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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttggttctttaaaaaaatgtgacaaatttttctcatttcatcatttctctgttttctgtcttcttttgcattttcctgaagttcaagttgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG

Basic information

species Glycine max
transcript GLYMA12G28730.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G138676_T02 (Zea mays), 3'ss of exon 8
gtatttggttctttaaaaaaatgtgacaaatttttctcatttcatcatttctctgttttctgtcttcttttgcattttcctgaagttcaagttgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
                        | |     | |    ||||  | |  ||||| ||  |  |||  ||||| || | ||||  | ||        || || |  ||||||||||||| |||||||| || || |||||||| |||||||||
------------------------gtctggcatgttcagtttc--cctccctctggttcttacctt--tttgc-ttcttctgatat-cattcatccatgtagGCTCTGTTTCCTGGAGAAAGTGGAGTCGACCAACTAGTTGAGATCATCAAG

upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 8
lower sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 8
----gtatttggttctttaaaaaaatgtgacaaatttttctcatttcatcatttctctgttttctgtcttcttttgcattttcctgaagttcaagttgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
         || || ||  |  |  | |      || |  |||||   |   |||  ||| ||      | || |||  || |         || |||   | |||||  |||||||||| ||||| |||||||||||||| ||||||||||| |||
gttaaagcatgatttttgcattagctatatgttgttctattcattcagtttattccttgtctt--actattttgtgcccttgct--------aatttgtcgtacagCCTCTGTTTCCTGGTGAGAGCGGAGTTGATCAGCTTGTTGAAATCATTAAG

upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 7
gtatttggttctttaaaa-aaatgtgacaaattt---ttctcatttcatcatttctctgttttctgtcttcttttgcattttcctgaagttcaagttgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
||| |    | || |    | ||||     | ||   ||| | ||||||||||||   ||  | |   |  ||  || |||  || |    ||  ||    | ||||| |||||||||||||| || ||||||||||| |||||||| |||||||||
gtagtacactgttaatttcagatgtagttgacttgccttcgcttttcatcatttccaagtcctgt---tatttaggcttttatctaa---ccatcttctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG

upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 6
--gtatttggttctttaaaaaaatgtgacaaatttttctcatttcatcatttctctgttttctgtcttcttttgcattttcctgaagttcaagttgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
    || || | || |     || |||   |  |||    |  |     |      | ||| ||| |  | | |  |||  |     ||    | |  |||||||| ||||||||||||||||||||||| |||||  | || ||||||||||||
gacgatatgttgctgtggcgcaa-gtgtagaggtttg---aagttgaggtgagggagctttatgtgtaatctgggttttgacgacgcttttgatgggattgcagCCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG

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|6719212|gb|AW306859.1|AW306859
EST:     TAGATATATGGTCAACTGGTTGTGTAATGGCTGAATTACTTCTTGGACAG                         CCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
genomic: TAGATATATGGTCAACTGGTTGTGTAATGGCTGAATTACTTCTTGGACAGgtatttggtt ... tgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
EST: gi|151408852|gb|EV278660.1|EV278660
EST:     TAGATATATGGTCAACTGGTTGTGTAATGGCTGAATTACTTCTTGGACAG                         CCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
genomic: TAGATATATGGTCAACTGGTTGTGTAATGGCTGAATTACTTCTTGGACAGgtatttggtt ... tgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
EST: gi|193630915|gb|FK585070.1|FK585070
EST:     AAGATATATGGTCAACTGGTTGTGTAATGGCTGAATTACTTCTTGGACAG                         CCCTTGTTTCCTGGAGAGAGTGG
genomic: A-GATATATGGTCAACTGGTTGTGTAATGGCTGAATTACTTCTTGGACAGgtatttggtt ... tgatttgcagCCCTTGTTTCCTGGAGAGAGTGG
EST: gi|208208274|gb|GE004247.1|GE004247
EST:     TAGATATATGGTCAACTGGTTGTGTAATGGCTGAATTACTTCTTGGACAG                         CCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
genomic: TAGATATATGGTCAACTGGTTGTGTAATGGCTGAATTACTTCTTGGACAGgtatttggtt ... tgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
EST: gi|13312538|gb|BG406189.1|BG406189
EST:     TAGATATATGGTCAACTGGTTGTGTAATGGCTGAATTACTTCTTGGACAG                         CCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
genomic: TAGATATATGGTCAACTGGTTGTGTAATGGCTGAATTACTTCTTGGACAGgtatttggtt ... tgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
EST: gi|208078311|gb|GD877523.1|GD877523
EST:     TAGATATATGGTCAACTGGTTGTGTAATGGCTGAATTACTTCTTGGACAG                         CCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
genomic: TAGATATATGGTCAACTGGTTGTGTAATGGCTGAATTACTTCTTGGACAGgtatttggtt ... tgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
EST: gi|13479623|gb|BG508966.1|BG508966
EST:     TAGATATATGGTCAACTGGTTGTGTAATGGCTGAATTACTTCTTGGACAG                         CCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
genomic: TAGATATATGGTCAACTGGTTGTGTAATGGCTGAATTACTTCTTGGACAGgtatttggtt ... tgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
EST: gi|7589778|gb|AW705545.1|AW705545
EST:     GTAATGGCTGAATTACTTCTTGGACAG                         CCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
genomic: GTAATGGCTGAATTACTTCTTGGACAGgtatttggtt ... tgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
EST: gi|193434108|gb|FK402332.1|FK402332
EST:     TAGATATATGGTCAACTGGTTGTGTAATGGCTGAATTACTTCTTGGACAG                         CCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
genomic: TAGATATATGGTCAACTGGTTGTGTAATGGCTGAATTACTTCTTGGACAGgtatttggtt ... tgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctctgttttctgtcttcttttgcattttcctgaagttcaagttgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG
                                          agttgat  putative branch site (score: 5)
                 ttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttggttctttaaaaaaatgtgacaaatttttctcatttcatcatttctctgttttctgtcttcttttgcattttcctgaagttcaagttgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT