGTGTTCCCTAGCATTGTG
genomic: CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAGgtatcaattt ... tgtgatatagGCTGGTTTTGCTGGAGATGATGCACCGAGGGCTGTGTTCCCTAGCATTGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACAAACAAACATCTTTTACCTTAAACAACAATGGCCGATGCCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAGgtatcaatttcccatgggatcataggttttcttttaccgattttgtcgatgactaatcttggcggcaaattaagtctttgtttaagggatctgagtccag

- - - - - - - - - - - - - - - - - - - - - - GAGGAT