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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATTGTGATGAGCACAAGAGTTTGTGCAGCAAGTATGGAGTTTCCGGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagcgcgtgtttaaatttttccatatcctttgtttaccaagttctgtgaattctgacagaaattcctttggcaaattag

Basic information

species Zea mays
transcript GRMZM2G128171_T04
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128171_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g23740.2 (Oryza sativa), 5'ss of exon 3
GTTGATTGTGATGAGCACAAGAGTTTGTGCAGCAAGTATGGAGTTTCCGGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagcgcg-----tgtttaaatttttccatat-cctttgtttaccaagttctgtgaattctgacagaaattcctttggcaaattag
|||||||| ||||||||||||||| |||||||||||||||||||||| ||||| |||||||| ||||||||||| ||||||||| |||||||||||||||||||  ||        |||| ||||  ||    |   ||        |||  | |     |  |||   | ||  ||    | |  |||
GTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAAgtgaggctgcataacttttgttcaaatacttttgaacatctacaccagacaaaattt-----tcatgatttatatcactacaaccatgtag

upper sequence: GRMZM2G128171_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA02G01750.1 (Glycine max), 5'ss of exon 3
GTTGATTGTGATGAGCACAAGAGTTTGTGCAGCAAGTATGGAGTTTCCGGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagcgcgtgtttaaatttttccatatcctttgtttaccaagttctgtgaattctgacagaaattcctttggcaaattag--------------------------------------------------
||||| ||||||||||||||||||||||||||||| |||||||| || ||||| |||||||| || ||||| || ||||||||  | || ||||||||||||||       ||| ||  ||     ||| | ||     |      | | | |||||  | ||  |||    || ||  | |                                                   
GTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAACCCAAAAAgtgaggagatttttgtcta--ttggaatataacattgacacaattttatatcttaattc--atagttatttacctgtcatttcacatttatcattccttttgcattcaatacttgattttggaaaattcccatag

upper sequence: GRMZM2G128171_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA06G24520.1 (Glycine max), 5'ss of exon 4
GTTGATTGTGATGAGCACAAGAGTTTGTGCAGCAAGTATGGAGTTTCCGGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagcgcgtgttta----aattt-------------ttccatatcctttgtt-taccaagtt--ctgtgaattctgacagaa-attcctttggcaaattag-------------------------
||||| ||||||||||||||||||||||||||||| |||||||| || ||||| |||||||| || ||||| || ||||||||  | || ||||||||||||||       ||| ||    ||| |             ||  ||||| |   |  ||   | ||  |||| | |||| |   |  |||||||| |||    |                          
GTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAACCCAAAAAgtgaggagatttttgtctattggaatataacattgacacaattttatatcttaattcatagttatttacctgtcatttctcatttatcattccttttgcattcaatacttgattttggaaaattcccatag

upper sequence: GRMZM2G128171_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA10G01820.1 (Glycine max), 5'ss of exon 4
GTTGATTGTGATGAGCACAAGAGTTTGTGCAGCAAGTATGGAGTTTCCGGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagcgcg---tgtttaaat---------------ttttccatatcctttgtttaccaagt-tctgtgaattctgacagaa-attcctttggcaaattag-------------------------
||||| ||||||||||| |||||||||||||||||||||||||| || ||||| |||||||| || ||||| || ||||||||  | ||  |||||||||||||          | ||  |||               ||||  || ||  ||  |    |  |  |||| | |||  |   |  |||||||| |||    |                          
GTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAAGCCAAAAAgtgaggagatcttctctattggaatataacatggagacgattttatatctcaattcatagttatttacctgtcatttcacatctatcattccttttgcattcaatatttgattttggaaaattcccatag

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|211242633|gb|FL145173.1|FL145173
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCC
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCC
EST: gi|211249334|gb|FL145212.1|FL145212
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211242622|gb|FL145162.1|FL145162
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211244855|gb|FL145175.1|FL145175
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211247098|gb|FL145196.1|FL145196
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGC
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGC
EST: gi|211249335|gb|FL145213.1|FL145213
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTG
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTG
EST: gi|211244858|gb|FL145178.1|FL145178
EST:     GGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCC-AAAATA                         GTATGAAGGACAACGCACTGCA
genomic: GGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAA-Agtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCA
EST: gi|211242621|gb|FL145161.1|FL145161
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTCA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211242632|gb|FL145172.1|FL145172
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCT
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCT
EST: gi|211249340|gb|FL145218.1|FL145218
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211251556|gb|FL145219.1|FL145219
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211247097|gb|FL145195.1|FL145195
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211249328|gb|FL145206.1|FL145206
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211251557|gb|FL145220.1|FL145220
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211242629|gb|FL145169.1|FL145169
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGGAAGCCCTTGCTGAATTTCTCAATACTG
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAG-AAGCCCTTGCTGAATTTCTCAATACTG
EST: gi|211249333|gb|FL145211.1|FL145211
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCMAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211249326|gb|FL145204.1|FL145204
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACA
EST: gi|211249332|gb|FL145210.1|FL145210
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211247093|gb|FL145191.1|FL145191
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAA
EST: gi|211249331|gb|FL145209.1|FL145209
EST:     GGGTATCNAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTWGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211249330|gb|FL145208.1|FL145208
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACCTG
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATAC-TG
EST: gi|211249337|gb|FL145215.1|FL145215
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACT
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACT
EST: gi|211247100|gb|FL145198.1|FL145198
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|78117464|gb|DV535851.1|DV535851
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211249329|gb|FL145207.1|FL145207
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCNGAATTTCTCAATACTGA
genomic: GG-TATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211251558|gb|FL145221.1|FL145221
EST:     GTATCCAACAATCCAATGGTTCCCGGAAAGGATCCTTGGAGCCCCAAAAA                         GTATGAAGGACAACGCACTGCAG
genomic: GTATCCAACAATCCAATGGTTCCCG-AAAGGATCCTTGGAGCCC-AAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAG
EST: gi|211247092|gb|FL145190.1|FL145190
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211247105|gb|FL145203.1|FL145203
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211244862|gb|FL145182.1|FL145182
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211244868|gb|FL145188.1|FL145188
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCT
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCT
EST: gi|211244856|gb|FL145176.1|FL145176
EST:     GGGTATCCAACAATCCAWTGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATTGTGATGAGCACAAGAGTTTGTGCAGCAAGTATGGAGTTTCCGGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagcgcgtgtttaaatttttccatatcctttgtttaccaagttctgtgaattctgacagaaattcctttggcaaattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG