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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatttgtatatctagtccttttgtgtaatggacttacttaagatgctaaaatattcttatgtggtgatgaatgtgcttgttttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAGCCTCTTACAAGATCAAAGGCCGACAATTTAGCAGCTCAAAGAGCCAGAG

Basic information

species Glycine max
transcript GLYMA07G11310.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G11310.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g46280.3 (Oryza sativa), 3'ss of exon 6
-------------------------------gtaatatttgta-tatctagt-ccttttgtgtaatggacttacttaagatgctaaaatattcttatgtggtgatgaatgtgcttgttttttagGAAAAGC------AAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAGCCTCTTACAAGATCAAAGGCCGACAATTTAGCAGCTCAAAGAGCCAGAG
                               |    ||||  | |||  | | |   || | | |   ||||  ||   || |    || |    |||| ||    ||||   || ||      ||| |||      ||||||| |||||||| || |||||||||||||| |||||||| ||  | |        || || || |     ||||| || || || ||||
gtaaaatagcagaatgacagttcagctcaaggctggatttacactatgcaatgcaaattatctcagttactt--ttgctatccctgtatctgagaatgtagtctgcaatgcatttcttccaattgaacagCTTTATCAAAAGGGGAGGATTGGAATTCTCTTGGATTTTGTCTGGTATGAACCATTCAGTGACAGCAATGCTGATAGGGCTGCAGCACAGAGGGCAAGAG

upper sequence: GLYMA07G11310.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G18080.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------------gtaatatttgtatatctagtcc--ttttgtgtaatggacttacttaagatgctaaaatattcttatg-tggtgatgaatgtgcttgttttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAGCCTCTTACAAGATCAAAGGCCGACAATTTAGCAGCTCAAAGAGCCAGAG
                      ||  | ||  | |   |  |    | |  || |||  || ||  ||    |||    |     | |  |  | ||     ||    ||||  |||  || |||||||||||| ||||||| || || ||||| |||||||||||||| ||||| |||   || || || ||| | |||||||||||||| ||||
gtaaacaaataacttctaatacgttttcttgatcttcttgatgtgatatgatgaaataaacctatatatatggctcttttgccagtgtactactaatcttaatgaaaattttccagGCGAAACAAAAGGGAAGGGTTGGGATACTTTTAGATTTCGTTTGGTATGAGCCGCTTACTAGAAGTAAAGCAGATAATCTTGCAGCTCAAAGAGCAAGAG

upper sequence: GLYMA07G11310.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G18070.2 (Arabidopsis thaliana), 3'ss of exon 3
----gtaatatttgtatatctagtccttttgtgtaatggacttacttaagatgctaaaatattcttatgtggtgatgaatgtgcttgttttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAGCCTCTTACAAGATCAAAGGCCGACAATTTAGCAGCTCAAAGAGCCAGAG
    ||||||    ||||             |||        || | || |||   |    | || | |   | |   |     |   || | |||| || |||||||||||| ||||||| ||  ||||||||||||||| |||||| ||||| ||     | || ||||||   || ||||||||||| ||||
gtatgtaataaccttataggctccttcaagttgtttctatgatattaaacatgtatatgattactaaagatctaactgacaaatt--cttctcagGAGAAACAAAAGGGAAGGGTTGGGATTCTACTGGATTTTGTTTGGTTTGAGCCACTTACGAGTAGTCAAGCAGACAATGACGCTGCTCAAAGAGCAAGAG

upper sequence: GLYMA07G11310.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g02680.t01 (Vitis vinifera), 3'ss of exon 6
--------------gtaatatttgtatatctagtccttttg-tgtaatggactt-acttaagatgctaaaatattcttatgtggtgatgaatgt--gcttgttttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAGCCTCTTACAAGATCAAAGGCCGACAATTTAGCAGCTCAAAGAGCCAGAG
               || | ||| | || ||      |||| ||| |||   || | | ||      | || ||  | ||    |||   ||    |  ||||| | || || | |||||||| |||||||| || |||||||||||||||||||||||||||||||||||||||||||| |||||  |||||||||||||| ||||||
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|192318423|gb|FK006543.1|FK006543
EST:     TGATATTGTCACATGCAGCTGCTGTTCAAAGATACCGAGAGAAGTATCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: TGATATTGTCACATGCAGCTGCTGTTCAAAGATACCGAGAGAAGTATCAAgtaatatttg ... tgttttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|151405282|gb|EV275096.1|EV275096
EST:     TGATATTGTCACATGCAGCTGCTGTTCAAAGATACCGAGAGAAGTATCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: TGATATTGTCACATGCAGCTGCTGTTCAAAGATACCGAGAGAAGTATCAAgtaatatttg ... tgttttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|21994135|gb|BQ785663.1|BQ785663
EST:     TGATATTGTCACATGCAGCTGCTGTTCAAAGATACCGAGAGAAGTATCAA                         GAAAAGCAAATTTGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: TGATATTGTCACATGCAGCTGCTGTTCAAAGATACCGAGAGAAGTATCAAgtaatatttg ... tgttttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|10237463|gb|BE806351.1|BE806351
EST:     TGATATTGTCACATGCAGCTGCTGTTCAAAGATACCGAGAGAAGTATCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: TGATATTGTCACATGCAGCTGCTGTTCAAAGATACCGAGAGAAGTATCAAgtaatatttg ... tgttttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
EST: gi|192318424|gb|FK006544.1|FK006544
EST:     TGATATTGTCACATGCAGCTGCTGTTCAAAGATACCGAGAGAAGTATCAA                         GAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG
genomic: TGATATTGTCACATGCAGCTGCTGTTCAAAGATACCGAGAGAAGTATCAAgtaatatttg ... tgttttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttacttaagatgctaaaatattcttatgtggtgatgaatgtgcttgttttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAGCCTCTTACAAGATCAAAGGCCGACAATTTAGCAGCTCAAAGAGCCAGAG
           tgctaaa  putative branch site (score: 2)
                                           cttgtttttt  putative PPT
              taaaatattcttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatttgtatatctagtccttttgtgtaatggacttacttaagatgctaaaatattcttatgtggtgatgaatgtgcttgttttttagGAAAAGCAAAAGGGAAGGATTGGGATCCTCTTGGATTTTGTTTGGTATGAGCCTCTTACAAGATCAAAGGCCGACAATTTAGCAGCTCAAAGAGCCAGAG

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