Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattactctcccttcagtagaattatttttaatatatcatcgatctctttatttttcttattagcaattaggcattatcaatgacgtgcattgttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCCATTCCAAACCAGCAGATAATTGGCAAGTTGGAAAGAGCCCTTGGAGCTA

Basic information

species Glycine max
transcript GLYMA06G42900.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G42900.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g27850.2 (Oryza sativa), 3'ss of exon 3
gtattactctcccttcagtagaattattttt-aatatatcatcgatctctttatttttcttattagcaattaggcat-tatcaa--------tgacgtgcattgttacttgca----gCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCCATTCCAAACCAGCAGATAATTGGCAAGTTGGAAAGAGCCCTTGGAGCTA
        | |  | ||     |  |||||  ||| |   | || |   || | ||||   |    || |    |||  |  ||        | |  |    |||   |||||    | |||||||||||||||| || ||||||||||||||||||||||| || || ||||| ||||||||||| || || ||| | ||||| || |||||| | |
-----gtgccctgtccaaccatacaattttagaatttcctagcgttacattaacttttaccacagccactcgcacatacactaaccttcaactaaaatatggtgtgttttgcaaacagATGATCAATGAGAAGCCCCAGGTGATCCAGGAGTACGAGTCAGGTAAAGCTATTCCGAACCAGCAGATCATCGGGAAGCTTGAAAGGGCTCTTGGAACAA

upper sequence: GLYMA06G42900.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G101480_T01 (Zea mays), 3'ss of exon 3
-gtattactctcccttcagtagaattatttttaatatatcatcgatctctttatttttcttattagcaattaggcattatcaatgacgtgcattgttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCCATTCCAAACCAGCAGATAATTGGCAAGTTGGAAAGAGCCCTTGGAGCTA
    |   |     |   |||| | |    || |||  |      |  ||| ||  ||    || ||   |       || |  ||  ||   ||||  |||||| |||||||||||||||| || |||||||||||||| |||||||| ||||| ||||| ||||||||||| ||||||||| | || || ||||| ||| | |
aaagtctatgctgttgttgtagtagttccattgatagctgggaagtagcttgatccttg--gttggcctctttatgagatgag-gatatgg--tgttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCAATTCCCAACCAGCAGATCATTGGCAAGCTCGAGAGGGCCCTGGGAACGA

upper sequence: GLYMA06G42900.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G800112_T02 (Zea mays), 3'ss of exon 3
gta-ttact--ctcccttcagtagaattatttttaatatatc--atcgatctctttatttttcttattagcaattaggcattatcaatgacgtgcattgttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCCATTCCAAACCAGCAGATAATTGGCAAGTTGGAAAGAGCCCTTGGAGCTA
||| ||  |     | ||  ||   |  | ||  |  ||| |  |    |  ||| ||  || || |   | ||||  ||      | || |||   ||||  ||| || |||| ||||||||||| || ||||| |||||||| || ||||| ||||| || || ||||||||||| ||| ||||| | || || ||||| ||| | |
gtacttggtggtatcattgggtttcagaacttcaaccatagctgagaagtagcttgatccttgtt-tggcctattaatca--gatgaggatgtgg--tgtttattgtagATGATAAATGAGAAGCCACAGGTGATTCAGGAGTATGAATCAGGCAAGGCAATCCCCAACCAGCAGATCATTAGCAAGCTCGAGAGGGCCCTGGGAACCA

upper sequence: GLYMA06G42900.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G800112_T01 (Zea mays), 3'ss of exon 3
gta-ttact--ctcccttcagtagaattatttttaatatatc--atcgatctctttatttttcttattagcaattaggcattatcaatgacgtgcattgttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCCATTCCAAACCAGCAGATAATTGGCAAGTTGGAAAGAGCCCTTGGAGCTA
||| ||  |     | ||  ||   |  | ||  |  ||| |  |    |  ||| ||  || || |   | ||||  ||      | || |||   ||||  ||| || |||| ||||||||||| || ||||| |||||||| || ||||| ||||| || || ||||||||||| ||| |||                        
gtacttggtggtatcattgggtttcagaacttcaaccatagctgagaagtagcttgatccttgtt-tggcctattaatca--gATGAGGATGTGG--TGTTTATTGTAGATGATAAATGAGAAGCCACAGGTGATTCAGGAGTATGAATCAGGCAAGGCAATCCCCAACCAGCAGATCATTAGCA------------------------

upper sequence: GLYMA06G42900.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G58680.1 (Arabidopsis thaliana), 3'ss of exon 3
gtattactctcccttcagtagaattatttttaatatatcatcgatctctttatt-tttcttattagcaattaggcattatcaatgacgtgcattgttact-tgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCCATTCCAAACCAGCAGATAATTGGCAAGTTGGAAAGAGCCCTTGGAGCTA
                | |   ||| || |   ||| |      |   |||| | | | |  | || ||||       ||  ||    ||  || | | | || ||||||||||||||||||| ||||||||||| || |||||||| || || || ||||| || || |||||  ||   ||| |||| || || ||||| ||||
--------------gtactttcatttttctctgtatctttctctttcttttactgtctttcgtcagtaattga-----attcattgtatgggttttgattctgtagCTGATCAATGAGAAGCCACAAGTGATCCAAGAATACGAGTCTGGGAAAGCAATTCCGAATCAACAGATCCTTTCAAAGCTGGAGAGGGCACTTGGTGCTA

upper sequence: GLYMA06G42900.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0028g02020.t01 (Vitis vinifera), 3'ss of exon 3
gtattactctcccttcagtagaattatttttaatatatcatcgatctctttatttttcttattagcaattaggcattatcaatgacgtgcattgttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCCATTCCAAACCAGCAGATAATTGGCAAGTTGGAAAGAGCCCTTGGAGCTA
                 ||| |  | | |    ||    ||   | || |  |       | | | |  |||   |    |||||  || |   ||  |||||| ||||||||||||| |||||| | || || ||||| || || || || || |||||||| || |||||||||| ||||||||| || || |||||||  |
-----------------gtaaatctttctcccttacccaatatgtatcctc-tccactgcactcgta--tagaactgcataatgaaatggagc-ttgtttgcagATGATCAATGAGAAACCTCAAATAATTCAAGAGTATGAATCTGGTAAAGCTATTCCAAATCAACAGATAATTGTCAAGTTGGAGAGGGCTCTTGGAGTGA

upper sequence: GLYMA06G42900.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0014g01260.t01 (Vitis vinifera), 3'ss of exon 3
gtattactctcccttcagtagaattatttttaatatatcatcgatctctttatttttcttattagcaattaggcattatcaatgacgtgcattgttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCCATTCCAAACCAGCAGATAATTGGCAAGTTGGAAAGAGCCCTTGGAGCTA
                    | ||   |  |  | | |  ||   |||| |   |   |  |    |||     || | |  |||      || |   |||||| |||| ||||||||||| |||||||| || ||||| ||||||||||| ||||||||||| || ||||||||   |||  ||||||| || ||||| |  |
--------------------gtatctctccttcttt-ttgtccggctctgttcctagttcgtacttaatctaatatca-ctttgatcgttgttatattttgcagATGATTAATGAGAAGCCCCAAGTGATACAAGAGTATGAGTCAGGAAAAGCCATTCCAAATCAACAGATAATCACCAAACTGGAAAGGGCTCTTGGTGTGA

upper sequence: GLYMA06G42900.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ33541 (Selaginella moellendorffii), 3'ss of exon 3
gtattactctcccttcagtagaattatttttaatatatcatcgatctctttattttt-cttattagc-aattaggcattatcaatgacgtgcattgttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCCATTCCAAACCAGCAGATAATTGGCAAGTTGGAAAGAGCCCTTGGAGCTA
                                 |  || || |||   ||  ||||| ||| || ||  ||| |   |  |   ||   ||| | ||      ||||||||||| ||||||||||| || ||||| ||||| || || ||||| ||||| || ||||||||||| ||   |||| | ||  | || || ||||| |
------------------------------gtttggatgattgattctttggttttttctttttggctgatttgttttccttgttggtttgcttggtc-----cagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCGGGAAAAGCCATCCCCAACCAGCAGATCATCTCCAAGCTCGAGCGCGCGCTGGGAGCCA

upper sequence: GLYMA06G42900.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ36890 (Selaginella moellendorffii), 3'ss of exon 3
gtattactctcccttcagtagaattatttttaatatatcatcgatctctttatttt-tcttattagc-aattaggcattatcaatgacgtgcattgttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCCATTCCAAACCAGCAGATAATTGGCAAGTTGGAAAGAGCCCTTGGAGCTA
                                 |  || || |||   ||  || | |||| || ||  ||| |   |  |   ||   ||| | ||      ||||||||||| ||||||||||| || ||||| ||||| || || ||||| ||||| || ||||||||||||||   |||| | ||  | || || ||||| |
------------------------------gtttggatgattgattctttggttgtgtctttttggctgatttgttttccttgttggtttgcttggtc-----cagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCCATCCCCAACCAGCAGATAATCTCCAAGCTCGAGCGCGCGCTGGGAGCCA

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|208201272|gb|GD996629.1|GD996629
EST:     TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA                         CTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
genomic: TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAAgtattactct ... ttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
EST: gi|10237885|gb|BE806773.1|BE806773
EST:     TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA                         CTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
genomic: TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAAgtattactct ... ttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
EST: gi|120492194|gb|EH220361.1|EH220361
EST:     TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA                         CTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
genomic: TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAAgtattactct ... ttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
EST: gi|192316373|gb|FK008162.1|FK008162
EST:     TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA                         CTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
genomic: TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAAgtattactct ... ttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
EST: gi|192302097|gb|FG993467.1|FG993467
EST:     TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA                         CTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
genomic: TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAAgtattactct ... ttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
EST: gi|254337318|gb|GR845101.1|GR845101
EST:     TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA                         CTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
genomic: TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAAgtattactct ... ttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
EST: gi|192329167|gb|FK019754.1|FK019754
EST:     TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA                         CTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
genomic: TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAAgtattactct ... ttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
EST: gi|192302223|gb|FG996617.1|FG996617
EST:     TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA                         CTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
genomic: TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAAgtattactct ... ttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
EST: gi|18735226|gb|BM528641.1|BM528641
EST:     TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA                         CTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
genomic: TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAAgtattactct ... ttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
EST: gi|192315428|gb|FK007774.1|FK007774
EST:     TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA                         CTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
genomic: TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAAgtattactct ... ttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
EST: gi|21888229|gb|BQ741433.1|BQ741433
EST:     TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA                         CTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
genomic: TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAAgtattactct ... ttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
EST: gi|7638872|gb|AW733264.1|AW733264
EST:     TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA                         CTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
genomic: TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAAgtattactct ... ttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
EST: gi|193318238|gb|FK287482.1|FK287482
EST:     TAATGCAAGCTAGGATGGACAAGAAACTTGCTCAGTCTCAGCTTGCTCAA                         CTGATCAATGAGAAGCCTCAGGTGATCCAGGAGTACGAGTCAGGAAAGGCC
genomic: TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAAgtattactct ... ttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
EST: gi|10231268|gb|BE800165.1|BE800165
EST:     TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA                         CTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
genomic: TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAAgtattactct ... ttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
EST: gi|7638873|gb|AW733265.1|AW733265
EST:     TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA                         CTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
genomic: TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAAgtattactct ... ttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
EST: gi|18719032|gb|BM523131.1|BM523131
EST:     GAAACTTACTCAGTCTCAGCTTGCTCAA                         CTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
genomic: GAAACTTACTCAGTCTCAGCTTGCTCAAgtattactct ... ttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
EST: gi|192316374|gb|FK008163.1|FK008163
EST:     TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA                         CTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
genomic: TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAAgtattactct ... ttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
EST: gi|17023513|gb|BM094547.1|BM094547
EST:     TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA                         CTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
genomic: TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAAgtattactct ... ttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
EST: gi|254339962|gb|GR858087.1|GR858087
EST:     TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAA                         CTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC
genomic: TAATGCAAGCTAGGATGGACAAGAAACTTACTCAGTCTCAGCTTGCTCAAgtattactct ... ttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttttcttattagcaattaggcattatcaatgacgtgcattgttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCCATTCCAAACCAGCAGATAATTGGCAAGTTGGAAAGAGCCCTTGGAGCTA
     tttcttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattactctcccttcagtagaattatttttaatatatcatcgatctctttatttttcttattagcaattaggcattatcaatgacgtgcattgttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCCATTCCAAACCAGCAGATAATTGGCAAGTTGGAAAGAGCCCTTGGAGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT