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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcccccctccctgggtttgtagtttgtactgttacttgcattcctccgtcttaattcgtaaccttgcatttttgcttctcctgcagGACTTCCTCTGAGATGTATGAGAGTAATTTGTAGTTATACAAGATTGCAATGACATGCTGGAAGATTAACATAGACATGTACGGATATAACGAAAGATTA

Basic information

species Zea mays
transcript GRMZM2G108115_T01
intron # 9
splice site 3'
intron type U2

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|211043445|gb|FL436669.1|FL436669
EST:     AGATCCCTTCAACGGTTCAAAAGAGTGTTTCCATGCCGAATCTTAAACTG                         GACTTCCTCTGAGATGTATGAGAGTAATTTGTAGTTATACAAGATTGCAAT
genomic: AGATCCCTTCAACGGTTCAAAAGAGTGTTTCCATGCCGAATCTTAAACTGgtatcccccc ... tctcctgcagGACTTCCTCTGAGATGTATGAGAGTAATTTGTAGTTATACAAGATTGCAAT
EST: gi|37391024|gb|CF632751.1|CF632751
EST:     AGATCCCTTCAACGGTTCAAAAGAGTGTTTCCATGCCGAATCTTAAACTG                         GACTTCCTCTGAGATGTATGAGAGTAATTTGTAGTTATACAAGATTGCAAT
genomic: AGATCCCTTCAACGGTTCAAAAGAGTGTTTCCATGCCGAATCTTAAACTGgtatcccccc ... tctcctgcagGACTTCCTCTGAGATGTATGAGAGTAATTTGTAGTTATACAAGATTGCAAT
EST: gi|149060175|gb|EE157145.2|EE157145
EST:     AGATCCCTTCAACGGTTCAAAAGAGTGTTTCCATGCCGAATCTTAAACTG                         GACTTCTTTTGAGATGTATGAGAGTAATTTGTAGTTATACAAGATTGCAAT
genomic: AGATCCCTTCAACGGTTCAAAAGAGTGTTTCCATGCCGAATCTTAAACTGgtatcccccc ... tctcctgcagGACTTCCTCTGAGATGTATGAGAGTAATTTGTAGTTATACAAGATTGCAAT
EST: gi|31350402|gb|CD434759.1|CD434759
EST:     ACATCCCTTCAACGGTTCAAAAGAGTGTTTCCATGCCGAATCTTAAACTG                         GACTTCCTCTGAGATGTATGAGAGTAATTTGTAGTTATACAAGATTGCAAT
genomic: AGATCCCTTCAACGGTTCAAAAGAGTGTTTCCATGCCGAATCTTAAACTGgtatcccccc ... tctcctgcagGACTTCCTCTGAGATGTATGAGAGTAATTTGTAGTTATACAAGATTGCAAT
EST: gi|31363348|gb|CD447705.1|CD447705
EST:     AGATCCCTTCAACGGTTCAAAAGAGTGTTTCCATGCCGAATCTTAAACTG                         GACTTCCTCTGAGATGTATGAGAGTAATTTGTAGTTATACAAGATTGCAAT
genomic: AGATCCCTTCAACGGTTCAAAAGAGTGTTTCCATGCCGAATCTTAAACTGgtatcccccc ... tctcctgcagGACTTCCTCTGAGATGTATGAGAGTAATTTGTAGTTATACAAGATTGCAAT
EST: gi|24934189|gb|CA452407.1|CA452407
EST:     AGATCCCTTCAACGGTTCANAAGAGTGTTTCCATGCCGAATCTTANACTG                         GACTTCCTCTGAGATGTATGAGAGTAATTTGTAGTTATACAAGATTTGCA-
genomic: AGATCCCTTCAACGGTTCAAAAGAGTGTTTCCATGCCGAATCTTAAACTGgtatcccccc ... tctcctgcagGACTTCCTCTGAGATGTATGAGAGTAATTTGTAGTTATACAAGATT-GCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacttgcattcctccgtcttaattcgtaaccttgcatttttgcttctcctgcagGACTTCCTCTGAGATGTATGAGAGTAATTTGTAGTTATACAAGATTGCAATGACATGCTGGAAGATTAACATAGACATGTACGGATATAACGAAAGATTA
                        tcgtaac  putative branch site (score: 2)
                              ccttgcatttttgctt  CT-rich tract
                 tcttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcccccctccctgggtttgtagtttgtactgttacttgcattcctccgtcttaattcgtaaccttgcatttttgcttctcctgcagGACTTCCTCTGAGATGTATGAGAGTAATTTGTAGTTATACAAGATTGCAATGACATGCTGGAAGATTAACATAGACATGTACGGATATAACGAAAGATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA