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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtcagtccttttactatcttgcttctttctagttgaactacaccagcaactttaagagaggaagtcttagcttactgattctgggacttttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTCACTCTAGATCATCTCAGTGTGAGGGGTAACAA

Basic information

species Glycine max
transcript GLYMA02G10640.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G10640.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g37430.1 (Oryza sativa), 3'ss of exon 2
tagtcagtccttttactatcttgcttctttctagttgaactacaccagcaactttaagagaggaagtcttagcttactgattctgggacttttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTCACTCTAGATCATCTCAGTGTGAGGGGTAACAA
|   |||  || ||   ||   |            | | || ||  ||  |||  |  | |     | |   | | || | |    |   | |     ||||||||||||||| |||||||| ||  ||||||| || ||||| ||  |||||||||||||||| || ||  | ||||| |||||||||||||| |||||
tcagcagagctattctcatgcggtcatgcctataatcacctccataagtgactccattatactccatatgcacatcctaacttccaggtctattttgtagGTGTTGATATCAGCATGAACACGCACCTGAAAACTGTGAAACTCACATTGAAAGGGAAAAATCCTGTTACCTTTGATCACCTCAGTGTGAGGGGAAACAA

upper sequence: GLYMA02G10640.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g39444.1 (Oryza sativa), 3'ss of exon 2
tagtcagtccttttactatcttgcttctttctagttgaa------ctacaccagcaa---ctttaagagaggaagtcttagcttactgattctgggacttttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTCACTCTAGATCATCTCAGTGTGAGGGGTAACAA
       || | || ||| ||| |||| |  | |||||        ||      |||     ||| |    | | | ||    | |||||||    || |||    ||||||| ||||| || |||||||| || ||||| || ||||| || ||  |||||||||||||||| || || || || || ||||||||||| || |||||
-------tcatgtttctagctttcttcatgttggttgaggtgtttttaggtggacaaggctgttatgtcctggaatgtttcaattctgattcatcaaccttt--tgcagGTGTGGATATAAGCATGAACACCCACTTGAAGACTGTTAAGCTCACATTGAAAGGGAAAAATCCTGTAACCCTTGACCACCTCAGTGTGAGAGGAAACAA

upper sequence: GLYMA02G10640.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G416061_T01 (Zea mays), 3'ss of exon 3
tagtcag--tccttttactatcttgcttctttctagttgaactacaccagcaactttaagagaggaagtct-tagctta--ctgattctgggacttttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTCACTCTAGATCATCTCAGTGTGAGGGGTAACAA
|  | |   |||  |||  ||  |    | ||| | |   | |  || || ||   ||  |     | ||  |||  ||  |||||| |  |   ||||    ||||||||| ||||| ||||| || ||| |||| || || || || || || |||||||||||||| || || || ||||| || ||||||||||| |||||
tttttaacatcccattaaaattctctcccattcca-tcagattttac-agtaatcctagaatgattattcagtagtgtattctgattttttggactttgt---agGTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAAAAGGGAAAAATCCTGTTACCCTTGATCACCTTAGTGTGAGGGGAAACAA

upper sequence: GLYMA02G10640.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 3
----tagtcag---tccttttactatcttgcttctttctagt-tgaactacaccagcaactttaagagaggaagtcttagcttactgattctgggacttttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTCACTCTAGATCATCTCAGTGTGAGGGGTAACAA
    | ||  |   ||||||| ||  | |  |  | | |||  || | |   | | |||||    ||  || | | |   |||  ||||     |||||      ||||||| ||| | || |||||||| ||||| ||| | || ||||| |||||||||||||| |||||||| ||  |||| ||  | ||||| ||||| |||||
tgtttggtttggtttcctttttctgccatcatcttgtttagaatgcaattatcaatcaactcactgactggtactatctacttg-tgat-----gactt--aatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGAAAGGGAAGAATCCAGTTACATTAGACCACTTAAGTGTCAGGGGAAACAA

upper sequence: GLYMA02G10640.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0104g00160.t01 (Vitis vinifera), 3'ss of exon 4
tagtcagtccttttactatcttgcttctttctagttgaac---tacaccagcaactttaagagaggaagtcttagcttactgattctgggacttttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTCACTCTAGATCATCTCAGTGTGAGGGGTAACAA
   |||      | ||||    | ||   |     |  |    |  |    ||  | |     ||| ||  |    ||| ||  | ||      |||  | |||||||||||| |||||||||||||||||||| ||||| ||||| ||  |||| |||||||||||||| |||||||||||  | ||||| || || |||||
--atcaaatagataactaggcagttttaatgggaattcatgcatgaattctcagttgtgttgaaggcagattctaattagtggctttgcc-tgcttgttatagGTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGAAGGGGAAAAATCCAGTGACTCTAGATCACTTGAGTGTTAGAGGCAACAA

upper sequence: GLYMA02G10640.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0015g01330.t01 (Vitis vinifera), 3'ss of exon 2
tagtcagtccttttactatcttgcttctttctagttgaactac--accagcaactttaagagaggaagtcttagcttactgattctgggacttttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTCACTCTAGATCATCTCAGTGTGAGGGGTAACAA
 ||| | |     ||      | | | ||   |    |||||   |  | |||   | |  |  ||  || | ||| | || |  ||     | ||  | |||||| ||||| |||||||||||||||||||| || || ||||| |||||||| |||||||||||||| ||| | ||||| || ||||||||||| |||||
-agtaacttgaagtaggtaagtccatgttatgacaaaaactatttagaatcaaagatgattggagagatcattgctga-tggtattgctttgtatgttatagGTGTGGATATTAGTATGAACACACATTTGAAGACTGTGAAACTGACTCTGAAGGGGAAAAATCCAGTGACTATGGATCACCTGAGTGTGAGGGGCAACAA

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|192326454|gb|FK015941.1|FK015941
EST:     CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|120496339|gb|EH224506.1|EH224506
EST:     CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|208121198|gb|GD920307.1|GD920307
EST:     CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|23727600|gb|BU761836.1|BU761836
EST:     CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|19052973|gb|BM731640.1|BM731640
EST:     CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|192315263|gb|FK007721.1|FK007721
EST:     CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAGACTAACTCTGA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|193570947|gb|FK529966.1|FK529966
EST:     CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG                         GTTGTTGATATCAGTATGAACACACATTTAGAAAACA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGT-GTTGATATCAGTATGAACACACATTT-GAAAACA
EST: gi|298192845|gb|HO033279.1|HO033279
EST:     CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAACACACATCTGAAAACAGTTAAACTAACTCTGA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|58015388|gb|CX702130.1|CX702130
EST:     CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|7284502|gb|AW597091.1|AW597091
EST:     CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|13791520|gb|BG654111.1|BG654111
EST:     CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|10847035|gb|BF069805.1|BF069805
EST:     CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|58025133|gb|CX711874.1|CX711874
EST:     CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|22932348|gb|BU549487.1|BU549487
EST:     TGTCAATTGAGCTCAAGAATNNCACTATTGTTCATGGCACCATTACAN                         GTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: TGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|58018364|gb|CX705106.1|CX705106
EST:     CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|22541357|gb|BU091200.1|BU091200
EST:     CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|19268713|gb|BM884969.1|BM884969
EST:     CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|192301564|gb|FG994776.1|FG994776
EST:     CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|58015707|gb|CX702449.1|CX702449
EST:     CGTGTCAATTGAGCTCAAGAATGGCAGTATTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGATCACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|9902219|gb|BE611187.1|BE611187
EST:     CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|14991002|gb|BI316675.1|BI316675
EST:     CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|298187789|gb|HO031746.1|HO031746
EST:     CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAGgtttcttttc ... tttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcaactttaagagaggaagtcttagcttactgattctgggacttttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTCACTCTAGATCATCTCAGTGTGAGGGGTAACAA
                             tactgat  putative branch site (score: 2)
                                           cttttgcc  putative PPT
     actttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagtcagtccttttactatcttgcttctttctagttgaactacaccagcaactttaagagaggaagtcttagcttactgattctgggacttttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTCACTCTAGATCATCTCAGTGTGAGGGGTAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - -tgcttct
- - - - - - - - - - - - - - - - - - - -ctacacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gattctg