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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgttgtttgtaaacacatacctaatctgccagggctccaatgctgcttggaaacttttggtattgctttagaagtcacacacacttttggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCAGAATCAAAGAAGGAGCTTGATGCCTTACTTTCAGATGAATCATTGGCAA

Basic information

species Glycine max
transcript GLYMA17G03540.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G03540.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S7_338V6.1 (Physcomitrella patens), 3'ss of exon 2
-attgttgtttgtaaacacatacctaatctgccagggctccaatgctgcttggaaacttttggtattgctttagaagtcacacacacttttggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCAGAATCAAAGAAGGAGCTTGATGCCTTACTTTCAGATGAATCATTGGCAA
 |  |      | |||    ||  ||  |||  |       | || || |||     | | |   ||| |      || ||  |    |||  || | ||||| || |   | |||||| |||| |||||    ||||||||||||||| |||| ||||||||||| || |||||| |  | ||||| || ||  |||   
gacagaaaaaagaaaaactttagttatcctgaaatattgatagtgttggttgtgtgttatggtggttgttgactctgtaactgatgtgttta-ttatacagGTTGACGGCATCGTTTACTTGGTGGATGCAGCGGACAAAGAGAGGTTTTCAGAGTCAAAGAAGGAACTGGATGCCCTGTTATCAGACGATTCGCTGGGCC
















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|298187403|gb|HO034552.1|HO034552
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
EST: gi|298178780|gb|HO024515.1|HO024515
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
EST: gi|24206013|gb|BU965266.1|BU965266
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
EST: gi|151393095|gb|EV262970.1|EV262970
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
EST: gi|19268925|gb|BM885181.1|BM885181
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
EST: gi|193719432|gb|FK650056.1|FK650056
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
EST: gi|20449793|gb|BQ253917.1|BQ253917
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
EST: gi|5760306|gb|AI965669.1|AI965669
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCTTTTGACAAAGAGAGGTTTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
EST: gi|19054264|gb|BM732931.1|BM732931
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
EST: gi|298170756|gb|HO015732.1|HO015732
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCCTTTTGACAA-GAGAGGTTTGC
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTT-GACAAAGAGAGGTTTGC
EST: gi|17401176|gb|BM177958.1|BM177958
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
EST: gi|298167563|gb|HO012826.1|HO012826
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTCGATGCCTTTGACAAAGAG
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAG
EST: gi|26269163|gb|CA820226.1|CA820226
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
EST: gi|17519809|gb|BM188851.1|BM188851
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
EST: gi|192302890|gb|FG998572.1|FG998572
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
EST: gi|192298804|gb|FG988640.1|FG988640
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
EST: gi|298189520|gb|HO037923.1|HO037923
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGTTGCCTTTGACAAAGAGAGGTTTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
EST: gi|16349217|gb|BI974812.1|BI974812
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
EST: gi|26057414|gb|CA800328.1|CA800328
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
EST: gi|19053720|gb|BM732387.1|BM732387
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
EST: gi|298186789|gb|HO037422.1|HO037422
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
EST: gi|192332154|gb|FK024600.1|FK024600
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA
EST: gi|10231278|gb|BE800157.1|BE800157
EST:     TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAG                         GTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTGTGCA
genomic: TGGGGGGCCATCAAGTTGCCCGCAGAGTCTGGAAAGACTATTACGCAAAGgtcgctcaat ... ggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttggaaacttttggtattgctttagaagtcacacacacttttggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCAGAATCAAAGAAGGAGCTTGATGCCTTACTTTCAGATGAATCATTGGCAA
       aaactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgttgtttgtaaacacatacctaatctgccagggctccaatgctgcttggaaacttttggtattgctttagaagtcacacacacttttggttttgcagGTGGATGCAGTAGTTTACCTGGTTGATGCCTTTGACAAAGAGAGGTTTGCAGAATCAAAGAAGGAGCTTGATGCCTTACTTTCAGATGAATCATTGGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - -tgtttgt
- - - - - - - -cacatac
- - - - - - - - - - - - - tctgcca
- - - - - - - - - - - - - - - - - - - ccaatgc
- - - - - - - - - - - - - - - - - - - - - - -tgcttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cttttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acacaca