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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcacaattctgtacatgcctctcttgtgattgatgctttaagaactacttcatgatggtgttgttgtttttgcagTATGCTTTTAATCTATTCTCACATAATGCGTCTGTTCTTTCAAAGGGATTTAATGAAGAAGAAATGAAAATGGTCAAGGAGACCAGGAAAATCTGG

Basic information

species Glycine max
transcript GLYMA05G34420.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G34420.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g55280.1 (Oryza sativa), 3'ss of exon 3
gtttgcacaattctgta-catgcctctcttgtgattgatgctttaagaactacttcatgatggtgttgttgtttttgcagTATGCTTTTAATCTATTCTCACATAATGCGTCTGTTCTTTCAAAGGGATTTAATGAAGAAGAAATGAAAATGGTCAAGGAGACCAGGAAAATCTGG
|||     |||||| ||  || |    |    |   |||  |||   |   |  |   ||   || |  |  || ||||||||||||||||| |||| |||||||||||  |  || ||  ||| || |  ||||| || || ||||| ||||| ||||||||||| |||||||||
gttc---taattctataatatcctggacacacgccagattattttcaagtcagct---gaatttgcttctccttgtgcagTATGCTTTTAATATATTTTCACATAATGCACCAATTGTTGAAAATGGGTACAATGAGGAGGAGATGAAGATGGTGAAGGAGACCAGAAAAATCTGG

upper sequence: GLYMA05G34420.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G076885_T01 (Zea mays), 3'ss of exon 3
----------------gtttgcacaattctgtacatgcctctcttgtgattgatgctttaagaactacttcatga-tggtgttgttgtttttgcagTATGCTTTTAATCTATTCTCACATAATGCGTCTGTTCTTTCAAAGGGATTTAATGAAGAAGAAATGAAAATGGTCAAGGAGACCAGGAAAATCTGG
                | ||| |  || |||  ||    | ||   | |||   |     ||  || | |  ||| |    ||||   || ||||||||||||||||| |||||||||| |||||  | ||||||   || || | ||| || || |||||||||||||| ||||||||||||||||| |||
gttgttccagcttacagattgaaatatcctgagcaga--tatcaaattattttagtcacgagttcttcatgctgaatatctttgtcccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG

upper sequence: GLYMA05G34420.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0011g05860.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------gtttgc--acaatt-ctgtacatgcctctct-tgtgattgatgctttaagaactacttcatgatggtgttgttgtttttgcagTATGCTTTTAATCTATTCTCACATAATGCGTCTGTTCTTTCAAAGGGATTTAATGAAGAAGAAATGAAAATGGTCAAGGAGACCAGGAAAATCTGG
                              ||||   | |||| |   | |||  | | | | | ||  |       ||||  || || | ||     | |  ||  ||||||||||||||||||| || ||||| |||||  |||||||| |||| || |  |||||||| ||||||||| | || || ||||| ||||||||||||
gtttgtctactcattatacatgtttaccaatttgacaagaattacaacaaatgattttgtattttatctagttgcctagaataacctcttaataca--tatacttcatgcagTATGCTTTTAATCTCTTTTCACACAATGCACCTGTTCTTCCAAATGGGTACAATGAAGAGGAAATGAAATTAGTAAAAGAGACAAGGAAAATCTGG

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|22929114|gb|BU546253.1|BU546253
EST:     GTGTTGGAAGGAAAACCACCCACTTGTAAAATATTTAACCGACAG                         TATGCTTTTAATCTATTCTCACATAATGCGTCTGTTCTTTCAAATGGATAT
genomic: GTGTTGGAAGGAAAACCACCCACTTGTAAAATATTTAACCGACAGgtttgcacaa ... gtttttgcagTATGCTTTTAATCTATTCTCACATAATGCGTCTGTTCTTTCAAAGGGATTT
EST: gi|7796755|gb|AW782149.1|AW782149
EST:     GTGTTGGAAGGAAAACCACCCACTTGTAAAATATTTAACCGACAG                         TATGCTTTTAATCTATTCTCACATAATGCGTCTGTTCTTTCAAATGGATAT
genomic: GTGTTGGAAGGAAAACCACCCACTTGTAAAATATTTAACCGACAGgtttgcacaa ... gtttttgcagTATGCTTTTAATCTATTCTCACATAATGCGTCTGTTCTTTCAAAGGGATTT
EST: gi|254326691|gb|GR832843.1|GR832843
EST:     TGGAAGGAAAACCACCCACTTGTAAAATATTTAACCGACAG                         TATGCTTTTAATCTATTCTCACATAATGCGTCTGTTCTTTCAAATGGATAT
genomic: TGGAAGGAAAACCACCCACTTGTAAAATATTTAACCGACAGgtttgcacaa ... gtttttgcagTATGCTTTTAATCTATTCTCACATAATGCGTCTGTTCTTTCAAAGGGATTT
EST: gi|254327092|gb|GR836701.1|GR836701
EST:     GTG-TGGAAGGAAAACCACCCACTTGTAAAATATTTAACCGACAG                         TATGCTTTTAATCTATTCTCACATAATGCGTCTGTTCTTTCAAATGGATAT
genomic: GTGTTGGAAGGAAAACCACCCACTTGTAAAATATTTAACCGACAGgtttgcacaa ... gtttttgcagTATGCTTTTAATCTATTCTCACATAATGCGTCTGTTCTTTCAAAGGGATTT
EST: gi|254327091|gb|GR836700.1|GR836700
EST:     -TGTTGGAAG-AAAACCACCCACTTGTAAAAATATTTAACCGACAG                         TATGCTTTTAATCTATTCTCA
genomic: GTGTTGGAAGGAAAACCACCCACTTGTAAAA-TATTTAACCGACAGgtttgcacaa ... gtttttgcagTATGCTTTTAATCTATTCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttgtgattgatgctttaagaactacttcatgatggtgttgttgtttttgcagTATGCTTTTAATCTATTCTCACATAATGCGTCTGTTCTTTCAAAGGGATTTAATGAAGAAGAAATGAAAATGGTCAAGGAGACCAGGAAAATCTGG
       gattgat  putative branch site (score: 4)
                                           ttgttttt  putative PPT
                tttaagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcacaattctgtacatgcctctcttgtgattgatgctttaagaactacttcatgatggtgttgttgtttttgcagTATGCTTTTAATCTATTCTCACATAATGCGTCTGTTCTTTCAAAGGGATTTAATGAAGAAGAAATGAAAATGGTCAAGGAGACCAGGAAAATCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA