Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtggtgttcataatttgtttatcttagtagtttgtacttttgcatagaggtttgtgttattgttcgtgatggatttgtgttgtttttgttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGCGAGATTTATGATACATATGGAGAAGATGCTCTTAAGGAAGGAATGGGTG

Basic information

species Glycine max
transcript GLYMA13G38790.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G38790.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g57340.1 (Oryza sativa), 3'ss of exon 1
tttgtggtgt-tcataatttgtttatcttagtagtttgtacttttgcatagaggtttgtgttattgttcgtgatggatttgtgttgtttttgttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGCGAGATTTATGATACATATGGAGAAGATGCTCTTAAGGAAGGAATGGGTG
|  ||  ||  |    | |  |||||||   ||   ||||   | |     |    | | ||  ||    ||    | |    || ||    |   |  |||| || ||  | ||||| || ||||| || |||||||||||||||||||| || || ||||||   || || ||||||||||| ||||| || |||||| 
tgagtactgaattgccaatgctttatctggttaagctgtatgatggggacaatagctttcttgatgag-atggcaaactaaaattcttgccttcatttcagTTCAAGGAATTGGCTCAGGCTTATGAAGTCCTGAGTGACCCTGAGAAGCGTGAAATCTATGATCAGTACGGTGAAGATGCTCTCAAGGAGGGGATGGGTC

upper sequence: GLYMA13G38790.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G134917_T01 (Zea mays), 3'ss of exon 1
tttgtggtgttcataatttgtttatct-tagta-gtttgtacttttgcatagaggtttgtgttattgttcgtgatgga---tttgtgttgtttttgttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGCGAGATTTATGATACATATGGAGAAGATGCTCTTAAGGAAGGAATGGGTG
     |||| | ||   ||||   ||| || |  || |  |   | | || ||| | |   ||  || | | |||| |   |  | |||  |  | ||| |  |||| || ||||| ||||| || |||||||| || ||||| ||||| ||||| ||||||||||||  |||||| || ||||| || ||||| |||||||| |
-----ggtgatgattgattgtaagtctgtaatctgtataaatggtcgaatggagctgttgatttctgattgagatgaaaactaagagttcatgcttttgtttcagTTCAAGGAGCTAGCTCAGGCTTATGAGGTCCTCAGTGATCCTGAAAAGCGGGAGATTTATGATCAATATGGTGAGGATGCCCTCAAGGAGGGAATGGGAG

upper sequence: GLYMA13G38790.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0080g01230.t01 (Vitis vinifera), 3'ss of exon 1
tttgtggtgttcataatttgtttatcttagtagtttgtacttttgcatagaggtttgtgttattgttcgtgatggatttgtgttgtttttgttgg--------tgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGCGAGATTTATGATACATATGGAGAAGATGCTCTTAAGGAAGGAATGGGTG
         |||| |  || |||| | |  | || | ||       ||  || |||  ||| |   | ||  ||||  ||  ||       ||||        || |||| ||||| |||||||| || |||||||||||||||||||||||||| || || || ||||||   ||||| |||||||| || ||||||||||||||||
-------gattcacaggttttttagcctgattgtat-taaagcaatatgaagtttttagttttccgttgtagtggaactgaatttgaaacattgggtgtctcttgcagTTCAAAGAACTTGCTCAGGCTTATGAGGTTCTGAGTGACCCTGAGAAACGTGAAATCTATGATCAGTATGGTGAAGATGCCCTCAAGGAAGGAATGGGTG

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|16105212|gb|BI892952.1|BI892952
EST:     GAAAGCTTTTCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAG                         TTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
genomic: GAAAGCCGC-CATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAGgtattttcaa ... gttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
EST: gi|209704620|gb|BW673408.1|BW673408
EST:     AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAG                         TTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
genomic: AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAGgtattttcaa ... gttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
EST: gi|213619574|gb|DB957406.1|DB957406
EST:     AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAG                         TTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
genomic: AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAGgtattttcaa ... gttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
EST: gi|209720721|gb|BW677539.1|BW677539
EST:     AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAG                         TTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
genomic: AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAGgtattttcaa ... gttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
EST: gi|10845809|gb|BF068851.1|BF068851
EST:     AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAG                         TTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
genomic: AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAGgtattttcaa ... gttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
EST: gi|19935305|gb|BQ080335.1|BQ080335
EST:     AGAAAGCCGCCATTAATAACCATCCTGACAAAGGCGGGGATCCCGAGAAG                         TTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
genomic: AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAGgtattttcaa ... gttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
EST: gi|209697332|gb|BW655573.1|BW655573
EST:     AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAG                         TTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
genomic: AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAGgtattttcaa ... gttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
EST: gi|6566370|gb|AW234039.1|AW234039
EST:     AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGTGATCCCGAGAAG                         TTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
genomic: AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAGgtattttcaa ... gttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
EST: gi|209705227|gb|BW673767.1|BW673767
EST:     AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAG                         TTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
genomic: AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAGgtattttcaa ... gttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
EST: gi|213593343|gb|DB966112.1|DB966112
EST:     AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAG                         TTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
genomic: AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAGgtattttcaa ... gttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
EST: gi|16346351|gb|BI971946.1|BI971946
EST:     AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAG                         TTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
genomic: AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAGgtattttcaa ... gttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
EST: gi|6567081|gb|AW234708.1|AW234708
EST:     AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGTGATCCCGAGAAG                         TTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
genomic: AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAGgtattttcaa ... gttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
EST: gi|11412469|gb|BF424480.1|BF424480
EST:     AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAG                         TTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
genomic: AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAGgtattttcaa ... gttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
EST: gi|151399061|gb|EV268932.1|EV268932
EST:     AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAG                         TTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
genomic: AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAGgtattttcaa ... gttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
EST: gi|213610686|gb|DB961161.1|DB961161
EST:     AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAG                         TTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
genomic: AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAGgtattttcaa ... gttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
EST: gi|23726442|gb|BU761214.1|BU761214
EST:     AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAG                         TTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
genomic: AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAGgtattttcaa ... gttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
EST: gi|213601665|gb|DB972401.1|DB972401
EST:     AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAG                         TTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
genomic: AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAGgtattttcaa ... gttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
EST: gi|209705099|gb|BW667758.1|BW667758
EST:     AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAG                         TTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
genomic: AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAGgtattttcaa ... gttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
EST: gi|192308577|gb|FK002473.1|FK002473
EST:     AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAG                         TTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC
genomic: AGAAAGCCGCCATTAAGAACCATCCTGACAAAGGCGGGGATCCCGAGAAGgtattttcaa ... gttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catagaggtttgtgttattgttcgtgatggatttgtgttgtttttgttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGCGAGATTTATGATACATATGGAGAAGATGCTCTTAAGGAAGGAATGGGTG
                                        tttttgtt  CT-rich tract
              ttattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtggtgttcataatttgtttatcttagtagtttgtacttttgcatagaggtttgtgttattgttcgtgatggatttgtgttgtttttgttggtgtagTTTAAAGAGCTTGCTCAAGCCTATGAGGTTCTGAGTGACCCTGAGAAGCGCGAGATTTATGATACATATGGAGAAGATGCTCTTAAGGAAGGAATGGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA