Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctctctctctctctctctctctctctctctctctctctcttttatgtttttgggttctcttttactctgatacatatgtttatttattttcgggtaatttaattatgctttttttaacaaaataaataaatttatgcgtttgtgttgttggcaattggtgtagATGGATCCCAAGTTTCTGAGGAATCAGAGGTACGCGAGGAAGCACAACAAGAAGAGTGGTGAAACAGCCACCGAGGAAGAGTGAAATGGCACTTTCTAAC

Basic information

species Glycine max
transcript GLYMA09G04280.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g28750.1 (Oryza sativa), 3'ss of exon 1
gtctctctctctctctctctctctctctctctctctctctcttttatgtttttgggttctcttttactctgatacatatgtt-tatttattttcgggtaatttaattatgctttttttaacaaaataaataaatttatgcgtttgtgttgttggcaattggtgtagATGGATCCCAAGTTTCTGAGGAATCAGAGGTACGCGAGGAAGCACAACAAGAAGAGTGGTGAAACAGCCACCGAGGAAGAGTGAAATGGCACTTTCTAAC
                                                             |   |     || || ||||  |   | || |   | |||| |||  || |   ||        |        |||   |  |   ||||       |  | |||||||| || ||||| || ||||| ||||||||| ||||||||||||||||||||||||||||  | |   |||||||  |                    
-------------------------------------------------------------tcggaaatcaattcaaatgtcctcgctgttatgttgaaattgaatcctgttgcctt-----gtttccgcgttcttacctgggttctttgtaaattgcttttatagATGGACCCAAAGTTCCTCAGGAACCAGAGGTACTCGAGGAAGCACAACAAGAAGAGTGGTGAGGCTGAATCCGAGGAGTAA-------------------

upper sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g19840.1 (Oryza sativa), 3'ss of exon 2
gtctctctctctctctctctctctctctctctctctctctcttttatgtttttgggttctcttttactctgatacatatgtttatttattttcgggtaatttaattatgctttttttaacaaaataaataaatttatgcgtttgtgttgttggcaattggtgtagATGGATCCCAAGTTTCTGAGGAATCAGAGGTACGCGAGGAAGCACAACAAGAAGAGTGGTGAAACAGCCACCGAGGA---AGAGTGAAATGGCACTTTCTAAC
                                                               |||   |||    | | |  ||  ||             || |      |||||  |    | |   | ||    |  |  | || ||  | ||   | |||||||| || ||||| |||||||| ||||| ||  | |||||||| |||||||||||||||||  | |   |||||||   |||  ||| | |  |||||    
---------------------------------------------------------------ttatcttgaattgtttatcaatcaatcagtattgtgcacaaatccaaaatttttgcctcctttac--acttctctcactgatctttttcaccatgtttatagATGGACCCAAAGTTCCTGAGGAACCAGAGATATTCCAGGAAGCATAACAAGAAGAGTGGTGAGGCTGAATCCGAGGAGTAAGATGGAAGTTGTCCTTTCG---

upper sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 2
gtctctctctctctctctctctctctctctctctctctctcttttatgtttttgggttctcttttactctgatacatatgtttatttattttcgggtaatttaattatgcttt--ttttaacaaaataaataaatttatgcgtttgtgttgttggcaattggtgtagATGGATCCCAAGTTTCTGAGGAATCAGAGGTACGCGAGGAAGCACAACAAGAAGAGTGGTGAAACAGCCACCGAGGAAGAGTGAAATGGCACTTTCTAAC
                                                            || ||||| |  | |  || |||  |   |  | | |  || |  |   | ||  ||||  |   | || | |   | ||| ||     ||||         || ||||||| |||||||| |||||||| | ||||||  | ||||||  ||||||||||||||||||  | |      ||||||      ||||   | | |   
--------------------------------------------------------acaactgttacttt--tgccaatttttcatctctaacagctgcttgagatgcaccttggtttttgctctacaactgaccctttgcattgaccatgtt---------tgcagATGGACCCCAAGTTCCTGAGGAACCTGAGGTATTCAAGGAAGGGCAACAAGAAGAGTGGTGAGGCTGAGGAGTAGGAAGGAAAGCATGGTTGTGTTTCCT

upper sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S28_307V6.1 (Physcomitrella patens), 3'ss of exon 2
gtctctctctctctctctctctctctctctctctctctctcttttatgtttttgggttctcttttactctgatacatatgtttatttattttcgggtaatttaattatgctttttttaacaaaataaataaatttatgcgtttgtgttgttggcaattggtgtagATGGATCCCAAGTTTCTGAGGAATCAGAGGTACGCGAGGAAGCACAACAAGAAGAGTGGTGAAACAGCCACCGAGGAAGAGTGAAATGGCACTTTCTAAC
       |   | | ||  | ||| ||| | |      || | ||  |      |  |  |  |    ||  ||| |   | | |   ||     | ||| | || || | | ||| |||            | |    |    | |  ||      ||  | ||||||| |||||||| || |||||||||||||| |||| ||||||||||  |    |||  |  |  |     |||||   |  | |    | |||    |
------gtgagtatatccgtttctttctttttgaacggctgtgttcggaccgcagagtgacactgtgccttctacctgc-tgtgtaccttacattgcaatgttatgatacgtatttgaacttctgttgctcttctgatagggcatatcttt-----ctgtggcagATGGACCCCAAGTTCCTAAGGAATCAGAGGTATGCGAAGAAGCACAACCGGTCTGGTGCGGCCAGTGAGGTTGAGGAGACGGAAGAGTAAATTTTAGGTC

upper sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S79_253V6.2 (Physcomitrella patens), 3'ss of exon 2
gtctctctctctctctctctctctctctctctctctctctcttttatgtttttgggttctcttttactctgatacatatgtttatttattttcgggtaatttaattatgctttttttaacaaaataaataaatttatgcgtttgtgttgttggcaattggtgtagATGGATCCCAAGTTTCTGAGGAATCAGAGGTACGCGAGGAAGCACAACAAGAAGAGTGGTGAAACAGCCACCGAGGAAGAGTGAAATGGCACTTTCTAAC
                                                         |  |    |  |   ||   || |  ||||       ||| ||     | ||| || |    |        |   |||   | ||    |     |    || |  ||||||| || ||||| ||||||||||||||||| |||| |||||||||| |||   ||| ||     |     |||   | |    |    |     |   
---------------------------------------------------------taccgagcag-caactagccatctcgattt-cccctaggtcatggccgtgtgcgttctccggctg------ttgtttttctcattgagataacgtgttgatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAGACAGGTGCTGCCGAGGAGGTTGAGTCCGCGGAGGAGTAGATCAAATGTG

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|6964053|gb|AW432746.1|AW432746
EST:     ACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAAAGGG--A                         -TGGATCCCAAGTTTCTGAGGAATCAGAGGTACCCGAGGAAGCACAACAAG
genomic: ACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAAAGGGGTAgtctctctct ... attggtgtagATGGATCCCAAGTTTCTGAGGAATCAGAGGTACGCGAGGAAGCACAACAAG
EST: gi|5677275|gb|AI938405.1|AI938405
EST:     ACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAAA-GGG--                         ATGGATCCCAAGTTTCTGAGGAATCAGAGGTACGCGAGGAAGCACAACAAG
genomic: ACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAAAGGGGTAgtctctctct ... attggtgtagATGGATCCCAAGTTTCTGAGGAATCAGAGGTACGCGAGGAAGCACAACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttaacaaaataaataaatttatgcgtttgtgttgttggcaattggtgtagATGGATCCCAAGTTTCTGAGGAATCAGAGGTACGCGAGGAAGCACAACAAGAAGAGTGGTGAAACAGCCACCGAGGAAGAGTGAAATGGCACTTTCTAAC
   ttttaac  putative branch site (score: 2)
     ttaacaaaataaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctctctctctctctctctctctctctctctctctctcttttatgtttttgggttctcttttactctgatacatatgtttatttattttcgggtaatttaattatgctttttttaacaaaataaataaatttatgcgtttgtgttgttggcaattggtgtagATGGATCCCAAGTTTCTGAGGAATCAGAGGTACGCGAGGAAGCACAACAAGAAGAGTGGTGAAACAGCCACCGAGGAAGAGTGAAATGGCACTTTCTAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA