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'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgccttgagatatttttatgtcaaactttgtacttttgcattcacaatgaaagagagaagaattcacatttatttttgtacaaacttaaggctatgttaacttgaaactctgaagtaaatacttttctttgctatacttgacacttagatattttcttccagTCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTGCATGGGGTTGATTTGGAGCCTGCCATTAACAATGCTGTTTTTCCTGGTC

Basic information

species Glycine max
transcript GLYMA13G29410.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G29410.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0008g00770.t01 (Vitis vinifera), 3'ss of exon 6
gtttgccttgagatatttttatgtcaaactttgtacttttgcattcacaatgaaagagagaagaattcacatttatttttgtacaaacttaaggc---tatgttaacttgaaactctgaagtaaatacttttctttgctatacttgac--acttagatattttcttccagTCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTGCATGGGGTTGATTTGGAGCCTGCCATTAACAATGCTGTTTTTCCTGGTC
                                                                       | ||||| || ||   | | |  |   |  ||   | |  |  | |  | |  | |  ||    ||||  |||| |   |||| |||  ||   |||||||| |  ||||||| |||||||| ||||| ||||||||||||||| |||| |  || ||||| || ||  ||||||| ||||||||||||||||| ||| 
---------------------------------------------------------------------ggtatatttgtgaacttgccttatacatgtgcgtatgcatatatttttccattgca-atcttcacatgcttgacttaattaacttggatgattctatccagTCTCTTAGAGGTCCTAGAGGTGGCATGATCTTCTTCAAGAAAGATTCTGTTCTGGGAGTTGACTTAGAATCTGCCATCAACAATGCTGTTTTTCCAGGTT
















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|58018378|gb|CX705120.1|CX705120
EST:     TTCTAATCCCTTTGAGTATTGTGATATTGTGA-CACCCACACCCCACAAG                         TCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTG
genomic: TTCTAATCCCTTTGAGTATTGTGATATTGTGACCA-CCACAACCCACAAGgtttgccttg ... tttcttccagTCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTG
EST: gi|254333982|gb|GR848900.1|GR848900
EST:     CCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAG                         TCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTG
genomic: CCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAGgtttgccttg ... tttcttccagTCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTG
EST: gi|298170634|gb|HO019258.1|HO019258
EST:     TTTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAG                         TCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTG
genomic: TTTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAGgtttgccttg ... tttcttccagTCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTG
EST: gi|18039880|gb|BM308174.1|BM308174
EST:     TTTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAG                         TCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAG
genomic: TTTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAGgtttgccttg ... tttcttccagTCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAG
EST: gi|7591183|gb|AW706921.1|AW706921
EST:     TTTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAG                         TCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTG
genomic: TTTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAGgtttgccttg ... tttcttccagTCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTG
EST: gi|58023902|gb|CX710643.1|CX710643
EST:     TTTCTAATCCCTCTGAGTATTGTGATATTGTGACCACCACAACCCACAAG                         TCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTG
genomic: TTTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAGgtttgccttg ... tttcttccagTCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTG
EST: gi|254335574|gb|GR847102.1|GR847102
EST:     TTTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAG                         TCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTG
genomic: TTTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAGgtttgccttg ... tttcttccagTCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTG
EST: gi|18735429|gb|BM528760.1|BM528760
EST:     TTTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAG                         TCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTG
genomic: TTTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAGgtttgccttg ... tttcttccagTCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTG
EST: gi|298195468|gb|HO043859.1|HO043859
EST:     TTTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAG                         TCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTG
genomic: TTTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAGgtttgccttg ... tttcttccagTCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTG
EST: gi|254346462|gb|GR856184.1|GR856184
EST:     TTTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAG                         TCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTG
genomic: TTTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAGgtttgccttg ... tttcttccagTCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTG
EST: gi|298190143|gb|HO032264.1|HO032264
EST:     TTTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAG                         TCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCA
genomic: TTTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAGgtttgccttg ... tttcttccagTCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCA
EST: gi|5127019|gb|AI748755.1|AI748755
EST:     TTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCCAACAAG                         TCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGT
genomic: TTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCC-ACAAGgtttgccttg ... tttcttccagTCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGT
EST: gi|298186489|gb|HO037122.1|HO037122
EST:     TTTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAG                         TCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTG
genomic: TTTCTAATCCCTTTGAGTATTGTGATATTGTGACCACCACAACCCACAAGgtttgccttg ... tttcttccagTCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgaagtaaatacttttctttgctatacttgacacttagatattttcttccagTCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTGCATGGGGTTGATTTGGAGCCTGCCATTAACAATGCTGTTTTTCCTGGTC
                            acttgac  putative branch site (score: 4)
                                          tattttcttcc  putative PPT
        taaatacttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgccttgagatatttttatgtcaaactttgtacttttgcattcacaatgaaagagagaagaattcacatttatttttgtacaaacttaaggctatgttaacttgaaactctgaagtaaatacttttctttgctatacttgacacttagatattttcttccagTCTTTACGAGGTCCAAGAGGTGGTATGATATTCTTCAAGAAAGATACTGTGCATGGGGTTGATTTGGAGCCTGCCATTAACAATGCTGTTTTTCCTGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT