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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaatatttcgaggatcaaattatggtttactcttttgtttaatggactcacttaaactactaaaatgttcttatgaggttatgaatgtgcttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAGCCTCTTACAAGATCAAAGGCTGACAATTTTGCAGCTCAAAGAGCCAGAG

Basic information

species Glycine max
transcript GLYMA09G30910.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g46280.3 (Oryza sativa), 3'ss of exon 6
----------------ctaat--atttcgaggatcaaattatggtttactcttttgtttaatggactcacttaaacta--ctaaaatgttcttatgaggttatgaatgtgcttcttttag-
                  | |  |  || ||| |  | |||   | | |  |     |||    | | ||||   |||  |    || |    |||  ||    ||||   |||||  |   ||| |||      ||||||| |||||||| || |||||||||||||| |||||||| ||  | |        || ||||| |    |||||| || || || ||||
gtaaaatagcagaatgacagttcagctcaaggctggatttacactatgcaatgcaaattatctcagttacttttgctatccctgtatctgagaatgtagtctgcaatgcatttcttccaattgaacagCTTTATCAAAAGGGGAGGATTGGAATTCTCTTGGATTTTGTCTGGTATGAACCATTCAGTGACAGCAATGCTGATAGGGCTGCAGCACAGAGGGCAAGAG

upper sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G18080.1 (Arabidopsis thaliana), 3'ss of exon 6
-----ctaata-tttcgaggatcaaattatggtttactc-------ttttgtttaatggactcacttaaactactaaaatgttcttatgaggtta---tgaatgtgcttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAGCCTCTTACAAGATCAAAGGCTGACAATTTTGCAGCTCAAAGAGCCAGAG
     | ||||  ||| |  |     |  || | | ||        | |  |  |||  ||  |  || |   ||    ||    | |     ||   | ||||    | ||  |||  || |||||||||||| ||||||| || || ||||| |||||||||||||| ||||| |||   || || || ||| |||||||||||||||| ||||
gtaaacaaataacttctaatacgttttcttgatcttcttgatgtgatatgatgaaataaacctatatatatggctcttttgccagtgtactactaatcttaatgaaaattttccagGCGAAACAAAAGGGAAGGGTTGGGATACTTTTAGATTTCGTTTGGTATGAGCCGCTTACTAGAAGTAAAGCAGATAATCTTGCAGCTCAAAGAGCAAGAG

upper sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G18070.2 (Arabidopsis thaliana), 3'ss of exon 3
ctaatatttcgaggatcaaattatggtttactcttttgtttaatggactcacttaaactactaaaatgtt-cttatgaggttatgaatgtgcttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAGCCTCTTACAAGATCAAAGGCTGACAATTTTGCAGCTCAAAGAGCCAGAG
    ||| |     || |  |||| |  | |  |   |||   |  |     ||||||   || |   || || | ||  | |   |     |  | | |||| || |||||||||||| ||||||| ||  ||||||||||||||| |||||| ||||| ||     | || ||||||   || ||||||||||| ||||
---gtatgt----aataaccttataggct-ccttcaagttgtttctatgatattaaacatgtatatgattactaaagatctaactgacaaattcttctcagGAGAAACAAAAGGGAAGGGTTGGGATTCTACTGGATTTTGTTTGGTTTGAGCCACTTACGAGTAGTCAAGCAGACAATGACGCTGCTCAAAGAGCAAGAG

upper sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g02680.t01 (Vitis vinifera), 3'ss of exon 6
ctaatatttcgaggatcaaattatggtttactcttttgtttaatgg-actcacttaaactact-------aaaatgtt--cttatgaggttatgaatgtgcttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAGCCTCTTACAAGATCAAAGGCTGACAATTTTGCAGCTCAAAGAGCCAGAG
   ||  |||     | |   | |  ||  |||| |  ||| |||  |     || |   | |       || ||| |   | |     | || || ||   | | | || || | |||||||| |||||||| || ||||||||||||||||||||||||||||||||||||||||||||||||||  | |||||||||||| ||||||
-gtatggttctgtttttagtgtttttttacctctctaatttgatgttatgtgtttgattcaatggaggagaagatgatgattgactgactgataaaagtatgtttctcagAAAGAACAAAAGGGGAGGATTGGAATTCTCTTGGATTTTGTTTGGTATGAGCCTCTTACAAGATCAAAGGCTGACAACCTAGCAGCTCAAAGATCCAGAG

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|193352813|gb|FK317321.1|FK317321
EST:     ATGCAGCTAGCTGTTCAAAGATACCGAGCGAAGTACCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: ATGCAGC-AGCTGTTCAAAGATACCGAGCGAAGTACCAAgtaatattag ... cttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|207795313|gb|GD765442.1|GD765442
EST:     GCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: GCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAAgtaatattag ... cttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|207806086|gb|GD778325.1|GD778325
EST:     TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAAgtaatattag ... cttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|193319663|gb|FK283504.1|FK283504
EST:     TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAAgtaatattag ... cttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|23727814|gb|BU761942.1|BU761942
EST:     TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAAgtaatattag ... cttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|193358539|gb|FK326621.1|FK326621
EST:     ATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: ATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAAgtaatattag ... cttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|193530291|gb|FK483690.1|FK483690
EST:     TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAACGAAGTACCAA                         GAAAGGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAAgtaatattag ... cttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|193319870|gb|FK287575.1|FK287575
EST:     TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAA                         G-AAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAAgtaatattag ... cttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|207810230|gb|GD782404.1|GD782404
EST:     TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAAgtaatattag ... cttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|58018438|gb|CX705180.1|CX705180
EST:     TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAAgtaatattag ... cttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|193364851|gb|FK330560.1|FK330560
EST:     ATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: ATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAAgtaatattag ... cttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|193436866|gb|FK402495.1|FK402495
EST:     ATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: ATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAAgtaatattag ... cttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|193356087|gb|FK322688.1|FK322688
EST:     ATGCAGCTAGCTGTTCAAAGATACCGAGCGAAGTACCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: ATGCAGC-AGCTGTTCAAAGATACCGAGCGAAGTACCAAgtaatattag ... cttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|193365984|gb|FK333317.1|FK333317
EST:     GTTC-AAGATACCGAGCGAAGTACCAA                         GAAAAGCAAAAGGGAAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGA
genomic: GTTCAAAGATACCGAGCGAAGTACCAAgtaatattag ... cttcttttagGAAAAGCAAAAGGG-AAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGA
EST: gi|193516306|gb|FK472546.1|FK472546
EST:     TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAAgtaatattag ... cttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|193430304|gb|FK393278.1|FK393278
EST:     TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAA                         GTAAAAGTCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATG
genomic: TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAAgtaatattag ... cttcttttagG-AAAAG-CAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATG
EST: gi|208274007|gb|GE071041.1|GE071041
EST:     TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAAgtaatattag ... cttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|14012034|gb|BG726965.1|BG726965
EST:     TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAAgtaatattag ... cttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|193333305|gb|FK300366.1|FK300366
EST:     TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAAgtaatattag ... cttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|193382822|gb|FK346705.1|FK346705
EST:     TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: TGATATTGTCGCATGCAGCAGCTGTTCAAAGATACCGAGCGAAGTACCAAgtaatattag ... cttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|207836084|gb|GD807411.1|GD807411
EST:     GAGCGAAGTACCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: GAGCGAAGTACCAAgtaatattag ... cttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactcacttaaactactaaaatgttcttatgaggttatgaatgtgcttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAGCCTCTTACAAGATCAAAGGCTGACAATTTTGCAGCTCAAAGAGCCAGAG
             tactaaa  putative branch site (score: 1)
                                           tgcttctttt  putative PPT
       ttaaactactaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaatatttcgaggatcaaattatggtttactcttttgtttaatggactcacttaaactactaaaatgttcttatgaggttatgaatgtgcttcttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAGCCTCTTACAAGATCAAAGGCTGACAATTTTGCAGCTCAAAGAGCCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgtg