Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaataaaactatatatatatatatacttctccccgcggagattcaaatcttagtttgtgagttttcttatgagtttcacaattttgtgttttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCTCTTGACACAATTTACAGCAACTTCATCGACGCGCTTCCTGTG

Basic information

species Glycine max
transcript GLYMA12G30490.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G30490.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 1
taaataaaactatatatatatatatacttctccccgcggagattcaaatcttagtttgtgagttttcttatgagtttcacaattttgtgttttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCTCTTGACACAATTTACAGCAACTTCATCGACGCGCTTCCTGTG
            | | |   | | |    ||||        |||  ||||| | ||  |     |||| || |    |     ||   | | ||    |||| || || ||||| || || ||||| || || || |||||||||||||| || ||||| || ||||||||||||||||||||||| ||||||
-----------gtctctccctctctctccctcctgctctcaatttcaatctcatttcat-----ttctgataacacgccttgattccggatctgcgt-agACGATCAACCTGGCGGCGATCTGCACGCCGGCCGACTACAACACGCGCCCCCTCGACACCATCTACAGCAACTTCATCGACGCGCTCCCTGTG

upper sequence: GLYMA12G30490.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G167872_T01 (Zea mays), 3'ss of exon 1
----------------------------------------------taaataaaacta-tata--tatatatatacttctccccgcggagattcaaatcttagtttgtgagt--tttcttatgagtttcacaat----tttgtgttttg---ttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCTCTTGACACAATTTACAGCAACTTCATCGACGCGCTTCCTGTG
                                              | | | | |||| ||||  |  ||||  ||||    ||    |  |||   ||  | |     | |  || | |     | ||    |     ||| ||  ||    |  |||| || || ||||| || || ||||| || ||||| |||||||||||||| || ||||| || ||||||||||||||||| || || || |||
gtgagagcctgctgccaccatatttcgggacccagatttcatctcatcagttatactagtataattcaatatgcacttggtacccaaaaagttctgctcccactcaagaattccttcccttcccatctcctgctgctgcttgggtggtggatctgaagACCATCAACCTGGCGGCTATCTGCACGCCGGCGGACTACAACACGCGCCCCCTCGACACCATCTACAGCAACTTCATCGATGCACTCCCAGTG

upper sequence: GLYMA12G30490.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 1
----------------------------------------------------taaataaaactatatatatatatatacttctccccgcggagattcaaatcttagtttgtgagttttcttatgagtttcacaattttgtgttttgttcca-gACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCTCTTGACACAATTTACAGCAACTTCATCGACGCGCTTCCTGTG
                                                    | | ||  |||    ||  || |  | ||  | |  ||||  | |  ||| |    ||  |   | ||     | | |     | ||   |  |  ||| ||| || || ||||| || || ||||| || || || |||||||| ||||| |||||||| || |||||||||||||||||||| || || |||
gtcagttagtgcctattcttccacctatcttccttttttctttctcgattgcttactactacttggaatgcatttcgaattgactc-acggatttcctcatcctctcctgccatgctgct-----gctgcttggatctgatctgcgcgccaagACCATAAACCTGGCCGCGATCTGCACGCCGGCCGACTACAACACTCGCCCACTTGACACCATCTACAGCAACTTCATCGACGCACTCCCAGTG

upper sequence: GLYMA12G30490.2 (Glycine max), 3'ss of exon 1
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 1
----------------------------------------taaataa-aactatatatatatatatacttctccccgcggagattcaaatcttagtttgtgagttttcttatgagtttcacaatt-ttgt-gttttg----ttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCTCTTGACACAATTTACAGCAACTTCATCGACGCGCTTCCTGTG
                                         ||||    | | |  | |   | ||     ||     |   | || ||| |    |||||  | |  |  | | ||   |  || |||| ||||||    || ||||| || ||||| ||||| || || ||||| || |||||||| ||||| ||||||||||| || |||||||| ||||| || || || || |||
gtatttgttcttcgtttcttcttagtaaatcgttaatgtgaaaatgttgaatgtgaagactcagatctgattcgttatgtgaaatcgaatttcgaattgtggatgtcttgtttaattaatctgttgttgttgttttggattttgcagACGATAAATCTAGCTGCGATCTGTACTCCAGCAGATTACAATACGCGTCCTCTTGACACTATCTACAGCAATTTCATTGATGCTCTCCCAGTG

upper sequence: GLYMA12G30490.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 3'ss of exon 1
taaataaaactatatatatatatatacttctccccgcggagatt-caaatcttagtttgtgagttttcttatgagtttcacaattttgtgttttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCTCTTGACACAATTTACAGCAACTTCATCGACGCGCTTCCTGTG
          |||      || | || ||||  |   |||  || ||  |||| | || ||| |    || ||          |||| | |  |  | |||||||| |||||||| || || || ||||||||||| ||||| || || ||||| || || ||||||||||| ||||| || || ||||| |||
----gttcgttattccccaatttctatttcttgcattggattttgcatttcttggattttgaatcaatttgtggc-------gttttctttggtaatgcagACTATCAATCTGGCGGCGATCTGTACTCCCGCGGACTACAATACTCGTCCTCTCGATACGATTTACAGCAATTTCATTGATGCCCTTCCAGTG

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|193464260|gb|FK429612.1|FK429612
EST:     CCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCGCTCCCGCGGATTACAACACGCGCCCT
genomic: CCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|13477512|gb|BG507365.1|BG507365
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|9203920|gb|BE330144.1|BE330144
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|209702171|gb|BW664233.1|BW664233
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|10710286|gb|BF010010.1|BF010010
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|193300324|gb|FK266693.1|FK266693
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|209710480|gb|BW662016.1|BW662016
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|7283473|gb|AW596080.1|AW596080
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|9264592|gb|BE352739.1|BE352739
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|209700873|gb|BW661277.1|BW661277
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|213610338|gb|DB962952.1|DB962952
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|11275155|gb|BF325478.1|BF325478
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|209729039|gb|BW651777.1|BW651777
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|209705408|gb|BW668027.1|BW668027
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|16348560|gb|BI974155.1|BI974155
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|7327204|gb|AW620926.1|AW620926
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|12774624|gb|BG239551.1|BG239551
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|193300363|gb|FK265388.1|FK265388
EST:     TACAAGCACGACTTCCCGTCTACGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: T-CAAGCACGA-TTCCCGTCT-CGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|7285776|gb|AW598263.1|AW598263
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|120529563|gb|EH257697.1|EH257697
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|163926309|gb|EH039167.1|EH039167
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|120529751|gb|EH257885.1|EH257885
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|213594831|gb|DB959858.1|DB959858
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|213619670|gb|DB965616.1|DB965616
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|15812879|gb|BI785154.1|BI785154
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|298164774|gb|HO014419.1|HO014419
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
EST: gi|213590885|gb|DB973710.1|DB973710
EST:     ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTG                         ACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT
genomic: ACATCAAGCACGATTCCCGTCTCGAAGGCCTCATCAAAATGTCAGATCTGgtaaattagt ... tttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatcttagtttgtgagttttcttatgagtttcacaattttgtgttttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCTCTTGACACAATTTACAGCAACTTCATCGACGCGCTTCCTGTG
                                            ttttgttcc  CT-rich tract
                 ttttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaataaaactatatatatatatatacttctccccgcggagattcaaatcttagtttgtgagttttcttatgagtttcacaattttgtgttttgttccagACTATTAATCTGGCTGCCATTTGCACTCCCGCGGATTACAACACGCGCCCTCTTGACACAATTTACAGCAACTTCATCGACGCGCTTCCTGTG

-aaataaa
- - - - - - - - - - - - - -ttctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - -gtttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgtg