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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgtttctccactcatacatgacaaagtcactgatattgctaactcgacaagtatattaattcagatatttgcaatatgatatttgttgtcttccatagGGTTCAAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGACAAGCTCGAAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC

Basic information

species Glycine max
transcript GLYMA03G36650.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G36650.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g30980.1 (Oryza sativa), 3'ss of exon 5
--tatgtttctccactcatacatgacaaagtcactgatattgctaactcgacaagtatattaattcagatatttgcaatatgatatttgttg-tcttccatagGGTTCAAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGACAAGCTCGAAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC
     | | ||  | |  ||  | | | | |  ||| |     ||  |     | | |    | |    ||  |  |   |||| |    || ||||   |||||||||||||| || || ||||| ||||||||||| ||||| ||||||||||||||||||| ||| || || || || |  ||  | |||||| |  || 
agccagctccttaagttgtat-taatatattagctgtttcctttatgtt--tgaattttcacagttgattacatagatcttgatgtgccctgatcttttgtagGGTTCAAGTGTACCTTTGGTTGTTAAATGGGCTGACACTGAGAAGGAAAGACAAGCTCGAAAAGCACAAAAGGCTCAATTTCACCCATCTAATATGTCAA

upper sequence: GLYMA03G36650.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g71200.1 (Oryza sativa), 3'ss of exon 5
tatgtttctccactcatacatgacaa-agtcactgatattgctaactcgacaagtatattaattcagatatttgcaatatgatatttgttg---tcttccatagGGTTCAAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGACAAGCTCGAAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC
   | | |        | ||| | |  |  || | | ||  ||  ||| |     |  ||| ||   ||   |  | ||| || | |  ||   | ||   ||||| || ||||| || || |||||||||||||| ||||| ||||||||||| || || |||| ||| || || || || |  ||| | |||||| | ||  
---gataccttgtgtctgcattatattatccagttacatccctt-ctcaaaccccacgttatttttcatgaatatattataatctcttctgatttatttgttagGGCTCTAGTGTGCCGTTGGTTGTCAAATGGGCCGATACAGAAAAGGAAAGGCAGGCCCGAAAAGCACAAAAGGCTCAATTGCAATCATCTAATATGCCTA

upper sequence: GLYMA03G36650.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G128809_T01 (Zea mays), 3'ss of exon 6
---tatgtttctc-cactcatacatgacaaagtcac-tgatattgctaactcgacaagtatattaattcagatatttgcaatatgatatttgttgtcttccatagGGTTCAAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGACAAGCTCGAAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC
   ||  |   |   ||     | |   | |||    |||||| | | |||   ||  | |   |  |||   || |  || |||   || ||  | ||   |||||||||||||||||||| ||||||||||||||||| |||||||||||||| |||||||||| ||| || ||| | |  | |||  |||||||  |     
taatagatcattgataccttggccttgtatagttgtatgatatagattactt--cagttctgaaatctcatgaatct--aacatggc-ttggtcattttggttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAAGCTCGAAAAGCGCAAAAATCTCCATTCCAGTCTTCTAACATGTTGA

upper sequence: GLYMA03G36650.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G177001_T01 (Zea mays), 3'ss of exon 5
-tatgtttctccactcatacatgacaaagtcactgatattgctaactcgacaagtatatta--attcagatatttgcaatatgatatttgttgtcttccatagGGTTCAAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGACAAGCTCGAAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC
 |||  ||     ||    | ||   | |  | ||||      |  ||   || |  || |  | | | | |  |  || |||    | ||  | ||   |||||||||||||||||||| ||||||||||||||||| |||||||||||||| || ||||||| ||| || ||||| || | |||  |||||||  |     
atatcattgataccttggtcttgt--atgatattgatcacttcagttctgaaatttcatgaccagttacacaaatctaacatgcc-ctggtcatttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCAGTCTTCTAACATGTTGA

upper sequence: GLYMA03G36650.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G005459_T01 (Zea mays), 3'ss of exon 5
----tatgtttctccactcatacatgacaaagtcactgatattgctaactcgacaagtatattaattcagatatttgcaatatgatatttgttgtcttccatagGGTTCAAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGACAAGCTCGAAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC
      | ||  |    ||||    ||||       ||| | |  | |   ||  | | ||   |||  |||||   |||   ||  | |  | | ||   |||||||| || || || || |||||||||||||||||||| ||||||||||| || ||||| | ||| || ||||| ||||| ||    ||| || ||||  
taaagctcttctttttttcattttagacagcccatttgacacttattatatgaacattgtacatattt-gatatcc-caac--gagctctaatatattttgtagGGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGGCAGGCTCGGAAAGCACAAAAAGCTCAGTCACAGCTATCTCATATACCCA

upper sequence: GLYMA03G36650.2 (Glycine max), 3'ss of exon 5
lower sequence: AT4G03110.1 (Arabidopsis thaliana), 3'ss of exon 5
tatgtttctccactca-tacatgacaaagtcactgatattgctaactcgacaagtatattaattcagatatttgcaatatgatatttgttgtcttccatagGGTTCAAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGACAAGCTCGAAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC
   ||   | |  |   ||| |   ||| | || |   ||  ||| ||   | || |   |||||    ||||      |  | || ||| |||||  |||||||||| |||||| ||||||||||||||||| || || |||   ||||||||  |  |||||  ||| || || || || ||     |     ||    
---gtaattgcttttgctactttgaaaacttaccg---tttgtaaatctgta-gtgtgaaaattccatcattt------ttcttttggttttcttct-tagGGTTCAACTGTTCCTTTAGTTGTCAAATGGGCAGACACAGAACGAGAAAGACACACAAGAAGACTTCAAAAGGCTCAATCTCACATCGCCCGACTAGGGA

upper sequence: GLYMA03G36650.2 (Glycine max), 3'ss of exon 5
lower sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 5
-tatgtttct-ccactcatacatgacaaagtcactgatattgctaactcgacaagtatattaattcagatatttgcaatatgatatt--tgttgtcttccat-agGGTTCAAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGACAAGCTCGAAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC
 |||||   |   ||  |||| |  |     || |  | ||    | |  | ||  |  |  ||  |||   |  |||||| | |||  | || |||||  | ||||  ||| |||||| ||  |||| |||||||| || || ||||||||||||||||||||||||  ||  ||||  || || || |  || |   |    |
gtatgtgcttattacatatacttctctcgaacattcttgtt----attttataaagacttgtatggagagtgtgacaatatcacattctttttttcttcttttagGGAGCAAATGTTCCTTTGATTGTTAAATGGGCAGACACAGAAAAGGAAAGACAAGCTCGAAGACTTCTAAAAGTTCAATCTCATGTCTCCAGACTCGATC

upper sequence: GLYMA03G36650.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0104g01150.t01 (Vitis vinifera), 3'ss of exon 5
tatgtttctccactcatacatgacaaagtcactgatat-tgctaactcgacaagtata--ttaattcagatatttgcaatatgatatttgttgtcttcca---tagGGTTCAAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGACAAGCTCGAAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC
      || ||| |  |           |    ||| | |||    |  | | | | |  || ||||    ||| |  || |||   ||  | |||       |||||||||||||||||  ||||||||||||||||||||||||||||||||||||||||||| |  ||||||||||| || || || || |||||| | ||| 
------tccccagttctgtgaagtgggatagtggatttctgccttataaaaatggagaagttgattcgatgattggttatctgaccattagtttctgttgcattagGGTTCAAGTGTTCCTCTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGACAAGCTCGGAAGGCTCAGAAAGCTCAATCTCAGGCATCTAATTTGCCAA

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|192326562|gb|FK017279.1|FK017279
EST:     AACAGGCTCTTACTGCTTTGGAGGCAATCAATGGAAAGCATAAAATGGAG                         GGTTCAAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGA
genomic: AACAGGCTCTTACTGCTTTGGAGGCAATCAATGGAAAGCATAAAATGGAGgtcagtgttt ... tcttccatagGGTTCAAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGA
EST: gi|19348677|gb|BM893209.1|BM893209
EST:     AACAGGCTCTTACTGCTTTGGAGGCAATCAATGGAAAGCATAAAATGGAG                         GGTTCAAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGA
genomic: AACAGGCTCTTACTGCTTTGGAGGCAATCAATGGAAAGCATAAAATGGAGgtcagtgttt ... tcttccatagGGTTCAAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgacaagtatattaattcagatatttgcaatatgatatttgttgtcttccatagGGTTCAAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGACAAGCTCGAAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC
          tattaat  putative branch site (score: 2)
                                          ttgtcttcc  putative PPT
     aagtatattaattcag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgtttctccactcatacatgacaaagtcactgatattgctaactcgacaagtatattaattcagatatttgcaatatgatatttgttgtcttccatagGGTTCAAGTGTTCCCTTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGACAAGCTCGAAGAGCTCAGAAAGCACAGTCCCAAGCTTCTAATGTACCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT