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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggattgccatggttttcttgttatttaaggatgaattttgtattattactaaaactaatttctcattatcatttcagCTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTTACTGCTAAACTTCAGGAGGTAGAAGACTGGCTATATGAGGATGGTGAAG

Basic information

species Glycine max
transcript GLYMA15G01750.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G01750.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G063676_T01 (Zea mays), 3'ss of exon 6
gtgaggattgccatggttttcttgttatttaaggatgaattttgtattattactaaaactaatttctcattatcatttcagCTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTTACTGCTAAACTTCAGGAGGTAGAAGACTGGCTATATGAGGATGGTGAAG
  |    | |  |||  |  |||| |  ||     ||   | |  |   |  ||||      ||| | ||| |   || ||||  | ||||  ||| | || |||||      |   |||| ||||   || | ||  || ||||||||||| ||||| ||||||||||| |||||||| |
--gtatgtggagatgcatgccttgatggttttccttgtgatataaacagtatctaatgtcc-ttttttattgta--tttagCTCTACGACAGGTACAACGATTTTGTGACACCTGAGGAGAAGGAAGGGTTGATTGGAAAGCTTCAGGAGGTTGAAGATTGGCTATATGAAGATGGTGAGG

upper sequence: GLYMA15G01750.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G023232_T01 (Zea mays), 3'ss of exon 6
gtgaggattgccatggttttcttgttatttaaggatgaattttgtattattactaaaactaatttctcattatcatttcagCTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTTACTGCTAAACTTCAGGAGGTAGAAGACTGGCTATATGAGGATGGTGAAG
        |    ||  |  |   |    ||| | ||  | || |    ||   |     | ||| |  |  ||  || ||||  ||||||| |||   || ||||||     |   || | ||||   || | |||||| ||||||||||| ||||||||||| ||||| ||||| || |
-------gtatattgagtcacgcata--ctaatgttg--tcttatgaagttgtgagcctgattttgttctcttctatttagCTATATGACAAGTACAGTGATTTTGTCACGTCTGAGGACAAGGAAGGTTTGATTGCTAAGCTTCAGGAGGTTGAAGACTGGCTCTATGAAGATGGCGAGG

upper sequence: GLYMA15G01750.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv09s0002g04680.t01 (Vitis vinifera), 3'ss of exon 5
gtgaggattgccatggttttc-ttgttatttaaggatgaattttgtattatt-----actaaaactaatttctcattatcattt----cagCTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTTACTGCTAAACTTCAGGAGGTAGAAGACTGGCTATATGAGGATGGTGAAG
|| ||  || | ||  | ||   |   |   ||  |     ||||||   ||     ||| | |   |    | |||||| | |    |||||| ||||||| || || || ||||||  |   |||||||||||    |||||||||||||| |||||||||||||| ||| | ||||| || ||||| |
gtaagtgtttctatcctattggctaagacagaattacagcatttgtaaccttcacctactgatatctacacatgattatcttctgccccagCTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTTACTGCTAAACTGCAGGAGGTAGAAGATTGGTTGTATGAAGACGGTGAGG

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|19346354|gb|BM891234.1|BM891234
EST:     AGGATAAGAAAAATGCAGTAGAGGCTTATGTTTATGACACGAGAAACAAG                         CTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTT
genomic: AGGATAAGAAAAATGCAGTAGAGGCTTATGTTTATGACACGAGAAACAAGgtgaggattg ... atcatttcagCTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTT
EST: gi|193462405|gb|FK425518.1|FK425518
EST:     TTATGACACGAGAAACAAG                         CTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTT
genomic: TTATGACACGAGAAACAAGgtgaggattg ... atcatttcagCTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTT
EST: gi|33388505|gb|CA851712.1|CA851712
EST:     AGGATAAGAAAAATGCAGTAGAGGCTTATGTTTATGACACGAGAAACAAG                         CTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTT
genomic: AGGATAAGAAAAATGCAGTAGAGGCTTATGTTTATGACACGAGAAACAAGgtgaggattg ... atcatttcagCTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTT
EST: gi|33390219|gb|CA853426.1|CA853426
EST:     AGGATAAGAAAAATGCAGTAGAGGCTTATGTTTATGACACGAGAAACAAG                         CTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTT
genomic: AGGATAAGAAAAATGCAGTAGAGGCTTATGTTTATGACACGAGAAACAAGgtgaggattg ... atcatttcagCTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTT
EST: gi|5770361|gb|AI973535.1|AI973535
EST:     AGGATAAGAAAAATGCAGTAGAGGCTTATGTTTATGACACGAGAAACAAG                         CTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTT
genomic: AGGATAAGAAAAATGCAGTAGAGGCTTATGTTTATGACACGAGAAACAAGgtgaggattg ... atcatttcagCTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTT
EST: gi|105634312|gb|DW247461.1|DW247461
EST:     AGGATAAGAAAAATGCAGTAGAGGCTTATGTTTATGACACGAGAAACAAG                         CTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTT
genomic: AGGATAAGAAAAATGCAGTAGAGGCTTATGTTTATGACACGAGAAACAAGgtgaggattg ... atcatttcagCTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTT
EST: gi|193560375|gb|FK516826.1|FK516826
EST:     GAATAAGAAAAATAGCAGTAGAGGCTTATGTTTATGACACGAGAAACAAG                         CTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTT
genomic: G-ATAAGAAAAAT-GCAGTAGAGGCTTATGTTTATGACACGAGAAACAAGgtgaggattg ... atcatttcagCTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTT
EST: gi|193548375|gb|FK504472.1|FK504472
EST:     GGATAAAGAAAAATGCAGTAGAGGCTTATGTTTATGACACGAGAAACAAG                         CTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTT
genomic: GGATAA-GAAAAATGCAGTAGAGGCTTATGTTTATGACACGAGAAACAAGgtgaggattg ... atcatttcagCTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTT
EST: gi|208274072|gb|GE071484.1|GE071484
EST:     AGGATAAGAAAAATGCAGTAGAGGCTTATGTTTATGACACGAGAAACAAG                         CTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATTATTT
genomic: AGGATAAGAAAAATGCAGTAGAGGCTTATGTTTATGACACGAGAAACAAGgtgaggattg ... atcatttcagCTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaaggatgaattttgtattattactaaaactaatttctcattatcatttcagCTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTTACTGCTAAACTTCAGGAGGTAGAAGACTGGCTATATGAGGATGGTGAAG
                                              tcatttc  CT-rich tract
           aattttgtattattac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggattgccatggttttcttgttatttaaggatgaattttgtattattactaaaactaatttctcattatcatttcagCTTAATGACAAATACCAAGAGTTTGTCGTTGATTCAGAGAGGGAATCATTTACTGCTAAACTTCAGGAGGTAGAAGACTGGCTATATGAGGATGGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG