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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGGTGGTTCTCACCAAGGATACAACCACAATTGTTGGTGATGGAAGTACCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccatctctctctttttctctccactgaaatgtttgcacatgcaaacgtggcatgggcaggtttcatgaagatatttcacagaaaacatgactga...

Basic information

species Glycine max
transcript GLYMA15G40110.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 8
CAAGGTGGTTCTCACCAAGGATACAACCACAATTGTTGGTGATGGAAGTACCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtct-ttccatctctctctttt--tctctccactgaaatgtttgcacatgcaaacgtggcatgggca-ggtttcatgaagatatttcacagaaaacatgactga
 |||||||| || | ||| ||  |||| ||||||||||||||||| ||||| ||||||| |||||  ||||| |||||||| || |  || || || ||||| | ||  |||| | |    |  |   |       |||  |  | |    |    |    | ||||   |         ||||| |||        | |    
AAAGGTGGTCCTTAACAAAGAGTCAACAACAATTGTTGGTGATGGCAGTACACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttatatctgtttaccatggttaatttggcacaatagtgcctcgcaaatttttttttttggcacaatagtggttctatattccaccatttctttaa----

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 7
CAAGGTGGTTCTCACCAAGGATACAACCACAATTGTTGGTGATGGAAGTACCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccatctctctctttttctctccactgaaatgt-ttgcacatgcaaacgtggcatgggcaggtttcatgaagatatttcacagaaaacatgactga
 ||||| || || || || ||  | || ||||||||||||||||| || |||||||||| ||| |  ||||| |||||||||||||  || || ||||||||||  || | ||    | | | |   ||||  | | |  ||| || |  || ||   | |  | | ||| |||||  || ||  |||             
AAAGGTTGTCCTTACGAAAGAGTCGACAACAATTGTTGGTGATGGCAGCACCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctgaccttttcctgttctatttgctcacttgactttactgctcaggtgaaagtctgaagctctgtttttatgaacctaatttgcag-------------

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G065023_T01 (Zea mays), 5'ss of exon 3
CAAGGTGGTTCTCACCAAGGATACAACCACAATTGTTGGTGATGGAAGTACCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccatctctctctttttctctccactgaaatgt-ttgcacatgcaaacgtggcatgggcaggtttcatgaagatatttcacagaaaacatgactga
 ||||| || || || || |   | || ||||||||||||||||| || |||||||||| ||| |  ||||| |||||||||||||  || || ||||||||||  || | ||    | | | |   ||||  | | |  ||| || |  || ||   | |  | | ||| |||||  || ||  |||             
AAAGGTTGTCCTTACGAAAGGGTCGACAACAATTGTTGGTGATGGCAGCACCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctgaccttttcctgttctatttgctcacttgactttactgctcaggtgaaagtctgaagctctgtttttatgaacctaatttgcag-------------

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 2
CAAGGTGGTTCTCACCAAGGATACAACCACAATTGTTGGTGATGGAAGTACCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtcttt--ccatctctctctttttctctccactgaaatgt-ttgcacatgcaaacgtggcatgggcaggtttcatgaagatatttcacagaaaacatgactga
 ||||| || || || || ||  | || ||||||||||||||||| || |||||||| | ||| |  ||||| |||||||||||||  || || |||||||||| |  || | ||    | | | | | ||||  | | |  ||| || |  ||  |   |  | | | ||| || ||  || ||   ||             
AAAGGTTGTCCTTACTAAAGAGTCGACAACAATTGTTGGTGATGGCAGCACCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgaccttttcctgttctctttgttcactcgattttactgctcaggtgaaaatctgaaagtctgcttttatcaacctaatttttag-------------

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 7
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 8
CAAGGTGGTTCTCACCAAGGATACAACCACAATTGTTGGTGATGGAAGTACCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccatctctctctttttctctccactgaaatgtttgcacatgcaaacgtggcatgggcag-gtttcatgaagatatttcacagaaaacatgactga
|||||| || || || ||||| |  || |||||||| |||||||| |  || || ||||||||||||||| | |||| |||||||||||| || |||||||| |         | | |   ||   || |  ||  || ||     || |   |    ||   |  ||||  | | | || | ||            | | 
CAAGGTTGTCCTGACAAAGGAAATGACAACAATTGTGGGTGATGGGACCACACAAGAAGCAGTGAACAAGCGTGTTGTACAGATTAGGAATCTTATTGAGgtat--------atgtttgagtcaaaccgcataagagtctgtgacagctacttttttttgtataaagtttgtttatgctaatacaactgcggttgtgcag-

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 7
lower sequence: AT5G56500.2 (Arabidopsis thaliana), 5'ss of exon 8
CAAGGTGGTTCTCACCAAGGATACAACCACAATTGTTGGTGATGGAAGTACCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgt-ctttccatctctctctttttctctccactgaaatgtttgcacatgcaaacgtggcatgggcaggtttcatgaagatatttcacagaaaacatgactga
 || ||||||||||| || ||||| || || || |||||||||||||||||  | ||||  ||||| |||||||||| |||||| | ||| || || ||||| | |  ||     |  |        ||| | || || ||  |  |      |    |      || ||  || ||                        
TAAAGTGGTTCTCACAAAAGATACTACAACGATAGTTGGTGATGGAAGTACTGAAGAAGTTGTGAAGAAGAGAGTTGAACAGATCAAGAATCTTATCGAGgtacatctcaaaaaacattgaaatgtcccaataaattggttttatgttacggtgattaagtctttgggtttgtgtag------------------------

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 8
CAAGGTGGTTCTCACCAAGGATACAACCACAATTGTTGGTGATGGAAGTACCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccatctctctctttttctctccactgaaatgtttgcacatgcaaacgtggcatgggcaggtttcatgaagatatttcacagaaaacatgactga-
 |||||||| || ||||||||||||||||| |||||||| ||||| || |||||||||||||| || ||| |||||||||| ||||| ||||| ||||||||      |||| ||| |  |      |||| | |       | | | |||  ||   | |      ||  |  |  | | | ||| |     ||| | | 
AAAGGTGGTGCTTACCAAGGATACAACCACCATTGTTGGAGATGGGAGCACCCAGGAAGCAGTAAATAAGCGAGTTGCACAAATTAGAAACCTCATTGAGgt------atctatctgtcctctcactcactcacacacacagaga-gtaaatatgtgtttgctgaactttgttgatctttcttacatatgtgttgattcag

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|16278868|gb|BI943136.1|BI943136
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccat ... aacattacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|193629072|gb|FK576466.1|FK576466
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATG
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccat ... aacattacagGCTGCTGAGCAAGAGTATG
EST: gi|16278211|gb|BI942785.1|BI942785
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccat ... aacattacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|208337500|gb|GE133496.1|GE133496
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccat ... aacattacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|193508759|gb|FK465915.1|FK465915
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccat ... aacattacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|208146316|gb|GD948421.1|GD948421
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTAT
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccat ... aacattacagGCTGCTGAGCAAGAGTAT
EST: gi|26046015|gb|CA783382.1|CA783382
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccat ... aacattacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|16279768|gb|BI943606.1|BI943606
EST:     GAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: GAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccat ... aacattacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|298192668|gb|HO033102.1|HO033102
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccat ... aacattacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|16276840|gb|BI942072.1|BI942072
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccat ... aacattacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|193661261|gb|FK603559.1|FK603559
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccat ... aacattacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|208166285|gb|GD965477.1|GD965477
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccat ... aacattacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|193658934|gb|FK602087.1|FK602087
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccat ... aacattacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|193523440|gb|FK478287.1|FK478287
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccat ... aacattacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|15589717|gb|BI674333.1|BI674333
EST:     GGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: GGAACCTAATTGAGgtctttccat ... aacattacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|208230249|gb|GE031696.1|GE031696
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccat ... aacattacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAA
EST: gi|207784127|gb|GD758437.1|GD758437
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccat ... aacattacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|17400588|gb|BM177370.1|BM177370
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccat ... aacattacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|208294352|gb|GE093051.1|GE093051
EST:     CCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccat ... aacattacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
EST: gi|207847652|gb|GD818243.1|GD818243
EST:     CCCAGGAAGCAGNGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAG                         GCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA
genomic: CCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccat ... aacattacagGCTGCTGAGCAAGAGTATGAGAAAGAAAAGCTGAATGAGAGAATTGCTAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGGTGGTTCTCACCAAGGATACAACCACAATTGTTGGTGATGGAAGTACCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtctttccatctctctctttttctctccactgaaatgtttgcacatgcaaacgtggcatgggcaggtttcatgaagatatttcacagaaaacatgactga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctctcc