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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcccagaatttgaacttgtgacctccatgactctgtgtcacaaggcagcaatctaacctccacgattcttacgtttgtttcaattgtttttgcttgcagAATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTCATCTTGGTTGCATTTATGAGTGGATGGAAAGAAGTGACAGCTGTCCTGT

Basic information

species Glycine max
transcript GLYMA08G27730.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G27730.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g41140.1 (Oryza sativa), 3'ss of exon 3
-ttcccagaatttgaacttgtgacctccatgactctgt-gtcacaaggcagcaatctaacctccacgattcttacgtttgtttcaattgtttttgcttgcagAATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTCATCTTGGTTGCATTTATGAGTGGATGGAAAGAAGTGACAGCTGTCCTGT
 ||    |||    ||    |||| || |      |||   ||| | | | |||| || |  ||     | ||    |  ||   |   | | |   |||||| || |||   |||||||| | |||||| |   | ||||| |||||||| || ||||| || ||||||||||||||||||||||||||    || |||||
gttgattgaaaaaaaaaac-tgacatcaaatctgttgttagcaccatg-aacaatttatctgcctaagattttgtactaattcttacattatatctatgcagATTATACTTCTGAGAATCCTAGGATAGTAATGCAGTGCTCACATCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGT

upper sequence: GLYMA08G27730.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G468260_T02 (Zea mays), 3'ss of exon 2
---ttcccagaatttgaacttgtgacctccatgactctg-tgtcacaaggcagcaatctaacctccacgattcttacgtttgtttcaattgtttttgcttgcagAATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTCATCTTGGTTGCATTTATGAGTGGATGGAAAGAAGTGACAGCTGTCCTGT
         |  ||  ||  | ||| |   |    | |  |||    |      ||||  |    ||| ||| |||    | | | |||     |   ||||||| ||   |   |||||||| | |||||| |   | ||||| || ||||| || ||||| || ||||||||||||||||||||||||||    || |||||
gaacgaaaggtgttcaaaactatgagcattacattttttctgttgatactttataatcacattctcactattgtta----tatattaatgtaactaaattgcagATTATGATTCTGAGAATCCTAGGATAGTAATGCAGTGCTCACACCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGT

upper sequence: GLYMA08G27730.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G38895.1 (Arabidopsis thaliana), 3'ss of exon 3
----ttcccagaatttgaacttgtgacctccatgactctgt-gtcacaag-gcagcaatctaacctccacgattcttacgtttgtttcaattgtttttgcttgcagAATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTCATCTTGGTTGCATTTATGAGTGGATGGAAAGAAGTGACAGCTGTCCTGT
       |||  | | | |    | || |  ||||  |  | ||  | || |||  ||  |||  |              ||||||| ||   | |      ||||| ||||||   ||||||||||||||| | || || || ||||| ||||| || ||| | || |||||||| |||||||| |||||||| |  || || ||
cattaggccattaatagtatagtttacgtagatgaggcaatcgttgcgagtgcattaaggtaatattggtttcatagttctttgttttaacaatat------gcagATTACACTTTGGAGAATCCGAAGATAATCACCAAGTGTTCTCACCATTTCCACCTTAGCTGTATTTATGAATGGATGGAGAGAAGTGAAACTTGCCCCGT

upper sequence: GLYMA08G27730.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G02290.1 (Arabidopsis thaliana), 3'ss of exon 3
ttcccagaatttgaacttgtgacctccatgactctgtgtcacaaggcagcaatctaacctccacgattcttacgtttgtttcaattgttt-ttgcttgcagAATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTCATCTTGGTTGCATTTATGAGTGGATGGAAAGAAGTGACAGCTGTCCTGT
                             |      |    | |  || || |||  |||    | | |||  || |   |   |||||  ||  |||||||||| ||   |||||| || ||||| ||||||||||| || || ||||| || ||| |||||||||||||||||||||| |||||||| | |||||| ||
-----------------------------gtaataataatcccattcaacagtct--cctttttgttccttcagtattcatatcttgttggttttttgcagAATATACATCAGAGAACCCAAAGATTGTGACAAAATGTTCACACCATTTCCACCTTAGTTGCATTTATGAGTGGATGGAGAGAAGTGAAAACTGTCCAGT

upper sequence: GLYMA08G27730.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G15790.2 (Arabidopsis thaliana), 3'ss of exon 3
ttcccagaatttgaacttgtgacctccatgactctgtgtcacaaggcagcaatctaacctccacgattcttacgtttgtttcaattgtttttgcttgcagAATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTCATCTTGGTTGCATTTATGAGTGGATGGAAAGAAGTGACAGCTGTCCTGT
      | |||     || | | ||   |   ||| | ||      ||        |  || | ||  ||||   |    | | ||  | |   ||| ||||||||    |||||| |||||||| || ||||| || ||||| ||||| || ||  ||||||||||||| |||||||| |||||||| | ||| |||||
------gtattca---ttttcatctttttttttctttttcttggatcaatgc----atttcaaagaagcttagtatcagattatttcgtgtgttttgtagAATACATATCAGAGAACCCGAAGATTGTTACAAAGTGTTCTCACCATTTCCACCTCAGTTGCATTTATGAATGGATGGAGAGAAGTGAAAACTGCCCTGT

upper sequence: GLYMA08G27730.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0083g01000.t01 (Vitis vinifera), 3'ss of exon 3
---ttcccagaatttgaacttgtgacctccatgactctgtgtcacaaggcagca-atctaacctccacgattcttacgtttgtttcaattgtttttgcttgcagAATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTCATCTTGGTTGCATTTATGAGTGGATGGAAAGAAGTGACAGCTGTCCTGT
   ||  ||  |||     |  |||      | ||| |   ||| |    || |  | | |       |||||| |  ||||||   | |  | ||   ||||||||| |||  ||| ||||| |||||| |||||||||||||||| |||||||| |||||||| || ||||| |||||||| |||||||| |  ||||| ||
atcttgtcattatt-aggttgatgattctgttaactgtac-tcaaatattagaatgttttagggtatagattctga--tttgttcatacttatcttttatgcagAATATACTCCAGAAAATCCCAAGATAATGACAAAATGCTCTCACCATTTTCACCTTGGTTGTATATATGAATGGATGGAGAGAAGTGAAACATGTCCAGT

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|214008544|gb|DB988205.1|DB988205
EST:     TGTCTATTCATCCTCAGAAGAGGAGGATGTCTGTCCAACTTGTCTTGAAG                         AATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTC
genomic: TGTCTATTCATCCTCAGAAGAGGAGGATGTCTGTCCAACTTGTCTTGAAGgtaagagtgt ... ttgcttgcagAATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTC
EST: gi|207789055|gb|GD762167.1|GD762167
EST:     CAACTTGTCTTGAAG                         AATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTC
genomic: CAACTTGTCTTGAAGgtaagagtgt ... ttgcttgcagAATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTC
EST: gi|192304400|gb|FG996722.1|FG996722
EST:     TGTCTATTCATCCTCAGAAGAGGAGGATGTCTGTCCAACTTGTCTTGAAG                         AATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTC
genomic: TGTCTATTCATCCTCAGAAGAGGAGGATGTCTGTCCAACTTGTCTTGAAGgtaagagtgt ... ttgcttgcagAATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTC
EST: gi|22928658|gb|BU545797.1|BU545797
EST:     TGTCTATTCATCCTCAGAAGAGGAGGATGTCTGTCCAACTTGTCTTGAAG                         AATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTC
genomic: TGTCTATTCATCCTCAGAAGAGGAGGATGTCTGTCCAACTTGTCTTGAAGgtaagagtgt ... ttgcttgcagAATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTC
EST: gi|207695267|gb|GD678064.1|GD678064
EST:     CAACTTGTCTTGTAAG                         AATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTT
genomic: CAACTTGTCTTG-AAGgtaagagtgt ... ttgcttgcagAATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTT
EST: gi|7684829|gb|AW755477.1|AW755477
EST:     TGTCTATTCATCCTCAGAAGAGGAGGATGTCTGTCCAACTTGTCTTGAAG                         AATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTC
genomic: TGTCTATTCATCCTCAGAAGAGGAGGATGTCTGTCCAACTTGTCTTGAAGgtaagagtgt ... ttgcttgcagAATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTC
EST: gi|192307749|gb|FK001693.1|FK001693
EST:     TGTCTATTCATCCTCAGAAGAGGAGGATGTCTGTCCAACTTGTCTTGAAG                         AATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTC
genomic: TGTCTATTCATCCTCAGAAGAGGAGGATGTCTGTCCAACTTGTCTTGAAGgtaagagtgt ... ttgcttgcagAATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagcaatctaacctccacgattcttacgtttgtttcaattgtttttgcttgcagAATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTCATCTTGGTTGCATTTATGAGTGGATGGAAAGAAGTGACAGCTGTCCTGT
                     ttcttac  putative branch site (score: 2)
                                          tttttgctt  putative PPT
                                 tttcaattgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcccagaatttgaacttgtgacctccatgactctgtgtcacaaggcagcaatctaacctccacgattcttacgtttgtttcaattgtttttgcttgcagAATACACTGAAGAGAATCCGAAGATAGTGACAAAATGCTCTCATCATTTTCATCTTGGTTGCATTTATGAGTGGATGGAAAGAAGTGACAGCTGTCCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- cccagaa
- - - - - - - - - -tgacctc
- - - - - - - - - - - - - catgact
- - - - - - - - - - - - - - - - - - tgtcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctccac