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

...cttgtgccgagttaattgatcgaatttgttctctgaatcctcaatataacctcttatacccttttctttaaaatttacttagcgagtattttttttccagTGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAGTGAAGTTTTTGAAGGCATAAATGTCAATAGCAATGAGCGCTGTATAATC

Basic information

species Glycine max
transcript GLYMA11G05340.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g10940.1 (Oryza sativa), 3'ss of exon 1
cttgtgccgagttaattgatcgaatttgttctctgaatcctcaatataacctcttatacccttttctttaaaat---ttacttagcgagtattttttttc---cagTGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAGTGAAGTTTTTGAAGGCATAAATGTCAATAGCAATGAGCGCTGTATAATC
    |        | |||   |||| ||   |   ||     |||  |||   ||||   |||||  |||   |   ||||  |  || | || || | |   |||||| || |||||||| |||||||||||||| || ||||| |||||||| |||||||| || ||||| || ||||| |  |   |||||||||| || || 
---ttaattgacaacttgggggaatgtgaagtaaaaaaa---aatcaaactatttattttcttttagttatgctctgttaccaatggattgttcttctccattcagTGAGCAGGATGATTACGAGGTTGTGCGAAAGGTAGGCAGAGGGAAATACAGTGAAGTCTTCGAAGGAATTAATGTGACAAATGATGAGCGCTGCATCATT

upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g09320.t01 (Vitis vinifera), 3'ss of exon 1
cttgtgccgagttaattgatcgaatttgttctc-tgaatcctcaat-ataacctcttatacc--cttttctttaaaatttacttagcgagtattttttt---tccagTGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAGTGAAGTTTTTGAAGGCATAAATGTCAATAGCAATGAGCGCTGTATAATC
        ||  |  ||    ||  | ||  || ||  |  | ||| |||  || |   | |    ||  | | ||  ||| ||      |  ||||||   ||||| ||||||||||| |||||||| || |||||||| || ||||| ||||| ||||| ||||||||||| |||||||| |  | ||||||  | ||  || ||
-------agaagtttttttgagacatggtcatcatgcgtagtgaatgatattctttggcatcagtcttgttcttaaccttatttgtatttttcttttttatatccagGGATCAAGATGACTATGAGGTCGTTCGAAAAGTTGGAAGGGGAAAATACAGTGAGGTTTTTGAAGGTATAAATGTGACAAACAATGAAAGATGCGTAGTC

upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0129g00410.t01 (Vitis vinifera), 3'ss of exon 1
cttgtgccgagttaattgatcgaatttgttctctg-aatcctcaatata-acctcttatacccttttctttaaaatttacttagcgagtattttttttccagTGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAGTGAAGTTTTTGAAGGCATAAATGTCAATAGCAATGAGCGCTGTATAATC
 |  |      ||  |   |    || |     || |||  |||| ||     | ||  ||   ||| | |   |||  |||  |   | ||||| | |||||||||| ||||| ||||||||||| || ||||| || ||||| ||||| || || |||||||||||||||||||| |||||||| ||||| || ||||||
ttgataatagtttgttctctttgtttagggaattgtaattttcaaaatctgtatgttgaactaatttttctctcattctcttccct--tctttttctcccagTGATCAGGATGACTATGAGGTTGTTCGGAAAGTTGGAAGGGGAAAATACAGCGAGGTTTTTGAAGGCATAAATGTTAATAGCAACGAGCGATGCATAATC

upper sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 2
-----cttgt-gccgagttaattgatcgaatttgttctctgaatcctcaatataacctcttatacccttttctttaaaatttacttagcgagtattttttttccagTGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAGTGAAGTTTTTGAAGGCATAAATGTCAATAGCAATGAGCGCTGTATAATC
     ||| | |  |||  |  |      ||| | | | ||  ||  |||   ||    || || |  |   | |  || | |  |    |    |   ||||||| || ||||| ||||| ||||| ||||| || |||||  | |||||||| ||||| |||||||||||  | || | |   |  | |||||| ||  | || 
gtattcttattgtagagcgacctttcattattgggtatatg--tcagcaagtgaagtagttgtatcagtaggtgttgaactgatctgttca----tcgatttccagGGACCAAGACGATTACGAGGTAGTGCGTAAGGTGGGGCGAGGGAAATACAGTGAGGTTTTTGAAGGTGTCAACGCCGTGAATAGTGAGCGTTGCGTTATG

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|193612756|gb|FK563137.1|FK563137
EST:     CTTCGCCCTAAAGAGTATTGGGATTACGAGTCTCTCACCCTTCAATGGGG                         TGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAG
genomic: CTTCGCCCTAAAGAGTATTGGGATTACGAGTCTCTCACCCTTCAATGGGGgtaatgttcc ... ttttttccagTGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAG
EST: gi|213592666|gb|DB955810.1|DB955810
EST:     CTTCGCCCTAAAGAGTATTGGGATTACGAGTCTCTCACCCTTCAATGGGG                         TGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAG
genomic: CTTCGCCCTAAAGAGTATTGGGATTACGAGTCTCTCACCCTTCAATGGGGgtaatgttcc ... ttttttccagTGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAG
EST: gi|5760973|gb|AI966336.1|AI966336
EST:     CTTCGCCCTAAAGAGTATTGGGATTACGAGTCTCTCACCCTTCAATGGGG                         TGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAG
genomic: CTTCGCCCTAAAGAGTATTGGGATTACGAGTCTCTCACCCTTCAATGGGGgtaatgttcc ... ttttttccagTGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAG
EST: gi|207720772|gb|GD701815.1|GD701815
EST:     CTTCGCCCTAAAGAGTATTGGGATTACGAGTCTCTCACCCTTCA-TGGG-                         TGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAA
genomic: CTTCGCCCTAAAGAGTATTGGGATTACGAGTCTCTCACCCTTCAATGGGGgtaatgttcc ... ttttttccagTGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAA
EST: gi|192297038|gb|FG990324.1|FG990324
EST:     CTTCGCCCTAAAGAGTATTGGGATTACGAGTCTCTCACCCTTCAATGGGG                         TGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAGTATAG
genomic: CTTCGCCCTAAAGAGTATTGGGATTACGAGTCTCTCACCCTTCAATGGGGgtaatgttcc ... ttttttccagTGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAG
EST: gi|192334448|gb|FK025569.1|FK025569
EST:     CTTCGCCCTAAAGAGTATTGGGATTACGAGTCTCTCACCCTTCAATGGGG                         TGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAG
genomic: CTTCGCCCTAAAGAGTATTGGGATTACGAGTCTCTCACCCTTCAATGGGGgtaatgttcc ... ttttttccagTGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAG
EST: gi|213592872|gb|DB969838.1|DB969838
EST:     CTTCGCCCTAAAGAGTATTGGGATTACGAGTCTCTCACCCTTCAATGGGG                         TGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAG
genomic: CTTCGCCCTAAAGAGTATTGGGATTACGAGTCTCTCACCCTTCAATGGGGgtaatgttcc ... ttttttccagTGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAG
EST: gi|5752761|gb|AI960048.1|AI960048
EST:     CTTCGCCCTAAAGAGTATTGGGATTACGAGTCTCTCACCCTTCAATGGGG                         TGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAG
genomic: CTTCGCCCTAAAGAGTATTGGGATTACGAGTCTCTCACCCTTCAATGGGGgtaatgttcc ... ttttttccagTGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataacctcttatacccttttctttaaaatttacttagcgagtattttttttccagTGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAGTGAAGTTTTTGAAGGCATAAATGTCAATAGCAATGAGCGCTGTATAATC
 atataac  putative branch site (score: 3)
                                         tattttttttcc  putative PPT
                ttttctttaaaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgtgccgagttaattgatcgaatttgttctctgaatcctcaatataacctcttatacccttttctttaaaatttacttagcgagtattttttttccagTGATCAAGATGATTATGAGGTTGTGCGAAAAGTGGGCAGGGGGAAATATAGTGAAGTTTTTGAAGGCATAAATGTCAATAGCAATGAGCGCTGTATAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
cttgtgc
- - - - - - - - - - - - - - - ctctgaa