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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatattttagcactgactctgcttcttatattgtagaatttttccatgtgaaaaattaggagataatagcaaattaacaatccatccttcatcttg...

Basic information

species Glycine max
transcript GLYMA03G40880.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G40880.3 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os10g28320.1 (Oryza sativa), 5'ss of exon 5
AGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaat-attttagcactg----actctgcttcttatattgtagaattt----------ttccatgtgaaaaattaggagataatagcaaattaacaatccatccttcatcttg---
 |||||||||||||||||||| |||||||||||  |||| || ||||| |||| |||||  |  | | |  | |  || ||  |    |     |||||| ||| |  ||  ||||     | ||| ||||| | |  |   | |||          ||| ||     |  | || | ||  ||  || |||  |     |     |  |     
GGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTTTGCTGGCAGGGCTGCTGTACAGAGCATACCATCTGAGAGTTGGCTGgtaaaattaaattcacactactataatcttcttct-acacagggaagtttgggtatagtcttctattctgcagttgagtacatccta-taacttagtatcttctttgctacttcacag

upper sequence: GLYMA03G40880.3 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G024315_T01 (Zea mays), 5'ss of exon 5
AGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatattttagcactgactctgcttcttatattgtagaatttttccatgtgaaaaattaggagataatag-caaattaacaatccatccttcatcttg---------------------------
|||  | |||||||||||||||||||| || |||||||| || || ||||||||||| | ||||||    ||| |  || ||||     |    ||||||  |  | ||  ||| | ||   ||    ||||  |    || ||   | || ||||  |  |  |  | | |    | | ||||  |   | |  |                             
AGAATTGGGCATTGGAATTGTACCATACAGTCCTCTTGGCCGTGGGTTTTTTGGTGGAAGAGGAGTGAAAGAACAAGTGTCTGCTGAATCTAATCTGgtatcaagtattgacacagtctac-ctcagaatatcatttctttcttttgt-tgcaaaaaaaacatttcttggtctgcatcaaaatctttttcttagttcacttacagattttactttggcttgtcag

upper sequence: GLYMA03G40880.3 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM5G813143_T02 (Zea mays), 5'ss of exon 5
AGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatattttagcactgactctgct-tcttatattgtagaatttttccatgtgaaaaattaggagataatagcaaattaacaatccatccttcatcttg
 |||||||| |||||||| || ||||||||||| ||||| || ||||| |||| |||||  | || | | |||  | | ||  ||   |   |  ||||| |  |  ||  ||||  |       | || ||  |||   || ||    |   |   |  | |  |    |   |  |    |   |    |    ||
GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaatttacactatcgtaataattttctacagtaatgttattgttagactatgttgtgtatgtgtgtgtggaaca-tggtttttaaaacggtatg

upper sequence: GLYMA03G40880.3 (Glycine max), 5'ss of exon 5
lower sequence: Vv14s0030g01960.t01 (Vitis vinifera), 5'ss of exon 5
AGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatattttagcactgactctgcttcttatattgtagaatttttccatgtgaaaaatt--aggagataatagcaaattaacaatccatccttcatcttg
 ||||||||||||||||| || |||||  | ||||||||||| || ||||||||||| |  |||||| |||||| | ||||||||      ||     |    |  |||     ||  |||| ||  | || || | ||| | |  | |  | |   |  |||| | || || | |||   ||| |  | || |     
GGAGCTTGGCATTGGAATAGTTCCATACTGTCCTCTTGGTCGTGGATTTTTTGGTGGTAGGGGAGTTGTGGAAAGTTTGCCTGCATACTTGgtatacattttgtcatttt-ttttgtttctgttttct-taatgcaaaatatctgaaagaaatattcttcaggaaacaa-agtatattctgaatgctccattta-----

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|58015079|gb|CX701821.1|CX701821
EST:     TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG                         ACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
genomic: TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatatt ... cacttggcagACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
EST: gi|58016837|gb|CX703579.1|CX703579
EST:     TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG                         ACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
genomic: TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatatt ... cacttggcagACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
EST: gi|22525360|gb|BU084171.1|BU084171
EST:     TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG                         ACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
genomic: TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatatt ... cacttggcagACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
EST: gi|10709064|gb|BF008788.1|BF008788
EST:     TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG                         ACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
genomic: TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatatt ... cacttggcagACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
EST: gi|7692973|gb|AW761072.1|AW761072
EST:     TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG                         ACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
genomic: TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatatt ... cacttggcagACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
EST: gi|192313023|gb|FK003661.1|FK003661
EST:     TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG                         ACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
genomic: TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatatt ... cacttggcagACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
EST: gi|209721585|gb|BW671726.1|BW671726
EST:     TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG                         ACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
genomic: TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatatt ... cacttggcagACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
EST: gi|21600510|gb|BQ610841.1|BQ610841
EST:     TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG                         ACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
genomic: TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatatt ... cacttggcagACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
EST: gi|26048905|gb|CA785358.1|CA785358
EST:     TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG                         ACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
genomic: TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatatt ... cacttggcagACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
EST: gi|6666289|gb|AW277748.1|AW277748
EST:     TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG                         ACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
genomic: TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatatt ... cacttggcagACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
EST: gi|10254586|gb|BE822352.1|BE822352
EST:     TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG                         ACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
genomic: TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatatt ... cacttggcagACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
EST: gi|10233104|gb|BE802049.1|BE802049
EST:     TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG                         ACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
genomic: TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatatt ... cacttggcagACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
EST: gi|14008706|gb|BG725310.1|BG725310
EST:     TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG                         ACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
genomic: TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatatt ... cacttggcagACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
EST: gi|254343582|gb|GR857338.1|GR857338
EST:     TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG                         ACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
genomic: TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatatt ... cacttggcagACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
EST: gi|192313024|gb|FK003662.1|FK003662
EST:     TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG                         ACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
genomic: TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatatt ... cacttggcagACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
EST: gi|18038680|gb|BM306974.1|BM306974
EST:     TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG                         ACTTTACATCATCCTCGGTTCCCAGCCGAGAACCTAAACCAGAACAAGAGA
genomic: TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatatt ... cacttggcagACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
EST: gi|20811954|gb|BQ296432.1|BQ296432
EST:     TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG                         ACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA
genomic: TTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatatt ... cacttggcagACTTTACATCATCCTCGGTTCCAAGCAGAGAACATAAACAAGAACAAGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatattttagcactgactctgcttcttatattgtagaatttttccatgtgaaaaattaggagataatagcaaattaacaatccatccttcatcttg

- - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG