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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAACCGCAGGACTGTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaatagaggcgggcatattgtgttgtgaaagcccaggatctgtcatcttgtaatcttatgagctactactctatgtag

Basic information

species Zea mays
transcript GRMZM5G820996_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G820996_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g33920.1 (Oryza sativa), 5'ss of exon 3
TGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAACCGCAGGACTGTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaatagaggcgggcatattgtgttgtgaaagc--ccaggatctgtcatcttgtaatcttatgagctactact----ctatgtag
|||| ||||| ||||||||||||||||||||||||||||||||||||||||| |||||||| ||||||||||| |||||||||| ||| |||||||| |||| |||| |||  |   |  ||||| || ||||||| |   || |||||||    ||||  |||||| |||| | |||    || || ||
TGAGGCCTGCTGAGTACAAGAGGTCCAGGTTGTCTAGGAACCGCAGGACTGTGAACCGTCCATATGGTGGAGTGCTCTCTGGAACTGCAGTTAGGGAAAGgtcagtacataatgctag--atattctgatgtgaaaactttcaagatctgta---ttgtggtcttattagctgcaactgtaactctgcag

upper sequence: GRMZM5G820996_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA18G49340.1 (Glycine max), 5'ss of exon 3
TGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAACCGCAGGACTGTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat-agaggcgggcatattgtgttgtgaaagcccaggatctgtcatcttgtaatcttatgagctac-tactcta--tgtag
| |||||||| || ||||||||||| || ||| |||||||||||||||| || |||||  | ||||| || ||  | || ||    |||||||| || ||||  ||   | | |       | ||| | || || ||        |||    |   ||||  |||  |||||  || |||   | |||
TAAGACCTGCTGAATACAAGAGGTCTAGATTGCCTAGGAACCGCAGGACCGTAAACCGAGCCTATGGAGGTGTTTTATCCGGGGGAGCTGTTAGAGAAAGgtatgttgctcaaaaatcactagattat-ttatgcaaattt----tcttagttgaagtaaatttaacagctatgtaatcttgctatag

upper sequence: GRMZM5G820996_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA01G05740.1 (Glycine max), 5'ss of exon 3
TGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAACCGCAGGACTGTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagta--aatagaggcg-ggcatat-tgtgttgtgaaagcccaggatctgtcatcttgtaatcttatgagctactactctatgtag
|||| ||||| |||||||||||||| |||||  | || ||||| |||||||| |||||| | |||||||||||  | ||||||| ||| || ||||||||||  ||   | ||||       ||  | | | || | | | | |      | | ||  | |  |   ||      ||  |   | |||
TGAGGCCTGCAGAGTACAAGAGGTCAAGGTTACCCAGAAACCGTAGGACTGTCAACCGTGCATATGGTGGAGTTTTATCTGGAAGTGCCGTCAGGGAGAGgtttgttttactagacttttaacagctatatattataataactcgtatgatttaattgtttgcttacatttatctctggttc-tatag

upper sequence: GRMZM5G820996_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA02G11920.1 (Glycine max), 5'ss of exon 3
TGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAACCGCAGGACTGTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaa------atagaggcgggcatattgtgttgtgaaagcccaggatctg-tcatcttgtaat-----cttatgagctactactctatgtag------------
|||| ||||| ||||||||||| || |||||  | || ||||| |||||||| |||||| | ||||| |||||  | ||||||| |||||| ||||||||||  ||        |      | |  ||||  |  |   ||  | || ||| |  | || | ||||       ||||    | ||  | | |||              
TGAGGCCTGCAGAGTACAAGAGATCAAGGTTACCCAGAAACCGTAGGACTGTCAACCGTGCATATGGCGGAGTTTTGTCTGGAAGTGCTGTCAGGGAGAGgtttgttttactctacttttacagttatatatttataataactcgcatgatttaattatatggtaaagttggtttatagcatgcttttatttgtgtctggttctatag

upper sequence: GRMZM5G820996_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G37360.1 (Glycine max), 5'ss of exon 3
TGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAACCGCAGGACTGTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat--agaggcgggcatattgtgttgtgaaagcccaggatctgtcatcttgtaatcttatgagctactactctatgtag--
|||||||||| || ||||||||||| || ||| || ||||||||||||| || |||||  | || || || ||  | || |||   |||||||| || ||||  ||   |  | | |     | ||  | ||||  ||        |||    |   ||||  |||    |   || ||   |||   
TGAGACCTGCTGAATACAAGAGGTCTAGATTGCCTCGGAACCGCAGGACCGTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTGTTAGAGAAAGgtatgttgctcaaaaagtctttagatgtttttgttgaaaatt---ttcttagttgaagtaaatttacagccatttattcatggtatag

upper sequence: GRMZM5G820996_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT3G28900.1 (Arabidopsis thaliana), 5'ss of exon 3
TGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAACCGCAGGACTGTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaatagaggcgggcatattgtgttgtgaaagcccaggatctgtcatcttgtaatcttatgagctactactctatgtag
|||||||||| |||||||| ||||| |||||| | ||||||   ||||| || || ||| | |||||||| || || |||||| |||||||||||||||||| |||  || |    |  |   |     |  |       ||  | |  || ||  |  |  | |   || ||  || |     
TGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAACGAGAGGACAGTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTGTTAGGGAGAGgtaagtgtattgtaaagacctcttaaaaattggtttctttagagtattgcaactaatcttactcttttct-ctgttccag----

upper sequence: GRMZM5G820996_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv01s0026g02410.t01 (Vitis vinifera), 5'ss of exon 3
TGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAACCGCAGGACTGTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaatagaggcgggcatattgtgttgtgaaagcccaggatctgtcatcttgtaa-tcttatgagctactactctatgtag----------------------------
| |||||||| || ||||||||||| || ||  |||||||||| |||||||| |||||| ||||||| || ||  | ||||||  |||||| ||||| ||||  || |  | ||       |  |||   |||      ||     | |||| | | || | ||| || | |||   ||    |                             
TAAGACCTGCAGAATACAAGAGGTCTAGATTACCTAGGAACCGTAGGACTGTGAACCGTGCTTATGGGGGTGTGTTGTCTGGAGGTGCTGTGAGGGAAAGgtatgttagcaaagt------ttctgttcagtgctcattcatatcatttcatatggaaagttttaagatcaactttgctggacatgtctttattttttcaattggttttgtag

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|211533043|gb|FL043886.1|FL043886
EST:     GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATT
genomic: GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctctatgtagAATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATT
EST: gi|30088131|gb|CB886336.1|CB886336
EST:     GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctctatgtagAATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|211352603|gb|FL470915.1|FL470915
EST:     GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctctatgtagAATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|211533048|gb|FL043891.1|FL043891
EST:     GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctctatgtagAATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|31405585|gb|CD484317.1|CD484317
EST:     GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctctatgtagAATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|60348609|gb|DN215582.1|DN215582
EST:     GTTAACCGTCCTTATGGTGGAGTACTTTTTGGAATTGCTGTTAGGGAGAG                         AATTATCCGTGCTTTTTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctctatgtagAATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|31405586|gb|CD484318.1|CD484318
EST:     GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctctatgtagAATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|4624308|gb|AI615141.1|AI615141
EST:     GTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctctatgtagAATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|211533047|gb|FL043890.1|FL043890
EST:     GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctctatgtagAATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|30306493|gb|CD001166.1|CD001166
EST:     GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctctatgtagAATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|60357248|gb|DN224221.1|DN224221
EST:     GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctctatgtagAATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|26557730|gb|CA829965.1|CA829965
EST:     GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATTATCCGTGCTTTCTTG
genomic: GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctctatgtagAATTATCCGTGCTTTCTTG
EST: gi|60395053|gb|DN227922.1|DN227922
EST:     GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctctatgtagAATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|16927550|gb|BM080619.1|BM080619
EST:     GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctctatgtagAATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|211533046|gb|FL043889.1|FL043889
EST:     GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctctatgtagAATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|60345851|gb|DN212824.1|DN212824
EST:     GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctctatgtagAATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|60354426|gb|DN221399.1|DN221399
EST:     GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctctatgtagAATTATCCGTGCTTTCTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|30087140|gb|CB885348.1|CB885348
EST:     GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATTATCCGTGCTTTCTTTGGTTGAGGAGCAGAAGATTGTCAAGAAGGTCC
genomic: GTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctctatgtagAATTATCCGTGCTTTCTT-GGTTGAGGAGCAGAAGATTGTCAAGAAGGTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAACCGCAGGACTGTTAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaatagaggcgggcatattgtgttgtgaaagcccaggatctgtcatcttgtaatcttatgagctactactctatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT