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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATCATTTCTATGGTTGACTTGATTGTCCACTTACAGGTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggactaggagcatgccatttcaagtttatgcactaaataattataaaactataatgaaaatgacatgtttaactattacggtccattaggaggccca...

Basic information

species Glycine max
transcript GLYMA08G17810.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G17810.2 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os02g42320.1 (Oryza sativa), 5'ss of exon 8
TATCATTTCTATGGTTGACTTGATTGTCCACTTACAGGTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggactaggagcatgccatttcaagtttatgcactaaataattataaaactataatgaaaatgacatgtttaactattacggtccattaggaggccca
                                      |||||||| || |||||||||||||||||  |||| || || || ||||||||||| |||||||| | || | ||  |||   |     | | | |   | ||  |||   |  ||         ||||   ||      || | |                
-------------------------------------ATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGGgtatgtcttgtag-gtgcttctgtttctatttccggaacatccttactgagttac--------tgactgattcgggggttgcag----------------

upper sequence: GLYMA08G17810.2 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G382240_T01 (Zea mays), 5'ss of exon 11
TATCATTTCTATGGTTGACTTGATTGTCCACTTACAGGTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggactaggagcatgccatttca-agttt---atgcactaaataattataaaactataatgaaaatgacatgtttaactattacggtccattaggaggccca
                                      |||||||| ||||||||||||||||||||  ||||||| ||||| |||||| |||| ||||||||   | |    | ||   || |  |||||   |    ||||||| |||  ||    |  || |  |   |  |  |                          
-------------------------------------ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtattgcaacccacttgtagttgcttagtttaaaacatcctaaatagttactaattggttctgcatcttggacttgcag-------------------------

upper sequence: GLYMA08G17810.2 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM5G824831_T03 (Zea mays), 5'ss of exon 10
TATCATTTCTATGGTTGACTTGATTGTCCACTTACAGGTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggactaggagcatgccatttcaagtttatgcactaaataattataaaactataatgaaaatgacatgtttaactattacggtccattaggaggccca
                                      |||||||| ||||||||||||||||||||  ||||||| ||||| |||||| |||| ||||||||   || |   ||| || | |     ||    | |  | || |||    ||| |  |  ||| |   |||     ||   || |    ||        
-------------------------------------ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtatcgctcg---catccc-tgttgtacttgcttagtttagaaatatc---ctaaatagttaataattggttccgg-atcttggacttgcag--------

upper sequence: GLYMA08G17810.2 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM5G850355_T02 (Zea mays), 5'ss of exon 10
TATCATTTCTATGGTTGACTTGATTGTCCACTTACAGGTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggactaggagcatgccatttca-agttt---atgcactaaataattataaaactataatgaaaatgacatgtttaactattacggtccattaggaggccca
                                      |||||||| |||||||| |||||||||||  ||||||| ||||| |||||| |||| ||||||||   | |    | ||   || |  |||||   |    ||||||| |||  ||    |  || |  |   |  |  |                          
-------------------------------------ATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtattgcaacccacttgtagttgcttagtttaaaacatcctaaatagttactaattggttctgcatcttggacttgcag-------------------------

upper sequence: GLYMA08G17810.2 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM5G850355_T04 (Zea mays), 5'ss of exon 9
TATCATTTCTATGGTTGACTTGATTGTCCACTTACAGGTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggactaggagcatgccatt-tcaagttta---tgcactaaataattataaaactataatgaaaatgacatgtttaactattacggtccattaggaggccca
                                      |||||||| |||||||| |||||||||||  ||||||| ||||| |||||| |||| ||||||||   | |    | ||   ||    ||||||       ||||||| |||  ||    |  || |  |   |  |  |  ||| | || | | |          
-------------------------------------ATACACAGAGGATATGGAACTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtattgcaacccacttgtagttgcttagtttaaaacatcctaaatagttactaattggttctgcatcttggacttgcagatatgaggggcaaatttcctc----

upper sequence: GLYMA08G17810.2 (Glycine max), 5'ss of exon 9
lower sequence: AT1G79210.1 (Arabidopsis thaliana), 5'ss of exon 10
TATCATTTCTATGGTTGACTTGATTGTCCACTTACAGGTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggactaggagcatgccatttcaagtttatgcactaaataattataaaactataatgaaaatgacatgtttaactattacggtccattaggaggccca
                                     ||||||||| |||||||| |||||||||||  | ||||| |||||||||||  ||||||||||||  |  |       |   |    || || ||  |||  ||    |  |    | |||       |    | ||||      | ||  ||   ||     
-------------------------------------GTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGGgtgagcat-------ttttaccaaaacttaatttactttatttcca-gagttcagaatttctcaaaagcctataacctccgtg-tcttttcacag-----

upper sequence: GLYMA08G17810.2 (Glycine max), 5'ss of exon 9
lower sequence: Vv01s0011g01960.t01 (Vitis vinifera), 5'ss of exon 9
TATCATTTCTATGGTTGACTTGATTGTCCACTTACAGGTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtagga-----ctaggagcatgccatttcaagtttatgc-actaaataattataaaactataatgaaaatgacatgtttaactattacggtccattaggaggccca
                                     |||||| ||||||||||| ||||||||||| ||||||||||| || ||||| || ||||| |||||         ||      |    ||| || |||  || |   |||  ||  |||||||| |    || | ||  |  |     |  |  |   |  |  |  | 
-------------------------------------GTACACTGATGATATGGAACTTGATGATGCTGTCCACACAGCTATTTTGACACTCAAGGAGGGgtatatgcatcttaaacttcttttcttttaaatttcagctaacgaatgtttg-aaaactatca----aaaggcacatcaagaagctttgaacttatctgttgttc-

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|6719574|gb|AW307221.1|AW307221
EST:     AGTCCACACAGCAATATTGACTCTGAAGGAAGG                         GTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATTGGAGC
genomic: AGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggactag ... tgtttcccagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATTGGAGC
EST: gi|214008378|gb|DB986320.1|DB986320
EST:     ATGGAGCTTGATGATGCAGTCCACACAGCAATATTGATTAGGAAGGAAGG                         GTTTGAGGGACAGATCCCAGGAAAAAACATTGAAATTGGCATAAATGGAGC
genomic: ATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggactag ... tgtttcccagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATTGGAGC
EST: gi|31468638|gb|CD410666.1|CD410666
EST:     ATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGG                         GTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATTGGAGC
genomic: ATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggactag ... tgtttcccagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATTGGAGC
EST: gi|19937016|gb|BQ081110.1|BQ081110
EST:     CTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGG                         GTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATTGGAGC
genomic: CTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggactag ... tgtttcccagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATTGGAGC
EST: gi|31462312|gb|CD404340.1|CD404340
EST:     ATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTTTGAAGGAAGG                         GTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATTGGAGC
genomic: ATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggactag ... tgtttcccagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATTGGAGC
EST: gi|14991049|gb|BI316722.1|BI316722
EST:     AGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGG                         GTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATTGGAGC
genomic: AGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggactag ... tgtttcccagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATTGGAGC
EST: gi|15200642|gb|BI424453.1|BI424453
EST:     ATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGG                         GTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATTGGAGC
genomic: ATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggactag ... tgtttcccagGTTTGAGGGACAGATCTCAGGAAAAAACATTGAAATTGGCATAATTGGAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATCATTTCTATGGTTGACTTGATTGTCCACTTACAGGTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggactaggagcatgccatttcaagtttatgcactaaataattataaaactataatgaaaatgacatgtttaactattacggtccattaggaggccca

- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA