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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggtacaaattaagtccttcatatctttgatagaattcttatatttctgttcttgctgttattttgcaaaagtaatcctgctgcatgtgatagtgggaggggagctagtgtttgctcaacactaaattagtattcaaaggaactgacatatagtttattctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATA

Basic information

species Glycine max
transcript GLYMA18G03360.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G03360.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 3'ss of exon 4
ggtacaaattaagtccttcatatctttgatagaattcttatatttctgttcttgctgttattttgcaaaagtaatcctgctgcatgtgatagtgggaggggagctagtgtttgctcaacactaaattagtattcaaaggaactgacatatagtttattctgtgtacaGAATGCCACTCAAAAA-AGTCAAAAGGTGTTTGTGCATGTGCCATCAG-AGATTGCTGCTCATGAAGTTGAGGAAATA-
                                                                                                   |    | ||| |||  ||        ||    ||||       | |  || |  || |  | |  ||||||||| ||||||||| ||||||||||||||||| ||||| || |||| | || ||||| || || |||||||||||  
---------------------------------------------------------------------------------------------------gtttattgtgcttgtccattgtcttgttctgtttca------ttaatgtacatgttgtctttt--acagAATGCTACTCAAAAACAGTCAAAAGGTGTTTGTTCATGTTCCTTCAGCAAATAGCTGCCCACGAGGTTGAGGAAATCG

upper sequence: GLYMA18G03360.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G061745_T03 (Zea mays), 3'ss of exon 4
ggtacaaattaagtccttcatatctttgatagaattcttatatttctgttcttgctgttattttgcaaaagtaatcctgctgcatgtgatagtgggaggggagctagtgtttgctcaacactaaattagtattcaaaggaactgacatatagtttattctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATA-
                                                                                 | |  | |   | |  | |  ||| | ||||        ||   | ||| || ||             | |||| |||  | |||||||||| ||||| |||||||| ||||| ||||| ||||| || ||||| ||||| ||||||||||||||||||||  
---------------------------------------------------------------------------------gtacataac--ttgctgagttgctggagtttttcacttgcttgctcagtgtttaat------------ttgttttttcctt-tacagAATGCAACTCAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG

upper sequence: GLYMA18G03360.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G368908_T03 (Zea mays), 3'ss of exon 1
ggtacaaattaagtccttcatatctttgatagaattcttatatttctgttcttgctgttattttgcaaaagtaatcctgctgcatgtgatagtgggaggggagctagtgtttgctcaacactaaattagtattcaaaggaactgacatatagtttattctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATA-
                                                                                 | ||||  | | ||  | |  ||| | || |        ||   | ||| || ||           |||  ||  | |  |   |||||||| || || |||||||| ||||| ||||| ||||| || ||||| ||||||||||||||||||||||||||  
---------------------------------------------------------------------------------gtatgtc-tgggggatgagatgctggagtgtttcacttgcttgctcagtgtttaa-----------tatttttgttgcccttcccagAATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG

upper sequence: GLYMA18G03360.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 4
ggtacaaattaagtccttcatatctttgatagaattcttatatttctgttcttgctgttattttgcaaaagtaatcctgctgcatgtgatagtgggaggggagctagtgtttgctcaacactaaattagtattcaaaggaactgacatatagtttattctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATA-
                                                               |   | |  || ||| |   || |  |       |   || |   || |||| |  |   ||| || || |  |  ||       | | ||  || | | | |||||||| ||||| ||||| || || || || || |||||| |  |||| ||||||||||||||||||||||||||  
--------------------------------------------------------------gtaagatacaaacccttccaaatattgtcccttttgtaaagtt---gtatgcttattat--aatcag-atgctgattaa-------acacttctttttctctccagAATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATTGCTGCTCATGAAGTTGAGGAAATCG

upper sequence: GLYMA18G03360.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G11270.1 (Arabidopsis thaliana), 3'ss of exon 4
ggtacaaattaagtccttcatatctttgatagaattcttatatttctgttcttgctgttat-tttgcaaaagtaatcctgctgcatgtgatagtgggaggggagctagtgtttgctcaacactaaattagtattcaaaggaactgacatatagtttattctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATA-
                             || |   |    | ||   ||||  |  || |  ||||   | |  |   | ||||| ||| |     |   ||  || | | |||   |   || ||   |||    |    |    ||      |  ||| | | |||||||| || || ||||| ||| |||| ||||| || |||||  |||| ||||| ||||||||||||||||||||  
----------------------------gtaaataccagccaatt---ttctaaccattttacttgctcgactg-ttaagttgcatctgacat----acttgatttactttctgcatta-gttatatccatatatctaattgccttgatccgaacttctctctctgcagAATGCTACCCAGAAAAGCCAACAGGTTTTTGTACACGTGCCTACAGAAATTGCAGCTCATGAAGTTGAGGAAATTG

upper sequence: GLYMA18G03360.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G11270.2 (Arabidopsis thaliana), 3'ss of exon 4
ggtacaaattaagtccttcatatctttgatagaattcttatatttctgttcttgctgttat-tttgcaaaagtaatcctgctgcatgtgatagtgggaggggagctagtgtttgctcaacactaaattagtattcaaaggaactgacatatagtttattctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATA-
                      |    ||   || |   |      | ||||  |  || |  ||||   | |  |   | ||||| ||| |     |   ||  || | | |||   |   || ||   |||    |    |    ||      |  ||| | | |||||||| || || ||||| ||| |||| ||||| || |||||  |||| ||||| ||||||||||||||||||||  
---------------------gtgaaagaggtaaatacca-gccaattttctaaccattttacttgctcgactg-ttaagttgcatctgacat----acttgatttactttctgcatta-gttatatccatatatctaattgccttgatccgaacttctctctctgcagAATGCTACCCAGAAAAGCCAACAGGTTTTTGTACACGTGCCTACAGAAATTGCAGCTCATGAAGTTGAGGAAATTG

upper sequence: GLYMA18G03360.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G05780.2 (Arabidopsis thaliana), 3'ss of exon 4
ggtacaaattaagtccttcatatctttgatagaattcttatatttctgttcttgctgttattttgcaaaagtaatcctgctgcatgtgatagtgggaggggagctagtgtttgctcaacactaaattagtattcaaaggaactgacatatagtttattctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATA-
                                                     | |       |   | |  || ||| |   || |  |       |   || |   || |||| |  |   ||| || || |  |  ||       | | ||  || | | | |||||||| ||||| ||||| || || || || || |||||| |  |||| ||||||||||||||||||||||||||  
-----------------------------------------------------gttaaggaggtaagatacaaacccttccaaatattgtcccttttgtaaagtt---gtatgcttattat--aatcag-atgctgattaa-------acacttctttttctctccagAATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATTGCTGCTCATGAAGTTGAGGAAATCG

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|208208309|gb|GE004702.1|GE004702
EST:     AATTGGGAATCCCAACAAAAGACATATTATGCTGTTGAAGAGGTTAAAGA                         GAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGAT
genomic: AATTGGGAATCCCAACAAAAG-CATATTATGCTGTTGAAGAGGTTAAAGAggtacaaatt ... tctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGAT
EST: gi|207798891|gb|GD770942.1|GD770942
EST:     GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGA                         GAATGCCACTCAAAAAAGTCAAGAGGTGTTTGTGCATGTGCCATCAGAGAT
genomic: GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGAggtacaaatt ... tctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGAT
EST: gi|208210642|gb|GE011717.1|GE011717
EST:     GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGA                         GAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGAT
genomic: GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGAggtacaaatt ... tctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGAT
EST: gi|193584905|gb|FK542364.1|FK542364
EST:     GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGA                         GAATGCCACTACAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGA
genomic: GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGAggtacaaatt ... tctgtgtacaGAATGCCACT-CAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGA
EST: gi|208122353|gb|GD920818.1|GD920818
EST:     GAATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGA                         GAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGAT
genomic: GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGAggtacaaatt ... tctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGAT
EST: gi|207716296|gb|GD697574.1|GD697574
EST:     GTTGAAGAGGTTAAAGA                         GAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGAT
genomic: GTTGAAGAGGTTAAAGAggtacaaatt ... tctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGAT
EST: gi|193390906|gb|FK353690.1|FK353690
EST:     GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGA                         GAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGAT
genomic: GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGAggtacaaatt ... tctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGAT
EST: gi|193649146|gb|FK599783.1|FK599783
EST:     GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGA                         GAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTG
genomic: GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGAggtacaaatt ... tctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTG
EST: gi|209700562|gb|BW670403.1|BW670403
EST:     GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGA                         GAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATC
genomic: GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGAggtacaaatt ... tctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATC
EST: gi|213595707|gb|DB968545.1|DB968545
EST:     GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGA                         GAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATC
genomic: GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGAggtacaaatt ... tctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATC
EST: gi|151407202|gb|EV277017.1|EV277017
EST:     GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGA                         GAATGCCACTC
genomic: GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGAggtacaaatt ... tctgtgtacaGAATGCCACTC
EST: gi|213587600|gb|DB971323.1|DB971323
EST:     GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGA                         GAATGCCACTCAAAAA-GTCAAAAG
genomic: GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGAggtacaaatt ... tctgtgtacaGAATGCCACTCAAAAAAGTCAAAAG
EST: gi|193359721|gb|FK324141.1|FK324141
EST:     GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGA                         GAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGAT
genomic: GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGAggtacaaatt ... tctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGAT
EST: gi|208065097|gb|GD862117.1|GD862117
EST:     GAATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGA                         GAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGAT
genomic: GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGAggtacaaatt ... tctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGAT
EST: gi|207729336|gb|GD709136.1|GD709136
EST:     GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGA                         GAATGCCACTCAAAAAAGTCAAAAGGTGTTT
genomic: GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGAggtacaaatt ... tctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTT
EST: gi|207761835|gb|GD734136.1|GD734136
EST:     GAATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGA                         GAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGAT
genomic: GAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGAggtacaaatt ... tctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGAT
EST: gi|193708925|gb|FK644603.1|FK644603
EST:     TTATGCTGTTGAAGAGGTTAAAGA                         GAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGAT
genomic: TTATGCTGTTGAAGAGGTTAAAGAggtacaaatt ... tctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcaacactaaattagtattcaaaggaactgacatatagtttattctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATA
                           aactgac  putative branch site (score: 2)
                                        tttattct  putative PPT
         taaattagtattcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtacaaattaagtccttcatatctttgatagaattcttatatttctgttcttgctgttattttgcaaaagtaatcctgctgcatgtgatagtgggaggggagctagtgtttgctcaacactaaattagtattcaaaggaactgacatatagtttattctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT