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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTGATGCCCAAACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAggtgtctatgaaatgatatttctgttagcttctgtgattatgttttgtgctactattagtacttactaatatctcccgagctgcagtgaatcagttttcacttatctcttaatctctggttatttggtttaattacctgttcttttctaca

Basic information

species Glycine max
transcript GLYMA18G05730.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G05730.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 5'ss of exon 3
TATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTGATGCCCAAACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAggtgtctatgaaatgatatttctgttagct-tctgtgattatgttttgtgctactattagtacttactaatatctcccgagctgcagtgaatcagttttcacttatctcttaatctctggttatttggtttaattacctgttcttttctaca
 ||| || |||||||||||||| ||||| |||||| | |||||||| || ||||| |||||  ||||||| |||||||| |||||||||||  | ||||||||       ||    ||||  |||  | | ||||| |  ||  ||   |  |   | | || ||  |  |   |    |  |  | |   ||||   | ||  ||   || |                                       
-ATTCATCGATGAGGTTGATGCTATAGCAACTGCTCGTTTTGATGCTCAGACTGGTGCTGACCGAGAAGTTCAGCGTATTCTTATGGAACTACTCAATCAGgt-------aaggtttattgttgtaggatatctgtaag-atacttgtggagaaactgaatatttgttgct---tgttaaatttgaatagctcagccat-acccatacattta---------------------------------------

upper sequence: GLYMA18G05730.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G090904_T01 (Zea mays), 5'ss of exon 3
TATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTGATGCCCAAACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAggtgtctatgaaatgatatttctgttagcttctgtgattatgttttgtgctactattagtacttactaatatctcccgagctgcagtgaatcagttttcacttatctcttaatctctggttatttggtttaattacctgttcttttctaca
  || ||||||||||||||||| |||||||||||| | |||||||| || ||||| |||||  ||||||| |||||||| |||||||| ||  | ||||||||       |||   ||  | |  ||   || |     |  ||| | |||  ||  || | ||| || ||| |    |  |     | | | |   | |   ||     |                                        
-TTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTGATGCTCAGACTGGTGCTGACCGAGAAGTTCAGCGTATTCTTATGGAGCTACTCAATCAGgt-------aaagcttagctattataagatcaggatggacttttagggct--taaaag-atttattactatgttagaaagtatttagcaactgacctgaagcattaaaaa----------------------------------------

upper sequence: GLYMA18G05730.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G038126_T01 (Zea mays), 5'ss of exon 3
TATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTGATGCCCAAACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAggtg----tctatgaaatgat--atttctgttagcttctgtgattatgttttgtgctactattagtacttactaatatctcccgagctgcagtgaatcagttttcacttatctcttaatctctggttatttggtttaattacctgttcttttctaca
  || ||||||||||||||||| |||||||||||| | |||||||| || ||||| |||||  ||||||| || || || |||||||| ||  | ||||||||     |     | |||||  | || |    | |     | |||| |  | || ||  |  | || |||  || |   | | | |   | ||||   ||| | | ||                                                
-TTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGCTTTGATGCTCAGACTGGTGCTGACCGAGAAGTTCAACGCATTCTTATGGAGCTACTCAATCAGgtaaagcttagctacatgatgaacttttaggggttaacaggtttat-tactatgttagaa--aatatttagcaacaggcctcaaac---attgaa---gttgttatttg-----------------------------------------------

upper sequence: GLYMA18G05730.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 5'ss of exon 3
TATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTGATGCCCAAACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAggtgtctatgaaatgatat---ttctgttagcttctgtgattatgttttgtgctactattagtacttactaatatctcccga-gctgcagtgaatcagttttcacttatctcttaatctctggttatttggtttaattac--ctgttcttttctaca-----------------------------------------
  || ||||||||||||||||| || || || ||||| |||||||||||||||||||||||||||||||| ||||| ||||| ||||| ||  | ||||||||   | | ||| |||||   |  | |     | ||   |||  |            | |  |     |  || ||   || ||   |   ||   | ||| | | || | |   |   || |||     | || || |  || || ||  ||| |                                         
-CTTCATTGATGAGGTTGATGCTATTGCTACCGCTAGGTTTGATGCCCAAACTGGAGCTGATAGAGAAGTTCAGCGAATCCTCATGGAGCTCCTCAATCAGgtaggtttaaaaggatatggatcttatagagatatggatttaattaaaaaaaaggcctgaaaatcagttgttaactggggatgccaaaaaaaaagggctttgattaatttgtctgt---tgattacagcatgtacttgcttctattgttagctaaaaatgtttaactttttggatttgggtctaaattcttctccag

upper sequence: GLYMA18G05730.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S36_183V6.1 (Physcomitrella patens), 5'ss of exon 3
TATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTGATGCCCAAACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAggtgtctatgaaatgatatttctgttagcttctgtgattatgttttgtgctactattagtacttactaatatctcccgagctgcagtgaatcagttttcacttatctcttaatctctggttatttggtttaattacctgttcttttctaca
 ||||||||||||| |||||||||| || || ||| | ||||| || ||||||||||| ||||| ||||| ||||||||| | ||||| |||||||||||||| |     || ||||  || || |||  |     ||| | |       |  |||   ||| |||       |     |  ||||||| || | ||  |       |   |  | || | |                             
-ATTTATTGATGAGATTGATGCAATTGCAACAGCTCGTTTTGACGCTCAAACTGGAGCAGATAGGGAAGTTCAGCGTATCTTGATGGAGCTTTTGAATCAGgtat-----aactgat--ttttggtagtct-----attctatcca----tgatatggatacctacgttggatt-----gtggcagtgagtccgattgtaaactatgcgagagttgtgttga-----------------------------

upper sequence: GLYMA18G05730.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S243_67V6.1 (Physcomitrella patens), 5'ss of exon 3
TATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTGATGCCCAAACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAggtgt------ctatgaaatgatatttctgttagcttctgtgattatgtttt-----gtgctactattagt--acttactaatatctcccgagctgcagtgaatcagttt----tcacttatctc-ttaatctctggttatttggtttaattacctgttctttt--ctaca-
  |||||||||||  |||||||||| || || ||| | || || || |||||||| || || ||||| || ||||||||||||||||||||| |||||||||| |       | | || |  |   | | ||  ||   | |   ||   |      |||   ||  |||   |   |  | |   | | |  | | | |   |    ||    ||| || |||| |  |  | ||| |  ||   |||  |   |  | || |   |||| 
-CTTTATTGATGAAATTGATGCAATTGCAACAGCTCGTTTCGACGCTCAAACTGGGGCAGACAGAGAGGTTCAGCGTATCCTTATGGAACTTCTGAATCAGgtatgaagtctttttaatttctcagttttttgtctgaagagtccattcctcaaatggtggacctcctaggtgatagatcatttatttctgtacagaactcggtagtcttcagttcatttttctcgtcgaagtttggctgcttttcttacatttttaatgttctggttacag

upper sequence: GLYMA18G05730.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S147_100V6.1 (Physcomitrella patens), 5'ss of exon 3
TATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTGATGCCCAAACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAggtgtctatgaaatgatatttctgttagcttctgtgattatgttttgtgctactattagtacttactaatatctcccgagctgcagtgaatcagttttcacttatctcttaatctctggttatttggtttaattacctgttcttttctaca
 ||||||||||||  |||||||||| || || ||  | || || || ||||||||||| || || || |||||||||||  | ||||||||||||||||||||    || | ||  |  |  |   |  ||     |  ||||| |  | |  ||     |  | | ||| |||   ||  || |||   |  ||||   ||||  | ||   || |  | ||     ||   |   || |          
-ATTTATTGATGAAATTGATGCAATCGCAACAGCCCGTTTCGACGCTCAAACTGGAGCAGACAGGGAGGTACAGCGTATATTAATGGAACTTTTGAATCAGgt----ataacatttttctggttcgaagtttgtcaagcatgttctccgattttagagcgatgttccaatgtctgttgaattgaagtct-tttgtttctgcttaggtgttgcgctttc-tcatacatgttttgtgtttggttgcag-----

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|6454816|gb|AW185499.1|AW185499
EST:     ACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCA                         GATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA
genomic: ACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAggtgtctatg ... cttttctacaGATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA
EST: gi|193513567|gb|FK469155.1|FK469155
EST:     ACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCA                         GATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA
genomic: ACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAggtgtctatg ... cttttctacaGATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA
EST: gi|207810299|gb|GD781983.1|GD781983
EST:     ACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCA                         GATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA
genomic: ACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAggtgtctatg ... cttttctacaGATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA
EST: gi|193629133|gb|FK578081.1|FK578081
EST:     ACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCA                         GATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA
genomic: ACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAggtgtctatg ... cttttctacaGATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA
EST: gi|58022279|gb|CX709020.1|CX709020
EST:     ACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCA                         GATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA
genomic: ACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAggtgtctatg ... cttttctacaGATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA
EST: gi|7146493|gb|AW508415.1|AW508415
EST:     ACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCA                         GATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA
genomic: ACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAggtgtctatg ... cttttctacaGATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA
EST: gi|18041397|gb|BM309691.1|BM309691
EST:     TATGGAACTTTTGAATCA                         CATGGATGGTTTTGACCATACGGTAAATGTTAAAGTTATAATGGCAACTAA
genomic: TATGGAACTTTTGAATCAggtgtctatg ... cttttctacaGATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA
EST: gi|192313767|gb|FK007639.1|FK007639
EST:     ACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCA                         GATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA
genomic: ACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAggtgtctatg ... cttttctacaGATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA
EST: gi|192313766|gb|FK007638.1|FK007638
EST:     ACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCA                         GATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA
genomic: ACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAggtgtctatg ... cttttctacaGATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA
EST: gi|16342518|gb|BI968113.1|BI968113
EST:     ACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCA                         GATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA
genomic: ACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAggtgtctatg ... cttttctacaGATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA
EST: gi|17401263|gb|BM178045.1|BM178045
EST:     ACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCA                         GATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA
genomic: ACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAggtgtctatg ... cttttctacaGATGGATGGTTTTGACCAAACGGTAAATGTTAAAGTTATAATGGCAACTAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTGATGCCCAAACTGGAGCTGATAGAGAAGTACAGCGTATCCTTATGGAACTTTTGAATCAggtgtctatgaaatgatatttctgttagcttctgtgattatgttttgtgctactattagtacttactaatatctcccgagctgcagtgaatcagttttcacttatctcttaatctctggttatttggtttaattacctgttcttttctaca

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT