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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattttcttttgctagaatcttctgttgatccaccatggtgtagaacgtactgctatcttaatgtgatttagctgatgtctcgattcgtcttttgtgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGGGAGTACTGGCAAAGGTCAACAATTGTCTTGGTGCTCTCTCGCAGCAAGC

Basic information

species Zea mays
transcript GRMZM2G147450_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147450_T03 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g47850.2 (Oryza sativa), 3'ss of exon 10
gtacattttcttttgctagaatcttctgttgatccaccatggtgtag-aacgta--ctgctatcttaatgtgatttagctgatgtctcgattc--gtcttttgtgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGGGAGTACTG-GCAAAGGTCAACAATTGTCTTGGTGCTCTCTCGCAGCAAGC----
|||||||| |||   | | |   | ||  |     |   || ||||  |||  |   ||   | | | ||| |  | | |||| |  | | ||  || | |||||||||||||| || ||||| ||||||||| | ||||||| |||||||||||||||        ||     ||| |||      | ||  | |  |      |    | |     
gtacatttccttgaacaatatagtacttctagagaaaagtgttgtaccaacacaacttgtgttatcactgttaagt-gttgattttactaatcctgtttcttgtgctttacagCTTTTGGTGAATTTATAGAGATGATGAAGAACAACAGATTGTGAGGCGCAAATATAAGATACAAGGGTT-----TGGTTCTTGAACCGGGAGGTGAGAGGTTCTA
















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|22552626|gb|BU102465.1|BU102465
EST:     TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAG                         CCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
genomic: TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAGgtacattttc ... tgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
EST: gi|21626214|gb|BQ621135.1|BQ621135
EST:     TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAG                         CCTTCGGTGAGTTTATAGAACTCATGAAGAGCAACAGATTGTGAGGGAGGG
genomic: TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAGgtacattttc ... tgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
EST: gi|148969715|gb|EE020587.2|EE020587
EST:     TCTCCAGTACCATCCTGAGTTTTCCCCAGGTCCGCATGATTCCGACACAG                         CCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
genomic: TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAGgtacattttc ... tgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
EST: gi|6021531|gb|AW066459.1|AW066459
EST:     TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAG                         CCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
genomic: TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAGgtacattttc ... tgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
EST: gi|211486296|gb|FL444470.1|FL444470
EST:     TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAG                         C-TTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
genomic: TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAGgtacattttc ... tgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
EST: gi|37392466|gb|CF633484.1|CF633484
EST:     TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAG                         CCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGG-AGGG
genomic: TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAGgtacattttc ... tgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
EST: gi|20802593|gb|BQ293643.1|BQ293643
EST:     TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAG                         CCTTCGGTGAGTTTATAGAGCTCATGAAGAACAACAGATTGTGAGGGAGGG
genomic: TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAGgtacattttc ... tgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
EST: gi|148934461|gb|EC878500.2|EC878500
EST:     TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAG                         CCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
genomic: TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAGgtacattttc ... tgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
EST: gi|45846984|gb|CN070927.1|CN070927
EST:     TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAG                         CCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGA-GGAGGG
genomic: TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAGgtacattttc ... tgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
EST: gi|21759933|gb|BQ635474.1|BQ635474
EST:     TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACCCAG                         CCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
genomic: TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAGgtacattttc ... tgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
EST: gi|12973319|gb|BG268421.1|BG268421
EST:     TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAG                         CCTTCGGTGAGTATATAGAGCTCATGAAGAGC
genomic: TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAGgtacattttc ... tgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGC
EST: gi|20208474|gb|BQ134563.1|BQ134563
EST:     TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAG                         CCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
genomic: TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAGgtacattttc ... tgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
EST: gi|5670854|gb|AI932117.1|AI932117
EST:     TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAG                         CCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
genomic: TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAGgtacattttc ... tgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
EST: gi|211122171|gb|FL463027.1|FL463027
EST:     TCTCCAGTACCATCCTGAGTCTTCTCCAGGTCCGCATGATTCCGACACAG                         C-TTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
genomic: TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAGgtacattttc ... tgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
EST: gi|213169758|gb|FM183377.1|FM183377
EST:     TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAG                         CCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGG-AGGG
genomic: TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAGgtacattttc ... tgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
EST: gi|149102853|gb|EE288195.2|EE288195
EST:     TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAG                         CCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
genomic: TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAGgtacattttc ... tgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
EST: gi|21759841|gb|BQ635382.1|BQ635382
EST:     TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAG                         AATACGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
genomic: TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAGgtacattttc ... tgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
EST: gi|74245055|gb|DT652969.1|DT652969
EST:     TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAG                         CCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
genomic: TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAGgtacattttc ... tgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
EST: gi|78544147|gb|DV621645.1|DV621645
EST:     TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAG                         CCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG
genomic: TCTCCAGTACCATCCTGAGTCTTCCCCAGGTCCGCATGATTCCGACACAGgtacattttc ... tgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgctatcttaatgtgatttagctgatgtctcgattcgtcttttgtgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGGGAGTACTGGCAAAGGTCAACAATTGTCTTGGTGCTCTCTCGCAGCAAGC
                                      tcttttgt  CT-rich tract
     atcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacattttcttttgctagaatcttctgttgatccaccatggtgtagaacgtactgctatcttaatgtgatttagctgatgtctcgattcgtcttttgtgctttacagCCTTCGGTGAGTTTATAGAGCTCATGAAGAGCAACAGATTGTGAGGGAGGGGAGTACTGGCAAAGGTCAACAATTGTCTTGGTGCTCTCTCGCAGCAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG