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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacccttttaagtttatgatataccattgctgttcctctgaagttctgtttttgcattacctgcacgtagttctgctgtcgaaggaaaataagtgactagttagaagtatattatgataaactctctccaacttcatctcatatatatctttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCACTTCAG

Basic information

species Zea mays
transcript GRMZM2G381051_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G381051_T03 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os05g03480.4 (Oryza sativa), 3'ss of exon 12
gtacccttttaagtttatgatataccattgctgttcctctgaagttctgtttttgcattacctgcacgtagttctgctgtcgaaggaaaataagtgactagttagaagtatattatgataaactctctccaacttcatc-------tcatatatatctttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCACTTCAG
                                                             ||   |  |      |||||      |  | |   | || |||       ||  || |||||| ||| || |||||||       | |||| | | ||  | ||||||||||||| || || |||||||||||||||||||  |||||||| ||||||||||||
------------------------------------------------------------tctattcacaacaaaactgtcttc---atctcatctaataattat-----catggtggtaaactgtcttcatcttcatctatataataatattttttttattattcagGATTGTGCTGGTGTGATTCTCTTTGCTGCTGAAAGGGCAACCCAGGTTGCACTTCAG
















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|211244133|gb|FL451950.1|FL451950
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|148952108|gb|EC897900.2|EC897900
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|24763821|gb|CA398992.1|CA398992
EST:     TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|40333869|gb|CK367939.1|CK367939
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGC-AAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|148928298|gb|EE284912.2|EE284912
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTTTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|211502819|gb|FL436168.1|FL436168
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|149073601|gb|EE161904.2|EE161904
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|14529291|gb|BI096424.1|BI096424
EST:     CAAAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: CAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|37375704|gb|CF624307.1|CF624307
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         TATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|148949902|gb|EC895400.2|EC895400
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|31352282|gb|CD436639.1|CD436639
EST:     TTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|60356707|gb|DN223680.1|DN223680
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|5871129|gb|AW017570.1|AW017570
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|15214937|gb|BI431104.1|BI431104
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|8576983|gb|BE129620.1|BE129620
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|40333885|gb|CK367955.1|CK367955
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         TATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|213182546|gb|FM191704.1|FM191704
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|78086928|gb|DV515321.1|DV515321
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|16925518|gb|BM078586.1|BM078586
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|86474638|gb|DY241008.1|DY241008
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|6095776|gb|AW120443.1|AW120443
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|86472558|gb|DY238928.1|DY238928
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|37394249|gb|CF634396.1|CF634396
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|6020797|gb|AW065725.1|AW065725
EST:     TTGNATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG                         GATTGTGCAGGAGCAATTCTCTTTGTTGTTGAAAATGCAACCCAAGNTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
EST: gi|37375650|gb|CF624276.1|CF624276
EST:     TTGTATACTCAGTTGCTAGGGACTGCGATAATGGC-AAGTTGATCGCAAG                         GATTGTGCAGGAGTAATTTTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA
genomic: TTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAGgtaccctttt ... ttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtatattatgataaactctctccaacttcatctcatatatatctttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCACTTCAG
                                        tatcttt  CT-rich tract
                                 tcatatatatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacccttttaagtttatgatataccattgctgttcctctgaagttctgtttttgcattacctgcacgtagttctgctgtcgaaggaaaataagtgactagttagaagtatattatgataaactctctccaacttcatctcatatatatctttgtgttcagGATTGTGCAGGAGTAATTCTCTTTGCTGCTGAAAATGCAACCCAAGTTGCACTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT