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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcacttcaccaaatgcttttaattattgttttctcctttattcaattttatggacatttctacttatcaagggcaaaatattctgacaaatttattgttatctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTATGGGATCTTGGAGGGCAACCTAGGTTCCGCAGCATGTGGGAACGTTACT

Basic information

species Glycine max
transcript GLYMA11G05080.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G05080.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g10370.1 (Oryza sativa), 3'ss of exon 2
gtaagt-tcacttcaccaaatgcttttaattattgttttctcctttattcaattttatggacatttctacttatcaagggcaaaatattctgacaaatttattgttatctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTATGGGATCTTGGAGGGCAACCTAGGTTCCGCAGCATGTGGGAACGTTACT
|||||| ||| ||    || |   |||| | | |   |      | ||    | | |||||      |          | ||  |   | |    |    ||  ||  ||  |     || |||||||| ||||| || ||||| ||||| ||||| |||||||| || |||||||||||||| |                                 
gtaagtatcagtttcttaatta--tttattcacttgctgaattataatgatttctcatggatcaccatgtaatctgcagACAGGAGGCTTTAGTGAGGACATGATT-CCTACT-----GTAGGATTCAACATGAGAAAGGTGACCAAAGGTAATGTCACAATAAAATTGTGGGATCTTGGAGGCC---------------------------------

upper sequence: GLYMA11G05080.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 2
gtaagttcacttcaccaaatgcttttaattattgttttctcctttattcaattttatggacatttctacttatcaagggcaaaatatt-----ctgacaaatttattgtt-atctgattccag-
||||||  | |   |   || |||||  |     |  | | ||  ||      | |   | |||| | |||   ||      | | ||     |||     |||| ||   || |||| ||    || |||||||||||||| ||||| || ||||| ||||| || |||||||| |||||||||||||| |                                 
gtaagt--attaggc---attcttttggtaccactcatatactggatgtttgatgaaatatatttatccttggtaaacatgtatttttgcagACTGGAGGCTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGAAAAGTTACGAAAGGAAATGTGACGATAAAGTTGTGGGATCTTGGAGGCC---------------------------------

upper sequence: GLYMA11G05080.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G007188_T01 (Zea mays), 3'ss of exon 2
gtaagttcacttcaccaaatgcttttaattattgttttct-cctttattcaattttatgga-catttctacttatcaagggcaaaatattctgacaaatttattgtt-atctgattccag-
||||||     |||     | |||   |    | |  |     | || | || | |||| | ||||  ||   ||  |         |  |||     |||| ||   || |||| ||    || |||||||||||||| || || || ||||||||||| || ||||| || |||||| ||||||| |                                 
gtaagtattaatcattcttttcttaccacccatatactggatgtataatgaaatatatgtatcattcataaacatgtattttttg-cagACTGGAGGTTTTAGTGAGGATATGATCCCTACTGTAGGATTCAATATGAGAAAGGTTACCAAAGGGAATGTGACGATAAAATTGTGGGATATTGGAGGCC---------------------------------

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|31464936|gb|CD406964.1|CD406964
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACTATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|151410326|gb|EV280141.1|EV280141
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|16349420|gb|BI975015.1|BI975015
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|209716493|gb|BW676943.1|BW676943
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|151405432|gb|EV275246.1|EV275246
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|193625198|gb|FK577382.1|FK577382
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|58023255|gb|CX709996.1|CX709996
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|254344316|gb|GR851119.1|GR851119
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|58016934|gb|CX703676.1|CX703676
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|120492024|gb|EH220191.1|EH220191
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|151412616|gb|EV282428.1|EV282428
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|254344317|gb|GR851120.1|GR851120
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|207732378|gb|GD708551.1|GD708551
EST:     ACTGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|192323170|gb|FK017396.1|FK017396
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|298177742|gb|HO023761.1|HO023761
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATATAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|254335359|gb|GR846856.1|GR846856
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|58022559|gb|CX709300.1|CX709300
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|57574961|gb|CX547936.1|CX547936
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|18733799|gb|BM527816.1|BM527816
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|120491696|gb|EH219863.1|EH219863
EST:     TATAGTGAGGACATGATTCCAACT                         GTGGGATTC-ATNATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTT
genomic: TATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAAT-ATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTT
EST: gi|192307680|gb|FK001624.1|FK001624
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|193425368|gb|FK387843.1|FK387843
EST:     TAGTTGCTACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: TAGTTGCTACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|193692589|gb|FK629360.1|FK629360
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|151395085|gb|EV264956.1|EV264956
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGAGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|151401783|gb|EV271596.1|EV271596
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|254335360|gb|GR846857.1|GR846857
EST:     ACCGGTGGATATAGTGAGGACATGATCCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|298167845|gb|HO013108.1|HO013108
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|120491652|gb|EH219819.1|EH219819
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|58023508|gb|CX710249.1|CX710249
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|10235042|gb|BE803930.1|BE803930
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|9203981|gb|BE330205.1|BE330205
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|192301117|gb|FG988012.1|FG988012
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|58022262|gb|CX709003.1|CX709003
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|120491738|gb|EH219905.1|EH219905
EST:     ACCGGTGGATATAGTGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
EST: gi|151409006|gb|EV278814.1|EV278814
EST:     ACCGGTGGATATAATGAGGACATGATTCCAACT                         GTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA
genomic: ACCGGTGGATATAGTGAGGACATGATTCCAACTgtaagttcac ... ctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctacttatcaagggcaaaatattctgacaaatttattgttatctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTATGGGATCTTGGAGGGCAACCTAGGTTCCGCAGCATGTGGGAACGTTACT
                  aaaatattctgacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcacttcaccaaatgcttttaattattgttttctcctttattcaattttatggacatttctacttatcaagggcaaaatattctgacaaatttattgttatctgattccagGTGGGATTCAATATGAGGAAAGTGACAAAAGGGAATGTTACAATAAAGTTATGGGATCTTGGAGGGCAACCTAGGTTCCGCAGCATGTGGGAACGTTACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG