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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cataagtgtttaattaacctgtttatccaaatacaccccaagtagtgatgagcaaaatgccataactatcatgattttctgatcctgacttactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAACCGCAGGACCGTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTG

Basic information

species Glycine max
transcript GLYMA18G49340.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G49340.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g06040.1 (Oryza sativa), 3'ss of exon 2
cataagtg-tttaattaacctgtttatccaaatacaccccaagtagtgatgagcaaaatgccataactatcatgattttctgat--cctgacttactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAACCGCAGGACCGTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTG
   || || || || |||  | | | |  |     | |  |||      ||   | | ||| ||| |  |  |  ||      |  | ||   ||  ||||||||||||||| | ||||||||||| ||||||||||| |||||| | ||||| ||||||||||| |||||  | || || |||||  | || ||    || |
---aattggttgaaataagttttctttgaaccggtatcttaagcttcattgttaacattgcaatatccttggttcttacaaagttgcttgtgctaaactgcagATTCCACACCTGAGACCTGCTGAGTACAAGAGGTCCAGATTGTCAAGGAATCGCAGGACCGTGAACCGTCCTTACGGTGGTGTCCTGTCTGGTACTGCAG

upper sequence: GLYMA18G49340.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g33920.1 (Oryza sativa), 3'ss of exon 2
cataagtgtttaattaacctgtttatccaaata--caccccaagtagtgatgagcaaaatgccataactatcatgattttctgatcctgacttactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAACCGCAGGACCGTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTG
    |  ||||  ||   |   ||| | | ||       |    |  |  |   |   ||      ||| | | |||||    |   |    |  ||| |||||||| ||||| || |||||||| ||||||||||| || ||| |||||||||||||||| || |||||  | ||||| || ||  | || ||    || |
-gataccgtttggttcttcatattaccgatattacttttctctatgctatttcactggatatttgtact-tgaggatttatacagtgttctattttctccagATTCCCCACTTGAGGCCTGCTGAGTACAAGAGGTCCAGGTTGTCTAGGAACCGCAGGACTGTGAACCGTCCATATGGTGGAGTGCTCTCTGGAACTGCAG

upper sequence: GLYMA18G49340.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G032564_T01 (Zea mays), 3'ss of exon 2
-------cataagtgtttaattaacctgtttatccaaatacaccccaagtagtgatgagcaaaatgccataactatcatgattttctgatcctgacttactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAACCGCAGGACCGTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTG
           ||| || | ||  |       |  || |      ||  ||   |  |   || |||       || |  |||| ||   | | | ||     ||||||||||||| | ||||||||||| ||||||||||| || ||| | |||||||||||||| || |||||  | ||||| |||||| | || ||    || |
tcagattaggcagtcttaagtttgcactgcagtataagtttgtgtcatttacataatatttaactgctgc--tcataaatatttcctatgcttcaatt-----gcagATTCCACACCTGAGACCTGCTGAGTACAAGAGGTCCAGGTTGGCAAGGAACCGCAGGACTGTGAACCGTCCATATGGTGGTGTTCTGTCTGGTACCGCAG

upper sequence: GLYMA18G49340.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G820996_T01 (Zea mays), 3'ss of exon 2
------cataagtgtttaattaacctgtttatccaaatacaccccaagtagtgatgagcaaaatgccataactatca-tgattttctgatcctgacttactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAACCGCAGGACCGTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTG
      ||||| |  | | |||       |   |   ||    |    |     ||| ||    | | ||||  ||| || |  |   || ||  |    |||  |||| || ||||| |||||||| || ||||||||||| || ||| |||||||||||||||| || |||||  | ||||| || ||  | || ||    ||||
actatccataaatcatcatttagttcacatggtctggtaatttctctatc----tgaacag---gtcttaacagtcaatgctaatgctattcttcccatatctctagATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAACCGCAGGACTGTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTG

upper sequence: GLYMA18G49340.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G152573_T04 (Zea mays), 3'ss of exon 2
------cata-agtgtttaattaacctgtttatccaaatacacccca--agtag--tgatgagcaaaatgccataactatcatgattttctgatcctgacttactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAACCGCAGGACCGTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTG
       ||  ||| || | || ||  |    |  || |     |||  |  ||  || | | |  | |  ||||| ||||  || |   |||             |||||||||||||| | ||||||||||| ||||||||||| || ||| | |||||||  ||||| || || ||  | ||||| |||||| | || ||    || |
tcagattatgcagtcttaagttcacgcgggagtataagtttgtgccattaacagcatgtttaactgattctcataaatatcgcgaatgcttgaat-----------tgcagATTCCACACCTGAGACCTGCTGAGTACAAGAGGTCCAGGTTGGCAAGGAACCAAAGGACTGTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAG

upper sequence: GLYMA18G49340.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0108g00850.t01 (Vitis vinifera), 3'ss of exon 2
----cataagtgtttaattaacctgtttatcca-aatacaccccaagtagtgatgagcaaaatgccataactatcatgattttctgatcctgacttactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAACCGCAGGACCGTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTG
    |   ||| || | ||    ||||||      ||     |||  || |  ||    || ||    || | |  |  ||| |   || |   |   |||||||||||| ||| | |||||||||||||||||||||||||||||||| |||||||| ||||| || ||||| ||||||||||||||||| || || || ||||
gtggccagagttttcacttg---tgtttacttgtgattagaaccatatattc-tgcttcaattgtgtcaatt-ttttcttttacaattctttgatctatctgcagATTCCTCACCTGAGACCTGCTGAATACAAGAGGTCTAGATTGCCAAGGAACCGTAGGACTGTGAACCGGGCCTATGGAGGTGTTTTGTCGGGTGGTGCTG

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|298192810|gb|HO033244.1|HO033244
EST:     AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTATGAAC
genomic: AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|192310364|gb|FK002244.1|FK002244
EST:     AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
genomic: AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|151398936|gb|EV268807.1|EV268807
EST:     AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
genomic: AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|163920689|gb|EH039970.1|EH039970
EST:     AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
genomic: AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|33388818|gb|CA852025.1|CA852025
EST:     AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
genomic: AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|192310365|gb|FK002245.1|FK002245
EST:     AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTTTAGATTGCCTAGGAAC
genomic: AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|7284738|gb|AW597288.1|AW597288
EST:     AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
genomic: AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|58024564|gb|CX711305.1|CX711305
EST:     AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
genomic: AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|58014987|gb|CX701729.1|CX701729
EST:     AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
genomic: AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|192313246|gb|FK003366.1|FK003366
EST:     AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
genomic: AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|24205811|gb|BU965064.1|BU965064
EST:     AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
genomic: AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|5753167|gb|AI960454.1|AI960454
EST:     GAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGGCA-GAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
genomic: GAGAGCAAGTGGACCTAAGTGCCCTGTCACTGG-CAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|7589597|gb|AW705368.1|AW705368
EST:     AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
genomic: AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|57575671|gb|CX548646.1|CX548646
EST:     AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
genomic: AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|208330531|gb|GE131356.1|GE131356
EST:     AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
genomic: AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|193483394|gb|FK451461.1|FK451461
EST:     AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
genomic: AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|7590502|gb|AW706253.1|AW706253
EST:     AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
genomic: AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|15662700|gb|BI700071.1|BI700071
EST:     GTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
genomic: GTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|6072282|gb|AW101669.1|AW101669
EST:     AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
genomic: AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|208136838|gb|GD937530.1|GD937530
EST:     AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
genomic: AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|193533122|gb|FK493684.1|FK493684
EST:     GAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCGAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAA
genomic: GAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCC-AAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAA
EST: gi|58024472|gb|CX711213.1|CX711213
EST:     AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
genomic: AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
EST: gi|192320359|gb|FK013449.1|FK013449
EST:     AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGG                         ATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC
genomic: AGAGAGCAAGTGGACCTAAGTGCCCTGTCACTGGCAAGAGGATCCAAGGGgtatttagtg ... tactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgagcaaaatgccataactatcatgattttctgatcctgacttactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAACCGCAGGACCGTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTG
                                         gacttac  putative branch site (score: 2)
                                           cttactct  CT-rich tract
                ataactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cataagtgtttaattaacctgtttatccaaatacaccccaagtagtgatgagcaaaatgccataactatcatgattttctgatcctgacttactctgcagATTCCACACTTAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAACCGCAGGACCGTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - -cctgttt
- - - - - - - - - - - - atccaaa
- - - - - - - - - - - - - - - - -cacccca
- - - - - - - - - - - - - - - - - - - - - - -tgatgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgact