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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcactatgaggatgatcaaaatttaatgcttctcaatgaaattgttcttaggatttgccttctccattcctaatacagaagtttttgtgttctttgcagGCTAAGGTAGTTGGAAAGTCGAGCTCTGCTGGTGGTGGTAACTTAGCTGGGTATGATGAATATGTACCAATGGTGGACAAAGCTGTTGATGCTGCCTGGA

Basic information

species Glycine max
transcript GLYMA12G04460.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G04460.1 (Glycine max), 3'ss of exon 10
lower sequence: AT4G39170.2 (Arabidopsis thaliana), 3'ss of exon 5
atcactatgaggatgatcaaaatttaatgcttctcaatgaaattgttcttaggatttgccttctccattcctaatacagaagtttttgtgttctttgcagGCTAAGGTAG---TTGGAAAGTCGAGCTCTGCTGGTGGTGGTAACTTAGCTGGGTATGATGAATATGTACCAATGGTGGACAAAGCTGTTGATGCTGCCTGGA---
                      | | ||   | |  |  |  ||||| |||     | | |  | | |   |   |          ||  |  ||||||||| ||||| |    |||  |  |||| | ||| ||| ||      || || || |||||||| ||||| |||||||| |||||||||||||| ||  ||||||   
---------------------gtatgatatattttcac-actttgtttttatagaatacatgattcgtggttttgaatcgtccaagtgattattttgcagGCAAAGGTTGGTTCTGGTGAAACGAGTTTTGCCGGTAGT------TTTGCAGGTTATGATGAGTATGTTCCAATGGTTGACAAAGCTGTTGACGCCACCTGGAAGG

upper sequence: GLYMA12G04460.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 3'ss of exon 11
atcactatgaggatgatcaaaatttaatgcttctcaatgaaattgttcttaggatttgccttctccattcctaatacagaagtttttgtgttctt--tgcagGCTAAGGTAGTTGGAAAGTCGAGCTCTGCTGGTGGTGGTAACTTAGCTGGGTATGATGAATATGTACCAATGGTGGACAAAGCTGTTGATGCTGCCTGGA------
   | |  | | ||      | |  ||||  |   | |||||     || |   | |    |    | |  |  | || |  ||| | || |     |||||||||||||||||||||||   |||| |||||      ||| ||| |  ||||||||||||||||| || ||||| ||||||||||||||||| |  ||||      
-gtattgagggcatttcttgagtgcaatgtctaagattgaaagaag-ctcacattgtatagtagttacttattcttcaaatatttctttggtggaaatgcagGCTAAGGTAGTTGGAAAGGTAAGCTATGCTG------GTAGCTTCGGGGGGTATGATGAATATGTTCCCATGGTCGACAAAGCTGTTGATGCAGGTTGGAAGAAGC
















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|208161112|gb|GD961718.1|GD961718
EST:     AAGTGACGAAGAGCTACTCACACCTGAGGTTGACACCTGTTCGGGAGGAA                         GCTAAGGTAGTTGGAAAGTCGAGCTCTGCTGGTGGTGGTAACTTAGCTGGG
genomic: AAGTGACGAAGAGCTACTCACACCTGAGGTTGACACCTGTTCGGGAGGAAgtaagtgttg ... ttctttgcagGCTAAGGTAGTTGGAAAGTCGAGCTCTGCTGGTGGTGGTAACTTAGCTGGG
EST: gi|7924506|gb|AW830532.1|AW830532
EST:     AAGTGACGAAGAGCTACTCACACCTGAGGTTGACACCTGTTCGGGAGGAA                         GCTAAGGTAGTTGGAAAGTCGAGCTCTGCTGGTGGTGGTAACTTAGCTGGG
genomic: AAGTGACGAAGAGCTACTCACACCTGAGGTTGACACCTGTTCGGGAGGAAgtaagtgttg ... ttctttgcagGCTAAGGTAGTTGGAAAGTCGAGCTCTGCTGGTGGTGGTAACTTAGCTGGG
EST: gi|19053078|gb|BM731745.1|BM731745
EST:     AAGTGACGAAGAGCTACTCACACCTGAGGTTGACACCTGTTCGGGAGGAA                         GCTAAGGTAGTTGGAAAGTCGAGCTCTGCTGGTGGTGGTAACTTAGCTGGG
genomic: AAGTGACGAAGAGCTACTCACACCTGAGGTTGACACCTGTTCGGGAGGAAgtaagtgttg ... ttctttgcagGCTAAGGTAGTTGGAAAGTCGAGCTCTGCTGGTGGTGGTAACTTAGCTGGG
EST: gi|193419035|gb|FK382265.1|FK382265
EST:     AAGTGACGAAGAGCTACTCACACCTGAGGTTGACACCTGTTCGGGAGGAA                         GCTAAGGTAGTTGGAAAGTCGAGCTCTGCTGGTGGTGGTAACTTAGCTGGG
genomic: AAGTGACGAAGAGCTACTCACACCTGAGGTTGACACCTGTTCGGGAGGAAgtaagtgttg ... ttctttgcagGCTAAGGTAGTTGGAAAGTCGAGCTCTGCTGGTGGTGGTAACTTAGCTGGG
EST: gi|22524635|gb|BU083446.1|BU083446
EST:     AAGCGATGAAGAGCTACTCACACCTGAGGTTGACACCTGTTCGGGAGGAA                         GCTAAGGTAGTTGGAAAGTCGAGCTATGCTGGTGGTGGTAACTTAGCTGGG
genomic: AAGTGACGAAGAGCTACTCACACCTGAGGTTGACACCTGTTCGGGAGGAAgtaagtgttg ... ttctttgcagGCTAAGGTAGTTGGAAAGTCGAGCTCTGCTGGTGGTGGTAACTTAGCTGGG
EST: gi|193547922|gb|FK504755.1|FK504755
EST:     GTTCGGGAGGAA                         GCTAAGGTAGTTGGAAAGTCGAGCTCTGCTGGTGGTGGTAACTTAGCTGGG
genomic: GTTCGGGAGGAAgtaagtgttg ... ttctttgcagGCTAAGGTAGTTGGAAAGTCGAGCTCTGCTGGTGGTGGTAACTTAGCTGGG
EST: gi|208268732|gb|GE069433.1|GE069433
EST:     AAGTGACGAAGAGCTACTCACACCTGAGGTTGACACCTGTTCGGGAGGAA                         GCTAAGGTAGTTGGAAAGTCGAGCTCTGCTGGTGGTGGTAACTTAGCTGGG
genomic: AAGTGACGAAGAGCTACTCACACCTGAGGTTGACACCTGTTCGGGAGGAAgtaagtgttg ... ttctttgcagGCTAAGGTAGTTGGAAAGTCGAGCTCTGCTGGTGGTGGTAACTTAGCTGGG
EST: gi|193359037|gb|FK325467.1|FK325467
EST:     AAGTGACGAAGAGCTACTCACACCTGAGGTTGACACCTGTTCGGGAGGAA                         GCTAAGGTAGTTGGAAAGTCGAGCTCTGCTGGTGGTGGTAACTTAGCTGGG
genomic: AAGTGACGAAGAGCTACTCACACCTGAGGTTGACACCTGTTCGGGAGGAAgtaagtgttg ... ttctttgcagGCTAAGGTAGTTGGAAAGTCGAGCTCTGCTGGTGGTGGTAACTTAGCTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttaggatttgccttctccattcctaatacagaagtttttgtgttctttgcagGCTAAGGTAGTTGGAAAGTCGAGCTCTGCTGGTGGTGGTAACTTAGCTGGGTATGATGAATATGTACCAATGGTGGACAAAGCTGTTGATGCTGCCTGGA
                       tcctaat  putative branch site (score: 2)
                                     tttttgtgttcttt  putative PPT
                                  aagttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcactatgaggatgatcaaaatttaatgcttctcaatgaaattgttcttaggatttgccttctccattcctaatacagaagtttttgtgttctttgcagGCTAAGGTAGTTGGAAAGTCGAGCTCTGCTGGTGGTGGTAACTTAGCTGGGTATGATGAATATGTACCAATGGTGGACAAAGCTGTTGATGCTGCCTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - gaggatg
- - - - - - - - - - - - - - gcttctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgtg