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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttcaacttccccaaattcatagtaatgtacagctctcataactattttttcactaataaataaataatttgaatttctgtttaattatgagccacatgaaaagagggtagaaaaataagactaaaaaaattggttagctagattttttgtttatgttttaatgagatcactttgttaaaagcttttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG

Basic information

species Glycine max
transcript GLYMA03G40880.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G40880.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g28320.3 (Oryza sativa), 3'ss of exon 4
gtcagttcaacttccccaaattcatagtaatgtacagctctcataactattttttcactaataaataaataatttgaatttctgtttaattatgagccacatgaaaagagggtagaaaaataagactaaaaaaattggttagctagattttttgtttatgttttaatgagatcactttgttaaaagcttttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCC-TGCAAGTACAGTCCTG--
                                                                                          | | |||  |     |||   ||  |  | | |  |       ||||     | | ||   ||     ||           ||| |      |   ||| | ||   || |||||||||||||||||||| |||||||||||  |||| || ||||| |||| |||||  |  | | |  | |  || || |   ||    | |  |  
------------------------------------------------------------------------------------------tgttagctcctattcaagtttgtgcatcatttactccttgttcattgaacctccacatcgcttcaccgtgccac-------tcattcgaagcattacttgtgtt--cagGGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTTTGCTGGCAGGGCTGCTGTACAGAGCATACCATCTGAGAGTTGGCTGGTA

upper sequence: GLYMA03G40880.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g28320.1 (Oryza sativa), 3'ss of exon 4
gtcagttcaacttccccaaattcatagtaatgtacagctctcataactattttttcactaataaataaataatttgaatttctgtttaattatgagccacatgaaaagagggtagaaaaataagactaaaaaaattggttagctagattttttgtttatgttttaatgagatcactttgttaaaagcttttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG
                                                                                          | | |||  |     |||   ||  |  | | |  |       ||||     | | ||   ||     ||           ||| |      |   ||| | ||   || |||||||||||||||||||| |||||||||||  |||| || ||||| |||| |||||  |  | | |  | |  || ||  |    |     |||
------------------------------------------------------------------------------------------tgttagctcctattcaagtttgtgcatcatttactccttgttcattgaacctccacatcgcttcaccgtgccac-------tcattcgaagcattacttgtgtt--cagGGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTTTGCTGGCAGGGCTGCTGTACAGAGCATACCATCTGAGAGTTGGCTG

upper sequence: GLYMA03G40880.3 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G024315_T01 (Zea mays), 3'ss of exon 4
gtcagttcaacttccccaaattcatagtaatgtacagctctcataactattttttcactaataaataaataatttgaatttctgtttaattatgagccacatgaaaagagggtagaaaaataagactaaaaaaattggttagctagattttttgtttatgttttaatgagatcactttgttaaaagcttttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG
                                                                                         |  | |  || ||| |  |    || ||| |    || ||| |||   |    |  ||| || |    |||| ||||     ||  | || |     |||        |||||  | |||||||||||||||||||| || |||||||| || || ||||||||||| | ||||||    ||| |  || ||||     |    |||
---------------------------------------------------------------------------------gaacaaggtcttaatacatatgtattgt---tacaaatacgtaaccaaacaaa---gcctaccggatattat---catgtattaa--gattctttatgctgtggacttc-------agAGAATTGGGCATTGGAATTGTACCATACAGTCCTCTTGGCCGTGGGTTTTTTGGTGGAAGAGGAGTGAAAGAACAAGTGTCTGCTGAATCTAATCTG

upper sequence: GLYMA03G40880.3 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G813143_T02 (Zea mays), 3'ss of exon 4
gtcagttcaacttccccaaattcatagtaatgtacagctctcataactattttttcactaataaataaataatttgaatttctgtttaattatgagccacatgaaaagagggtagaaaaataagactaaaaaaattggttagctagattttttgtttatgttttaatgagatcactttgttaaaagcttttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG
                                                                                         ||   ||    |   ||     |    |   |     |   |   |||||| | |  |  |     | |||  || ||  |     ||||| | ||    ||      || |||||||| |||||||| || ||||||||||| ||||| || ||||| |||| |||||  | || | | |||  | | ||  ||   |   |  ||
-----------------------------------------------------------------------------------------ttgcaagttctaattaacttatgcttcatttt-----tcttatctttggttcgttgaacatcgatatcatgcatttatctg-----tttgtcataaatgcttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG

upper sequence: GLYMA03G40880.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0030g01960.t01 (Vitis vinifera), 3'ss of exon 4
gtcagttcaacttccccaaattcatagtaatgtacagctctcataactattttttcactaataaataaataatttgaatttctgtttaattatgagccacatgaaaagagggtagaaaaataagactaaaaaaattggttagctagattttttgtttatgttttaatgagatcactttgttaaaagcttttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG
                                                                                           | |    | |||    ||           || | ||| ||        |  ||   | | ||  ||||   |  |||| ||    || | |     ||  ||    || ||||||||||||||||| || |||||  | ||||||||||| || ||||||||||| |  |||||| |||||| | ||||||||            
-------------------------------------------------------------------------------------------aaggattatatgctt-gatacctttcttgtatggctacaact-----ctctctctctctcttaattataaat--atgacatgctgttttcatttatttaaatatgcagGGAGCTTGGCATTGGAATAGTTCCATACTGTCCTCTTGGTCGTGGATTTTTTGGTGGTAGGGGAGTTGTGGAAAGTTTGCCTGCATACTTG------

upper sequence: GLYMA03G40880.3 (Glycine max), 3'ss of exon 4
lower sequence: EFJ35213 (Selaginella moellendorffii), 3'ss of exon 4
gtcagttcaacttccccaaattcatagtaatgtacagctctcataactattttttcactaataaataaataatttgaatttctgtttaattatgagccacatgaaaagagggtagaaaaataagactaaaa--aaattggttagctagattttttgtttatgttttaatgagatcactttgttaaaagcttttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGC----CTGCAAGTACAGTCCTG
                                                                                                                        |  | || ||   ||  |  ||   |  |  |  ||||  |  |  | |    ||| |||  | ||     ||  | | |||||||||||||| ||||| || ||||| |||||||| || |||||||| ||    |||||||   || | || ||  | |    |    | | | ||| | 
-----------------------------------------------------------------------------------------------------------------------gttggtctcaacccaagctctttttatcaagatcatgttcttactagagttctttcatttttctcaa----ctttctcacagAGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTTCTCCGGCAAAGCGATTGTTGAGAAGCTACAAAGCGATGATTCCCGTCTT-

upper sequence: GLYMA03G40880.3 (Glycine max), 3'ss of exon 4
lower sequence: EFJ24149 (Selaginella moellendorffii), 3'ss of exon 4
gtcagttcaacttccccaaattcatagtaatgtacagctctcataactattttttcactaataaataaataatttgaatttctgtttaattatgagccacatgaaaagagggtagaaaaataagactaaaa--aaattggttagctagattttttgtttatgttttaatgagatcactttgttaaaagcttttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGC----CTGCAAGTACAGTCCTG
                                                                                                                        |  | || ||   ||  |  ||   |  |  |  ||||  |  |  | |     || |||  | ||     ||  |   |||||||||||||| ||||| || ||||| |||||||| || |||||||| ||    |||||||   || | || ||  | |    |    | | | ||| | 
-----------------------------------------------------------------------------------------------------------------------gttggtctcaacccaagctctttttatcaagatcatgttcttactagagttcttccatttttctcaa----ctttctcgcagAGAGCTTGGCATCGGAATAGTTCCATACAGCCCTCTCGGACGAGGCTTCTTCTCCGGCAAAGCGATTGTTGAGAAGCTACAAAGCGATGATTCCCGTCTT-

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:     TGGTCCCTATGGACTCGTGACATTGAAGAGGAGATAATTCCTCTCTGCAG                         AGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
genomic: TGGTCCCTATGGACTCGTGACATTGAAGAGGAGATAATTCCTCTCTGCAGgtcagttcaa ... ttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
EST: gi|58016837|gb|CX703579.1|CX703579
EST:     TGGTCCCTATGGACTCGTGACATTGAAGAGGAGATAATTCCTCTCTGCAG                         AGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
genomic: TGGTCCCTATGGACTCGTGACATTGAAGAGGAGATAATTCCTCTCTGCAGgtcagttcaa ... ttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
EST: gi|22525360|gb|BU084171.1|BU084171
EST:     TGGTCCCTATGGACTCGTGACATTGAAGAGGAGATAATTCCTCTCTGCAG                         AGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
genomic: TGGTCCCTATGGACTCGTGACATTGAAGAGGAGATAATTCCTCTCTGCAGgtcagttcaa ... ttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
EST: gi|10709064|gb|BF008788.1|BF008788
EST:     TGGTCCCTATGGACTCGTGACATTGAAGAGGAGATAATTCCTCTCTGCAG                         AGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
genomic: TGGTCCCTATGGACTCGTGACATTGAAGAGGAGATAATTCCTCTCTGCAGgtcagttcaa ... ttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
EST: gi|192313023|gb|FK003661.1|FK003661
EST:     TGGTCCCTATGGACTCGTGACATTGAAGAGGAGATAATTCCTCTCTGCAG                         AGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
genomic: TGGTCCCTATGGACTCGTGACATTGAAGAGGAGATAATTCCTCTCTGCAGgtcagttcaa ... ttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
EST: gi|26048905|gb|CA785358.1|CA785358
EST:     TGGTCCCTATGGACTCGTGACATTGAAGAGGAGATAATTCCTCTCTGCAG                         AGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
genomic: TGGTCCCTATGGACTCGTGACATTGAAGAGGAGATAATTCCTCTCTGCAGgtcagttcaa ... ttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
EST: gi|14008706|gb|BG725310.1|BG725310
EST:     TGGTCCCTATGGACTCGTGACATTGAAGAGGAGATAATTCCTCTCTGCAG                         AGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
genomic: TGGTCCCTATGGACTCGTGACATTGAAGAGGAGATAATTCCTCTCTGCAGgtcagttcaa ... ttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
EST: gi|254343582|gb|GR857338.1|GR857338
EST:     TGGTCCCTATGGACTCGTGACATTGAAGAGGAGATAATTCCTCTCTGCAG                         AGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
genomic: TGGTCCCTATGGACTCGTGACATTGAAGAGGAGATAATTCCTCTCTGCAGgtcagttcaa ... ttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
EST: gi|192313024|gb|FK003662.1|FK003662
EST:     TGGTCCCTATGGACTCGTGACATTGAAGAGGAGATAATTCCTCTCTGCAG                         AGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
genomic: TGGTCCCTATGGACTCGTGACATTGAAGAGGAGATAATTCCTCTCTGCAGgtcagttcaa ... ttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
EST: gi|18038680|gb|BM306974.1|BM306974
EST:     TGGTCCCTATGGACTCGTGACATTGAAGAGGAGATAATTCCTCTCTGCAG                         AGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
genomic: TGGTCCCTATGGACTCGTGACATTGAAGAGGAGATAATTCCTCTCTGCAGgtcagttcaa ... ttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
EST: gi|20811954|gb|BQ296432.1|BQ296432
EST:     ATTCCTCTCTGCAG                         AGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT
genomic: ATTCCTCTCTGCAGgtcagttcaa ... ttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattttttgtttatgttttaatgagatcactttgttaaaagcttttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG
                ttttaat  putative branch site (score: 3)
                                          cttttatt  putative PPT
     ttttgtttatgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagttcaacttccccaaattcatagtaatgtacagctctcataactattttttcactaataaataaataatttgaatttctgtttaattatgagccacatgaaaagagggtagaaaaataagactaaaaaaattggttagctagattttttgtttatgttttaatgagatcactttgttaaaagcttttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTG

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