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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagttttttttatttgtttcttaaatttattttagttttagctttttttttcctccttgtatagttatatgttgtgttttggctgtttttctgtattt...

Basic information

species Glycine max
transcript GLYMA02G35500.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G35500.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G174204_T01 (Zea mays), 5'ss of exon 3
GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagttttttttatttgtttcttaaatttattttagttttagctttttttttcctccttgtatagttatatgttgtgttttggctgtttttctgtattt------
    | |||  ||||||||| | | | |||||||||   |||||||| |||||||||||||||||||||| |||  || ||   || | ||   ||||||||  ||  ||  | | |  |   |   ||   |  | || ||||     ||| |  || |  | ||        
TTGATTGGTGCTAAGGGCAAGAGGTTCGCCAAGAAACGCTATGCTGAGAAGGCGCAGATGAAGAAGACgtaagtgcttgtttgctgctcct---atttattt-ggtgatacttgtgtaatagata--tgagcaactttaagttgatgcatggatacttcttagaatgatgcgcg

upper sequence: GLYMA02G35500.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv08s0105g00280.t01 (Vitis vinifera), 5'ss of exon 3
GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagtttttttta-tttgtttcttaaatttattttagttttagctttttttttcctccttgtatagttatatgttgtgttttggctgtttttctgtattt--
||||||||||||||||| || ||| |||| ||||||  |||||| |||||||||||||||||||| |||||||| |  |||| ||  | |  | | ||| | ||  | ||   | |  |||| ||  ||   ||| || || ||   ||     || | |    |||    
GCTCTGGGTATTAAGGGTAAGATGTTTGCAAAGAAACGTTATGCAGAAAAGGCGCAGATGAAGAAAACgtgagtgtaatttaattcatgttattattttttatttctcttctgtatgatttttctttttcattagataaatatt---ttcaaattgatctataatatccat
















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|192313831|gb|FK007647.1|FK007647
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagttttt ... gtgtcaacagTTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|15203872|gb|BI426640.1|BI426640
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagttttt ... gtgtcaacagTTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|4307640|gb|AI444076.1|AI444076
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagttttt ... gtgtcaacagTTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|7478670|gb|AW666357.1|AW666357
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagttttt ... gtgtcaacagTTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|6071298|gb|AW100685.1|AW100685
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagttttt ... gtgtcaacagTTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|23733288|gb|BU764826.1|BU764826
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagttttt ... gtgtcaacagTTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|17519530|gb|BM188572.1|BM188572
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagttttt ... gtgtcaacagTTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|298194398|gb|HO041046.1|HO041046
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagttttt ... gtgtcaacagTTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|15203893|gb|BI426661.1|BI426661
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagttttt ... gtgtcaacagTTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|8285802|gb|BE023361.1|BE023361
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagttttt ... gtgtcaacagTTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|120491259|gb|EH219426.1|EH219426
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagttttt ... gtgtcaacagTTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|192328211|gb|FK020444.1|FK020444
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagttttt ... gtgtcaacagTTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|21995126|gb|BQ786654.1|BQ786654
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagttttt ... gtgtcaacagTTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|192313774|gb|FK007646.1|FK007646
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagttttt ... gtgtcaacagTTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|7588724|gb|AW704513.1|AW704513
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagttttt ... gtgtcaacagTTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|151402809|gb|EV272622.1|EV272622
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGTAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagttttt ... gtgtcaacagTTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
EST: gi|6668126|gb|AW279577.1|AW279577
EST:     AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGAC                         TTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT
genomic: AAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagttttt ... gtgtcaacagTTTGGCTATGCATGAAGAATCATCGTCTAGGCGCAAGACTGATGATAATGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCTGGGTATTAAGGGCAAAATGATTGCCAAGAAAAATTATGCTGAAAAGGCGCAGATGAAGAAGACgtgagttttttttatttgtttcttaaatttattttagttttagctttttttttcctccttgtatagttatatgttgtgttttggctgtttttctgtattt

- - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcctcc