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

...tggtggaaatttctctatgtatcatgtgtattttcatgtcttggactcgtgctttaatttggtctctttgactgagattccttgttctttatgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTTGCAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCT

Basic information

species Glycine max
transcript GLYMA18G47770.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g36190.1 (Oryza sativa), 3'ss of exon 3
-tggtggaaatttctctatgtatcatgtgt-at-tttcatgtcttggactcgtgctttaatttggtctctttgactga-gattccttgttctttatgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTTGCAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCT
       |   |   ||     | || | | || | |||| ||| | |||      ||| | |  ||       |||  ||||   ||||||   |  |  |||||||||||||||| ||||| ||||| ||||| || ||||| ||||| || ||||||||||| ||||||||||| |||||||||||  | || ||   || 
tcttcaaatgctcaactggaagttatttttcatatctcatttctagcactgccatcttattct--tcaaaacatctgctgattatctgttctacttt-tccagCAACGATCTGCAACAAAGGTTACATTTCCTCTAGTTTGGACCAACACTTGCTGCAGCCATCCTCTGTACCGTGAGTCTGAGCTTATACAGGAAAACTACC-

upper sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G108285_T01 (Zea mays), 3'ss of exon 3
-tggtggaaatttctctatgtatcat--gtgtattttcatgtcttggact--cgtgctttaatttggtctctttgactgagattccttgttctttatgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTTGCAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCT
 |  |  |  ||| | | | | | |       |||   |||| |  ||||  | |  | |  |    |   |||   | ||  || || | ||      || ||||| | || || || ||||| || || ||| | || ||||| || ||||| |||||||| || ||||||||||| |||||||||||  | |||||   || 
gtattaaatgtttgtttgtttttgaacaacacattccaatgtttgtgactatcctattcttttcaaattgtttttgataagtatcattctactc----gtgcagCAAAGGTCCGCGACAAAGGTTACCTTTCCTTTAGTTTGGACCAATACCTGCTGCAGCCACCCTCTGTACCGTGAGTCTGAGCTTATCCAGGAGAACTACC-

upper sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G133082_T01 (Zea mays), 3'ss of exon 3
-tggtggaaatttctctatgtatcatgtgtattttcatgtcttggactcgtgctttaatttggtctctttgactgagattccttgttc-tttatgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTTGCAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCT
 |  || |    | | | | ||   |  |  | |  |  ||   |  |  | | | | | || |  |       || |||      || | |    |  ||||| | |||||||| || || ||||| || ||||| |||||||||||||| || |||||||| || ||||| || || ||| | ||||| || |||     
ttactgcattgctatttctctaaacta-gcttgtctaaatcaaagggtatttcctaagtctgtttaccgcagaagatattgtaaaatcatatcctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGCTGTAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTG-

upper sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G145029_T01 (Zea mays), 3'ss of exon 3
----tg-gtggaaatttctctatg-tatcatgtgtattttcatgtcttggactcgtgctttaatttggtctctttgactgagattccttgttctttatgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTTGCAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCT
    ||  | |  |||||||||   || | ||  ||  || | || |         ||||   |            | ||  |   | | |||||||      ||||| | |||||||| || || ||||| || ||||| |||||||||||||| || |||||||| || ||||| || || ||| | ||||| || |||     
ctactgcattgttatttctctaaactagcttgactaaattgaagtgtattttctaagcttgtttaccaaagaagatattgtaacatcatattctttac-----agCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGCTGTAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTG-

upper sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G16440.1 (Arabidopsis thaliana), 3'ss of exon 3
tggtggaaatttctctatgtatcatgtgtattttcatgtcttggactcg--tgcttta----atttggtctctttgactgagattccttgttctttatgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTTGCAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCT
      |  |  || |||     |  ||  |  |   || ||||  | |  ||||| |    || ||  |    |     |  || ||| |||| |       ||||||| ||   ||| ||||| || ||||| ||||||||||||||||| |||||||||||||| || ||||||||||| ||||||||||| |||||||  | 
-----cacgtagctttatcataaaaatggttggttgggttttggcgttgcttgcttcagagtatgtgaccatcctactgaaattttcttcttctcttatggacagCAACGGTCAAAAACAAAGGTTACTTTCCCACTTGTGTGGACAAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCCGAGCTTATTGAAGAGAATGTGC-

upper sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G02780.1 (Arabidopsis thaliana), 3'ss of exon 3
tggtggaaatttctctatgtatcatgtgtattttcatgtcttggactcgtgctt-taatttggtctctttg--actgagattccttgttctttatgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTTGCAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCT
  || |  ||     |  |   |    ||  |   |  |  | |    ||  |  |||| |||    | ||  |      |   || ||||   |     ||||| | ||    || ||||| || |||||||| |||||||| ||||| |||||||||||||| || ||||||||||| ||||||||  | || ||||| | 
--gttgctatgatgatgggatgctctcgtgatcgtagatggttggtgggttttaataatctggctcatatgtcatctgactggtttcttctcgtttgaacagCAAAGGTCAAACACAAAGGTTACGTTCCCTCTAGTGTGGACTAACACTTGTTGCAGCCATCCTCTTTACCGTGAATCAGAGCTTATCCAGGACAATGCAC-

upper sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0206g00020.t01 (Vitis vinifera), 3'ss of exon 1
tggtggaaatttctctatgtatcatgtgtattttcatgtcttggactcgtgctttaatttggtctctttgactgagattccttgttctt-tatgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTTGCAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCT-------
|   |||   |       |  |  | || | | |      ||  ||||          ||  ||| ||  | |||   |   |         || || ||| |   |||  | |     | | ||   ||  |   ||   |    | ||  |  ||      ||| ||   |||    ||||  | | |||    | | |       
tttcggaggctgacgagggcttactttgcagtcttggaggtttcactcaacagccgtgttattcttttatattgaatctggatacaaacacctgctgcagCCATCCTCTTTACCGTGAATCAGAT---CTTATTAATGAGAATGTGCTTGGAGT-GCGGAATGCTGCACAAAGAA----AGCTATTGGGTGAACTCGGCATTCCTGCT

upper sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0023g00600.t01 (Vitis vinifera), 3'ss of exon 3
tggtggaaatttctctatgtatcatg-tgtattttcatgtcttggactcgtgctttaatttgg---tctctttgactgagattccttgttctttatgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTTGCAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCT
   ||       ||   | ||||| | | ||   |  | |  |  ||    ||   ||||||    || | |    ||   || ||   | ||| |  |  ||||| | ||||| || ||||| ||||||||| | ||||||||||||||||| ||||||||||| || ||||||||||| |||||||||||||||||||| | 
--ttgtttcaccctgattctatcaagatatagcattct-ttgtaaacatcagccagaatttgagaatcacatgctgtgttctttctgcatgtttcttgtacagCAAAGGTCTGCCACAAAGGTGACATTCCCTTTGGTGTGGACAAACACCTGCTGCAGCCATCCTCTTTACCGTGAATCAGAGCTTATTGATGAGAATGCGC-

upper sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S28_399V6.1 (Physcomitrella patens), 3'ss of exon 3
tggtggaaatttctctatgtatcatgtgtattttcatgtcttggactcgtgctttaatttggtctctttgactgagattccttgttctt-----tatgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTTGCAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGA-GAATGCCCT
         | | |   |  |   ||  |   |   || |||| |    ||  |   ||| | | | | |||  |   |  ||  | ||     |||  |  || |||| || || || || || || || || ||||||||||| ||||| |||||||||||||||||||||||||| ||||| |||||||| ||  ||| ||  
---ccaccgtgtatggttagagattggattagtgagtgacttgcagggatgtctcc-tttagacccatggacaaaatcttatttatgttgatattatatttcagAAACGTTCGGCTACGAAAGTGACCTTTCCACTTGTGTGGACCAACACTTGTTGCAGCCATCCACTGTACCGTGAGTCTGAACTTATTGAGGATAAATACC--

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|37997447|gb|CF809036.1|CF809036
EST:     AGCTTTCAGTGTATTCCTGTTCAACTCTAAGTATGAGTTGCTTCTTCAGC                         AACGATCTGCAACCAAGGTAACATTCCCTTCTTGTGTGGACAAACACCNTG
genomic: AGCTTTCAGTGTATTCCTGTTCAACTCTAAGTATGAGTTGCTTCTTCAGGtaagtttctt ... atgatgaagcAACGATCTGCAACCAAGGTAACATTCCC-TCTTGTGTGGACAAACACC-TG
EST: gi|26057349|gb|CA800263.1|CA800263
EST:     AGCTTTCAGTGTATTCCTGTTCAACTCTAAGTATGAGTTGCTTCTTCAGC                         AACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTT
genomic: AGCTTTCAGTGTATTCCTGTTCAACTCTAAGTATGAGTTGCTTCTTCAGGtaagtttctt ... atgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTT
EST: gi|18733450|gb|BM527614.1|BM527614
EST:     AGCTTTCAGTGTATTCCTGTTCAACTCTAAGTATGAGTTGCTTCTTCAGC                         AACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTT
genomic: AGCTTTCAGTGTATTCCTGTTCAACTCTAAGTATGAGTTGCTTCTTCAGGtaagtttctt ... atgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTT
EST: gi|19934737|gb|BQ079767.1|BQ079767
EST:     AGCTTTCAGTGTATTCCTGTTCAACTCTAAGTATGAGTTGCTTCTTCAGC                         AACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTT
genomic: AGCTTTCAGTGTATTCCTGTTCAACTCTAAGTATGAGTTGCTTCTTCAGGtaagtttctt ... atgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTT
EST: gi|15000069|gb|BI320883.1|BI320883
EST:     CAGTGTATTCCTGTTCAACTCTAAGTATGAGTTGCTTCTTCAGC                         AACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTT
genomic: CAGTGTATTCCTGTTCAACTCTAAGTATGAGTTGCTTCTTCAGGtaagtttctt ... atgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTT
EST: gi|208176085|gb|GD974316.1|GD974316
EST:     TATGAGTTGCTTCTTCAGC                         AACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTT
genomic: TATGAGTTGCTTCTTCAGGtaagtttctt ... atgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTT
EST: gi|19271109|gb|BM887365.1|BM887365
EST:     AGCTTTCAGTGTATTCCTGTTCAACTCTAAGTATGAGTTGCTTCTTCAGC                         AACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTT
genomic: AGCTTTCAGTGTATTCCTGTTCAACTCTAAGTATGAGTTGCTTCTTCAGGtaagtttctt ... atgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgtgctttaatttggtctctttgactgagattccttgttctttatgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTTGCAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCT
                    ctttgac  putative branch site (score: 4)
                                ttccttgttctttat  putative PPT
       tttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggtggaaatttctctatgtatcatgtgtattttcatgtcttggactcgtgctttaatttggtctctttgactgagattccttgttctttatgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTTGCAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
tggtgga
- - - - - - - ctatgta
- - - - - - - - - - -tcatgtg
- - - - - - - - - - - - - - - - -tcatgtc
- - - - - - - - - - - - - - - - - - - - - - -ctcgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgactg