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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttcatacagtatcccacattctatcggtgacttgatgttatgtggctgcagttcacttttacactgactgtttttccatttcttttcaatcagAGGCATCAAGGTCACCAGTACGCAATGCTTCAGGGCGTTGATGAATCAGTGGGAGCAGAGCTGGGGGAACATCATGAGGAAGCACATGACCATGAGGAGT

Basic information

species Zea mays
transcript GRMZM2G104418_T01
intron # 6
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|94475016|gb|EB703974.1|EB703974
EST:     CTTGGATGTTGATTCCAAAACCTCTTCTATTGAAGAAGCAACATCAGCAA                         AGGCATCAAGGTCACCAGTACGCAATGCTTCAGGGCGTTGATGAATCAGTG
genomic: CTTGGATGTTGATTCCAAAACCTCTTCTATTGAAGAAGCAACATCAGCAAgtacgttcat ... tttcaatcagAGGCATCAAGGTCACCAGTACGCAATGCTTCAGGGCGTTGATGAATCAGTG
EST: gi|32807350|gb|CD959584.1|CD959584
EST:     CTTGGATGTTGATTCCAAAACCTCTTCTACTGAAGAAGCAACATCAGCAA                         AGGCATCAAGGTCACCAGTACGCAATGCTTCAGGGCGTTGATGAATCAGTG
genomic: CTTGGATGTTGATTCCAAAACCTCTTCTATTGAAGAAGCAACATCAGCAAgtacgttcat ... tttcaatcagAGGCATCAAGGTCACCAGTACGCAATGCTTCAGGGCGTTGATGAATCAGTG
EST: gi|78080517|gb|DV508929.1|DV508929
EST:     CTTGGATGTTGATTCCCAAACCTCTTCTATTGAAGAAGCAACATCAGCAA                         AAGCATCAAGGTCACCAGTA
genomic: CTTGGATGTTGATTCCAAAACCTCTTCTATTGAAGAAGCAACATCAGCAAgtacgttcat ... tttcaatcagAGGCATCAAGGTCACCAGTA
EST: gi|67025519|gb|CO454268.1|CO454268
EST:     AAACCTCTTCTATCCGAAGAAGCAACATCAGCAA                         AGGCATCAAGGTCACCAGTACGCAATGCTTCAGGGCGTCCATGAATCAGTG
genomic: AAACCTCTTCTAT-TGAAGAAGCAACATCAGCAAgtacgttcat ... tttcaatcagAGGCATCAAGGTCACCAGTACGCAATGCTTCAGGGCGTTGATGAATCAGTG
EST: gi|211366578|gb|FK956887.1|FK956887
EST:     CTTGGATGTTGATTCCAAAACCTCTTCTATTGAAGAAGCAACATCAGCAA                         AGGCATCAAGGTCACCAGTACGCAATGCTTCAGGGCGTTGATGAATCAGTG
genomic: CTTGGATGTTGATTCCAAAACCTCTTCTATTGAAGAAGCAACATCAGCAAgtacgttcat ... tttcaatcagAGGCATCAAGGTCACCAGTACGCAATGCTTCAGGGCGTTGATGAATCAGTG
EST: gi|76283841|gb|DV023409.1|DV023409
EST:     CTTGGATGTTGATTCCAAAACCTCTTCTATTGAAGAAGCAACATCAGCAA                         AGGCATCAAGGTCACCAGTACGCAATGCTTCAGGGCGTTGATGAATCAGTG
genomic: CTTGGATGTTGATTCCAAAACCTCTTCTATTGAAGAAGCAACATCAGCAAgtacgttcat ... tttcaatcagAGGCATCAAGGTCACCAGTACGCAATGCTTCAGGGCGTTGATGAATCAGTG
EST: gi|211366579|gb|FK956888.1|FK956888
EST:     CTTGGATGTTGATTCCAAAACCTCTTCTATTGAAGAAGCAACATCAGCAA                         AGGCATCAAGGTCACCAGTACGCAATGCTTCAGGGCGTTGATGAATCAGTG
genomic: CTTGGATGTTGATTCCAAAACCTCTTCTATTGAAGAAGCAACATCAGCAAgtacgttcat ... tttcaatcagAGGCATCAAGGTCACCAGTACGCAATGCTTCAGGGCGTTGATGAATCAGTG
EST: gi|91050182|gb|EB160600.1|EB160600
EST:     CTTGGATGTTGATTCCAAAACCTCTTCTATTGAAGAAGCAACATCAGCAA                         AGGCATCAAGGTCACCAGTACGCAATGCTTCAGGGCGTTGATGAATCAGTG
genomic: CTTGGATGTTGATTCCAAAACCTCTTCTATTGAAGAAGCAACATCAGCAAgtacgttcat ... tttcaatcagAGGCATCAAGGTCACCAGTACGCAATGCTTCAGGGCGTTGATGAATCAGTG
EST: gi|78123326|gb|DV541710.1|DV541710
EST:     CTTGGATGTTGATTCCAAAACCTCTTCTATTGAAGAAGCAACATCAGCAA                         AGGCATCAGGGTCACCAGTACGCAGTGCTTCGGGGCGTTGATGAATCAGTG
genomic: CTTGGATGTTGATTCCAAAACCTCTTCTATTGAAGAAGCAACATCAGCAAgtacgttcat ... tttcaatcagAGGCATCAAGGTCACCAGTACGCAATGCTTCAGGGCGTTGATGAATCAGTG
EST: gi|32809734|gb|CD961968.1|CD961968
EST:     CTTGGATGTTGATTCCAAAACCTCTTCTACTGAAGAAGCAACATCAGCAA                         AGGCATCAAGGTCACCAGTACGCAATGCTTCAGGGCGTTGATGAATCAGTG
genomic: CTTGGATGTTGATTCCAAAACCTCTTCTATTGAAGAAGCAACATCAGCAAgtacgttcat ... tttcaatcagAGGCATCAAGGTCACCAGTACGCAATGCTTCAGGGCGTTGATGAATCAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtggctgcagttcacttttacactgactgtttttccatttcttttcaatcagAGGCATCAAGGTCACCAGTACGCAATGCTTCAGGGCGTTGATGAATCAGTGGGAGCAGAGCTGGGGGAACATCATGAGGAAGCACATGACCATGAGGAGT
                       cactgac  putative branch site (score: 2)
                             ctgtttttccatttct  CT-rich tract
                                       atttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttcatacagtatcccacattctatcggtgacttgatgttatgtggctgcagttcacttttacactgactgtttttccatttcttttcaatcagAGGCATCAAGGTCACCAGTACGCAATGCTTCAGGGCGTTGATGAATCAGTGGGAGCAGAGCTGGGGGAACATCATGAGGAAGCACATGACCATGAGGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG