Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGACTTTGTTGATCGGGGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtttccatgtatgcttgcatcatctgccttaacttgttcacgtgactttgagttatactatggtcccttcacaattatatcttgacgtttaag...

Basic information

species Glycine max
transcript GLYMA0048S00290.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA0048S00290.2 (Glycine max), 5'ss of exon 3
lower sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 3
GGAGACTTTGTTGATCGGGGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtttccatgtatgct-tgcatcatctgccttaacttgttcacgtgactttgagttatactatggtcccttcacaattatatcttgacgtttaag-
|| || || |||||| | |||||||| ||||||||||| |||||||| ||||| ||||| ||||| ||||| | | ||||| |  |   | ||| | || |   | |     |   | |   |  |  | | ||| |    | |       |  |   ||   |||||| 
GGGGATTTCGTTGATAGAGGTTACAACAGTCTTGAAGTTTTCACCATTCTTTTGCTTCTTAAAGCAAGgtaagat-tttccgtagaaattgtgcgttatatatgtca-tggatcgtcatccttccgtttcacactgtatatcatagttctcttgagaatgctctttaagc

upper sequence: GLYMA0048S00290.2 (Glycine max), 5'ss of exon 3
lower sequence: AT3G19980.1 (Arabidopsis thaliana), 5'ss of exon 3
GGAGACTTTGTTGATCGGGGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtttccatgtatgcttgcatcatctgccttaacttgttcacgtgactttgagttatactatggtcccttcacaattatatcttgacgtttaag--
|| ||||| || ||| | |||||||| || |||||||| ||||| || ||||||||||| ||||||||||| | || |   |  | | || |      |||   | | |   ||   || |||| |||| |  | || | | | |  |||   | |||   |||||    
GGGGACTTCGTGGATAGAGGTTACAACAGCCTTGAAGTCTTCACTATTCTTTTACTTCTTAAAGCTAGgtaaggtgctcataaatgttctggagattcctgttatcattgaatc-tttgcctttaagtttttttttg-ttcgtgcttaatacgaacttattgtttattaa

upper sequence: GLYMA0048S00290.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 5'ss of exon 3
GGAGACTTTGTTGATCGGGGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtttccatgtatgcttgcatcatctgccttaacttgttcacgtgactttgagttatactatggtcccttcacaattatatcttgacgtttaag--------
|| || ||||||||||| || |||||||| |||||||| ||||| |||||||| ||||| ||||| ||||||||  ||| |||| | | ||   |    ||||   ||||| |  | ||  ||||   |  | | | |    || || ||  || |||||  | |           
GGTGATTTTGTTGATCGAGGGTACAATAGCCTTGAAGTCTTCACAATCCTTTTGCTTCTGAAAGCCAGgtatgtcttttacatgcaagttttactagcttgcc---acttggt-gcctgcatttgg--tggattgttgcttgtttactatc-ta-cttgatatctgcagtctgttt

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|193398959|gb|FK363859.1|FK363859
EST:     GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAG                         ATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGA
genomic: GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtt ... aacttcatagATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGA
EST: gi|209728247|gb|BW651682.1|BW651682
EST:     GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAG                         ATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
genomic: GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtt ... aacttcatagATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
EST: gi|298172509|gb|HO019549.1|HO019549
EST:     GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAG                         ATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
genomic: GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtt ... aacttcatagATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
EST: gi|151410851|gb|EV280666.1|EV280666
EST:     GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAG                         ATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
genomic: GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtt ... aacttcatagATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
EST: gi|213603385|gb|DB966616.1|DB966616
EST:     GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAG                         ATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
genomic: GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtt ... aacttcatagATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
EST: gi|192323250|gb|FK018961.1|FK018961
EST:     GGTTACAATAGTCTTGAAGTATTCACCATTCTTTTACTTCTAAAAGCTAG                         ATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
genomic: GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtt ... aacttcatagATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
EST: gi|298178347|gb|HO024082.1|HO024082
EST:     GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAG                         ATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
genomic: GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtt ... aacttcatagATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
EST: gi|193578884|gb|FK536690.1|FK536690
EST:     GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAG                         ATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
genomic: GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtt ... aacttcatagATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
EST: gi|192296025|gb|FG989419.1|FG989419
EST:     GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAG                         ATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
genomic: GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtt ... aacttcatagATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
EST: gi|298187406|gb|HO034555.1|HO034555
EST:     GATTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAG                         ATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
genomic: GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtt ... aacttcatagATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
EST: gi|208275394|gb|GE079386.1|GE079386
EST:     GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAG                         ATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAA
genomic: GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtt ... aacttcatagATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAA
EST: gi|193307179|gb|FK271075.1|FK271075
EST:     GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAG                         ATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
genomic: GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtt ... aacttcatagATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
EST: gi|298190555|gb|HO032676.1|HO032676
EST:     GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAG                         ATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
genomic: GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtt ... aacttcatagATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
EST: gi|298188878|gb|HO035571.1|HO035571
EST:     GGTTACAATAGTCTTGAAGTATTCACCATCCCTTTACTTCTAAAAGCTAG                         ATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTGGACAACT
genomic: GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtt ... aacttcatagATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
EST: gi|254340656|gb|GR854384.1|GR854384
EST:     GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAG                         ATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
genomic: GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtt ... aacttcatagATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
EST: gi|308098123|gb|HO761294.1|HO761294
EST:     GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAG                         ATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT
genomic: GGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtt ... aacttcatagATACCCAGCTAATATTACCCTTCTACGTGGAAACCATGAAAGTAGACAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGACTTTGTTGATCGGGGTTACAATAGTCTTGAAGTATTCACCATCCTTTTACTTCTAAAAGCTAGgtatgttgtttccatgtatgcttgcatcatctgccttaacttgttcacgtgactttgagttatactatggtcccttcacaattatatcttgacgtttaag

- - - - - - - - - - - - - - -  TTGAAG