Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattgactgacctctacaatttcaaggacctgtagtggtgattcacttgttttttcattccctaatgttccaaattctgacatgatatttttgttttcagATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTA

Basic information

species Glycine max
transcript GLYMA03G39500.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g56000.1 (Oryza sativa), 3'ss of exon 2
aattgactgacctctacaatttcaaggacctgtagtggtgattcacttgtt-ttttcattccctaatgtt-------ccaaattctgacatgatatttttgttttcagATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTA
        | | | |  | |      ||     || |  || |   | ||  || | ||||   ||  ||       | || ||   |  |  || ||    ||||||||||||||||| || || || ||||| || ||||| |||||| | ||||| ||||| || || ||||||||||||||||| |||||  | |||||||| |
--------gtcttttcgagtccttgagaatgtcagagcagaattcttcgtagttctaattctgcaagattgtgggggcaaatttacaagttcttacttcctatttcagATATTGGAAATGAACCCCGAGGATGAGGCTGAAGAGGATGGTGCGAACATCGATCTGGATTCACAAAGGAAAGGAAAATGCGTTGTTTTGAAGACATCCA

upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 2
--aattgactgacctctacaatttcaaggacctgtagtggtgattcacttgttttt---tcattccctaatgttccaaattctgacatgatatttttg--ttttcagATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTA
   |||  | ||  | | |  ||||     ||| |    ||||   | |||||||      ||| | || |||  | |  |      || | || |    | || ||||  ||||||| || || || |||||||| || || |||||| | || |||||| | ||||| ||||||||||||||||||||||| || ||||| || |
gctattaccagaaat-tgctgtttc-----cctattaatgtgaccta-ttgttttggaacaattgcgtattgtaaccatatggtttctgcttttctcaactgtttagATTCTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAATATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACTTCCA

upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 2
aattgactgacctctaca-atttcaaggacctgtagtggtgattcacttgttttttca-----ttccctaatgttccaaattctgacatg-atatttttgttttcagATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTA
       | |  | | || ||||||| |   |  ||  || |   |  ||  |   ||       |  ||  |   | | | || | ||  || |      ||| |||| |||||||| || || || ||||| || |||||||||||| | ||||| ||||| ||||| ||||||||||||||||||||||| || |||||||| |
-------taagattttcatatttcaaagtttttaagatgtaaggaagctgcatacccaaggtggacgatatgggctccattacttatatacatctcaactgttttagATTTTGGAAATGAACCCTGAGGATGAGGCTGAAGAAGATGGTGCTAACATCGATCTGGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACATCCA

upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G032505_T03 (Zea mays), 3'ss of exon 2
-----aattgactgacctctacaatttcaaggacctgtagtggtgattcacttgttttttcattccctaatgttccaaattctgacatgatatttttgttttcagATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTA
      |||   ||  || |   |      |   |||||    | ||| | ||  ||| |   |  || || | |   |  ||| | |  | |      ||| |||| |||||||| || || || |||||||| || || |||||| | ||||||||| | ||||| ||||||||||||||||||||||| || ||||| || |
ttccatattatttggtctttgtcaggcagggtgtctgtac--attatttattttgtttctgggttactcatatac---agcctgcctttttctcaactattttagATCTTGGAAATGAACCCTGAGGATGAAGCTGAGGAGGATGGTGCTAACATTGATTTAGACTCACAAAGGAAAGGAAAATGTGTTGTTCTGAAGACCTCCA

upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 2
------aattgactgacctctacaatttcaaggacctgtagtggtgattcacttgttttttcattccctaatgttccaaattctgacatgatatttttgttttcagATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTA
      || |   |  | | |   ||||   | |  | |  |   || ||  ||   | ||   |    |||  |     || ||  |  ||||  | | | | |||| ||||| || |||||||||||||| || || ||||||||| | || |||||||||||||| ||| |||||||||||||||||||| | || || ||||
gtattcaactagttttcttatcttatttttggtattt-tcctacagagtc--ttacctatttgatttg-aattctaactgttgtgttaccatatcat-gctattagATTTTGGAGATGAATCCAGAAGATGATGCTGAGGAAGATGGTGCAAATATTGATCTTGACTCGCAACGGAAAGGAAAATGTGTTGTGTTGAAAACGTCTA

upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 2
-----aattgactgacctctacaatttcaaggacctgtagtggtgattcacttgttttttcattccctaatgttccaaattctgacatgatatttttgttttcagATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTA
     |||||          |   ||    | | ||| |||  |  |  ||||| || | || | | |  | ||     ||||    |    ||  |||||| |||| |||||||| || ||||| ||||| ||||| ||||||||| | || |||||||||||||| || ||||| ||||||||||||||  | || |||||||
ataggaattggtgagtgaacaggcttaattgaagctgaagttctagta-acttggttct-cactacattttttttt---ttcttttttctggttaatgtttttagATCTTGGAAATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATTGATCTTGACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTA

upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 2
-aattgactgacctctacaatttcaaggacctgtagtggtgattcacttgttttttcattccctaatgttccaaattct--gacatgatatttttgtttt-cagATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTA
  |   | |  |        ||| |     |   ||   | ||||   | |||  |     ||   |||   | ||| |   |  |||| |   ||   | |||||||||||  | ||||||||||||||||| ||||| |||||| | ||  ||||| | ||||| ||||||| |||||| ||||| ||  | |||||||| |
cgagaaagtagctctcgtgtttttat---tccacagct-taattcctgtttttcgttgcaaccggttgtcagatattttttaagttgatttcggtgccctgcagATATTGGACGTCAATCCAGAAGATGAAGCTGAAGAGGATGGTGCTAATGTTGATTTGGACTCTCAAAGGAGAGGAAAGTGTGTCGTCTTGAAGACATCCA

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|209727631|gb|BW663793.1|BW663793
EST:     AAGTTAAACTTAATAAGCAATTGCCCTACCTCGTTGGTAACATTGTTGAG                         ATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATT
genomic: AAGTTAAACTTAATAAGCAATTGCCCTACCTCGTTGGTAACATTGTTGAGgttatttaat ... ttgttttcagATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATT
EST: gi|23727048|gb|BU761539.1|BU761539
EST:     AAGTTAAACTTAATAAGCAATTGCCCTACCTCGTTGGTAACATTGTTGAG                         ATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATT
genomic: AAGTTAAACTTAATAAGCAATTGCCCTACCTCGTTGGTAACATTGTTGAGgttatttaat ... ttgttttcagATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATT
EST: gi|209718165|gb|BW657811.1|BW657811
EST:     AAGTTAAACTTAATAAGCAATTGCCCTACCTCGTTGGTAACATTGTTGAG                         ATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATT
genomic: AAGTTAAACTTAATAAGCAATTGCCCTACCTCGTTGGTAACATTGTTGAGgttatttaat ... ttgttttcagATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATT
EST: gi|298168340|gb|HO014515.1|HO014515
EST:     AAGTTAAACTTAATAAGCAATTGCCCTACCTCGTTGGTAACATTGTTGAG                         ATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATT
genomic: AAGTTAAACTTAATAAGCAATTGCCCTACCTCGTTGGTAACATTGTTGAGgttatttaat ... ttgttttcagATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATT
EST: gi|17400340|gb|BM177122.1|BM177122
EST:     AAGTTAAACTTAATAAGCAATTTTTCTACCTCGTTGGTAACATTGTTGAG                         ATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATT
genomic: AAGTTAAACTTAATAAGCAATTGCCCTACCTCGTTGGTAACATTGTTGAGgttatttaat ... ttgttttcagATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgttttttcattccctaatgttccaaattctgacatgatatttttgttttcagATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTA
                             ttctgac  putative branch site (score: 2)
                                          tttttgttttc  putative PPT
                                    atgatatttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattgactgacctctacaatttcaaggacctgtagtggtgattcacttgttttttcattccctaatgttccaaattctgacatgatatttttgttttcagATATTGGAAATAAATCCAGAAGATGAAGCAGAAGAAGATGGTTCCAACATTGATCTTGACTCCCAAAGGAAAGGAAAATGTGTTGTGCTAAAGACATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - ctgacct
- - - - - - - - - - - - - - - - -agtggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgac