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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggatcttgctcaatatttttccttacaagtttaaacatcttatcggtacaatttcattttttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG

Basic information

species Zea mays
transcript GRMZM2G381051_T03
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 11
lower sequence: LOC_Os05g03480.2 (Oryza sativa), 3'ss of exon 11
--gtaggatcttgctcaatatttttccttacaagtttaaacatcttatcggtacaatttcattttttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG
   |       | ||||| | || | || ||| |||||| ||| |  |   |  |  ||  ||| ||   | || |||||||| ||||| |||||||||||||| || ||||| |||||||| ||||||
gtatgcatatcttctcaagacttatactgacaggtttaagcatatccttactgaagctttctttgttgt-ttagGTCATTTGTTTACTCGGTTGCTAGGGACTGTGACAATGGTAAAGTTGACCGCAAG
















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|148952108|gb|EC897900.2|EC897900
EST:     GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|24763821|gb|CA398992.1|CA398992
EST:     GGGAAAATGGCCGATATGTACACCTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|40333869|gb|CK367939.1|CK367939
EST:     GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGC-AAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|148928298|gb|EE284912.2|EE284912
EST:     GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|211502819|gb|FL436168.1|FL436168
EST:     CACTTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: CACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|149073601|gb|EE161904.2|EE161904
EST:     GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|37375704|gb|CF624307.1|CF624307
EST:     GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|148949902|gb|EC895400.2|EC895400
EST:     GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|31352282|gb|CD436639.1|CD436639
EST:     GGGAAAATGGCCGATATGTACACCTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCGGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|60356707|gb|DN223680.1|DN223680
EST:     GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|5871129|gb|AW017570.1|AW017570
EST:     GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|15214937|gb|BI431104.1|BI431104
EST:     GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|8576983|gb|BE129620.1|BE129620
EST:     GGGCAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGG-AAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|40333885|gb|CK367955.1|CK367955
EST:     GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|213182546|gb|FM191704.1|FM191704
EST:     GAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|78086928|gb|DV515321.1|DV515321
EST:     GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|16925518|gb|BM078586.1|BM078586
EST:     GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|86474638|gb|DY241008.1|DY241008
EST:     GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|6095776|gb|AW120443.1|AW120443
EST:     GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|86472558|gb|DY238928.1|DY238928
EST:     ATACAGGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: ATACAGGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|37394249|gb|CF634396.1|CF634396
EST:     GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|6020797|gb|AW065725.1|AW065725
EST:     GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG                         ATCATTTGNATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG
EST: gi|37375650|gb|CF624276.1|CF624276
EST:     GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG                         ATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGC-AAGTTGATCG
genomic: GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAGgtaggatctt ... tttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttccttacaagtttaaacatcttatcggtacaatttcattttttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG
     tccttac  putative branch site (score: 2)
                                     tttcattttttccatc  putative PPT
                                tacaatttcatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggatcttgctcaatatttttccttacaagtttaaacatcttatcggtacaatttcattttttccatcagATCATTTGTATACTCAGTTGCTAGGGACTGCGATAATGGCAAAGTTGATCGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG