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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttggtatctatcaccaaattatgtgaatcttttaaccttggttccgagtattgttattgacttgaatgcagcatttgctcttgtgtttaacattgcagGGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGGAAACAACGAATGATTTCTGGTGCCTTGACTGATCAAGAAGTTCGAACTGCAAGGATTGAGG

Basic information

species Glycine max
transcript GLYMA12G30540.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G30540.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G057504_T01 (Zea mays), 3'ss of exon 8
-------------------------------------------atttggtatctatcaccaaattatgtga-----atcttttaacct--tggttccgagtattgttattgacttgaatgcagcatttgctcttgtgt---ttaacattgcagGGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGGAAACAACGAATGATTTCTGGTGCCTTGACTGATCAAGAAGTTCGAACTGCAAGGATTGAGG
                                            |  ||    |||||  | | |||  ||     | | ||  || |  || | ||  |  |   |  | | ||   |   | ||| |   |  | |    |  |  | ||||| || || || ||  |||||||||| ||||| || || || || |||||||||||||| || |||||||| |||||||| || |||||| | || || |
gtatcttttttttgcatcaaatctcatcataatccagattttgctggggccattatcagaagaatatacgaggcagacccttcgacattctgatgccccgattctcttgttattttttttttgtattggtcatgatataatatggccgtccagGGCACTGTCGAAGAACGAATGGAGGCTGTGCAGGCTCGAAAGCAGCGAATGATTTCTGGAGCTTTGACTGACCAAGAAGTCCGCACTGCACGTATAGAAG

upper sequence: GLYMA12G30540.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv06s0061g01190.t01 (Vitis vinifera), 3'ss of exon 19
atttggtatctatcaccaaattatgtgaatcttt-taaccttggttccgagtattgttattgacttgaa---tgcagca--tttgctcttgtgtttaacattgcagGGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGGAAACAACGAATGATTTCTGGTGCCTTGACTGATCAAGAAGTTCGAACTGCAAGGATTGAGG
      || | || ||  |   || ||  |  || | || || |  |    | |      ||| | |||   |||| ||   | |      | | |   || |||||| || || ||||| || |||  |||||||||||| || || || |||||||| |||||||||||||||||||||||||| |||| |||| | |||||||
-----ataacaattacacaggcatatggctaattatgacatttggac-atttctctaagatgagtagaactttgcaacaacctagtaaaaatatcttggatggcagGGAACGGTGGAGGAAAGGATGCTGGCAGTGCAAGCTCGTAAGCAGCGAATGATATCTGGTGCCTTGACTGATCAAGAAGTCCGAAGTGCACGCATTGAGG
















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|193321928|gb|FK287436.1|FK287436
EST:     ATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAG                         GGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGTAAACAACGAATG
genomic: ATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAGgtatatttaa ... aacattgcagGGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGGAAACAACGAATG
EST: gi|193597499|gb|FK551915.1|FK551915
EST:     ATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAG                         GGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGGAAACAACGAATG
genomic: ATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAGgtatatttaa ... aacattgcagGGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGGAAACAACGAATG
EST: gi|193333255|gb|FK298789.1|FK298789
EST:     ATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAG                         GGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGTAAACAACGAATG
genomic: ATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAGgtatatttaa ... aacattgcagGGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGGAAACAACGAATG
EST: gi|207838025|gb|GD810359.1|GD810359
EST:     GTATTGGACAAAACAAAAGAAAGGTTGCCATTAGACGGTTTATTGTGAAG                         GGGACAGTTGAGGAGAGAATGGAGGCAGTG
genomic: GTATTGGACAAA-CAAA-GAA-GGTTGCCATTAGACGGTTTATTGTGAAGgtatatttaa ... aacattgcagGGGACAGTTGAGGAGAGAATGGAGGCAGTG
EST: gi|193599772|gb|FK551567.1|FK551567
EST:     ATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAG                         GGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGTAAACAACGAATG
genomic: ATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAGgtatatttaa ... aacattgcagGGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGGAAACAACGAATG
EST: gi|193429943|gb|FK395017.1|FK395017
EST:     ATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAG                         GGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGTAAACAACGAATG
genomic: ATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAGgtatatttaa ... aacattgcagGGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGGAAACAACGAATG
EST: gi|193356432|gb|FK320905.1|FK320905
EST:     TCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTAGAAG                         GGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGTAAACAACGAAT
genomic: TCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGT-GAAGgtatatttaa ... aacattgcagGGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGGAAACAACGAAT
EST: gi|208227925|gb|GE025963.1|GE025963
EST:     ATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAG                         GGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGTAAACAACGAATG
genomic: ATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAGgtatatttaa ... aacattgcagGGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGGAAACAACGAATG
EST: gi|193443396|gb|FK409170.1|FK409170
EST:     ATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAG                         GGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGTAAACAACGAATG
genomic: ATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAGgtatatttaa ... aacattgcagGGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGGAAACAACGAATG
EST: gi|193334976|gb|FK300964.1|FK300964
EST:     ATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAG                         GGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGGAA-CAACGAATG
genomic: ATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAGgtatatttaa ... aacattgcagGGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGGAAACAACGAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgagtattgttattgacttgaatgcagcatttgctcttgtgtttaacattgcagGGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGGAAACAACGAATGATTTCTGGTGCCTTGACTGATCAAGAAGTTCGAACTGCAAGGATTGAGG
     tattgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttggtatctatcaccaaattatgtgaatcttttaaccttggttccgagtattgttattgacttgaatgcagcatttgctcttgtgtttaacattgcagGGGACAGTTGAGGAGAGAATGGAGGCAGTGCAAGCACGGAAACAACGAATGATTTCTGGTGCCTTGACTGATCAAGAAGTTCGAACTGCAAGGATTGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - -caccaaa
- - - - - - - - - - - - - - - - - - - - tggttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgca