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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatcttgaaggcactactatctgtttctgtgattgttaattttagtaggatatagtctgaccacattgtattgttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG

Basic information

species Zea mays
transcript GRMZM2G050961_T02
intron # 3
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|13558469|gb|BG549825.1|BG549825
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|13558000|gb|BG549356.1|BG549356
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGGAGTTGAGGCTGGGAAGAAGGTT
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGTT
EST: gi|148943634|gb|EC888698.2|EC888698
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|211482968|gb|FK973427.1|FK973427
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGNTGGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGG-AAGAAG
EST: gi|15198996|gb|BI423600.1|BI423600
EST:     TGTTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|148943633|gb|EC888697.2|EC888697
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|211485846|gb|FK973438.1|FK973438
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGA
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGA
EST: gi|166409968|gb|EG192262.1|EG192262
EST:     CTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGTT
genomic: CTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGTT
EST: gi|29577011|gb|CB617123.1|CB617123
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|19058136|gb|BM736803.1|BM736803
EST:     TGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|211061029|gb|FL204116.1|FL204116
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGCGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|6342692|gb|AW165516.1|AW165516
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|29167933|gb|CB411193.1|CB411193
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|15499585|gb|BI596098.1|BI596098
EST:     TGTTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAA
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|19058714|gb|BM737381.1|BM737381
EST:     TGTTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|13382241|gb|BG458916.1|BG458916
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|166483222|gb|EG111081.1|EG111081
EST:     CCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATAGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGT
genomic: CCAAAATCTGCTGTTAAGTTTGAGAGATATCTGAT-GGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGGT
EST: gi|29947167|gb|CB816515.1|CB816515
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|211058063|gb|FL204109.1|FL204109
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|32849976|gb|CD989657.1|CD989657
EST:     TGTTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|13558470|gb|BG549826.1|BG549826
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|6431818|gb|AW172022.1|AW172022
EST:     AAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGNGAAGTTGAGGCTGGGAAGAAG
genomic: AAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|13237244|gb|BG355258.1|BG355258
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|29544990|gb|CB605168.1|CB605168
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
EST: gi|26559456|gb|CA831691.1|CA831691
EST:     TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAG                         ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
genomic: TATTGCTACCAAAATCTGCTGTTAAGTTTGAGAGATATCTGATGGGTGAGgtgagatctt ... ttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgattgttaattttagtaggatatagtctgaccacattgtattgttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG
                          gtctgac  putative branch site (score: 3)
     tgttaattttagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatcttgaaggcactactatctgtttctgtgattgttaattttagtaggatatagtctgaccacattgtattgttcatgctagATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG