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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgattattagtacaattaaatttgtcatgtaatatagtttcatagtatatgagaatgtttctggtgcacgaagtttgtctaactaaaagtatgtatcagGATATGGCAGATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAATGAAATTCCAGATAAAAGAAATGCCACCTACAAGGAAAGATTCAGTAGCT

Basic information

species Zea mays
transcript GRMZM2G374779_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G374779_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g01150.1 (Oryza sativa), 3'ss of exon 9
ttgattattagtacaattaaatttgtcatgtaatatagtttcata---gtatatgagaatgtttctggtgcacgaagtttgtctaac-taaaagtatgtatcagGATATGGCAGATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAATGAAATTCCAGATAAAAGAAATGCCACCTACAAGGAAAGATTCAGTAGCT
    || ||      || | | ||     | |||| | ||| ||     | ||||  ||||||||   |    ||||||||  |||| |     |   | |||||||||  |||||||| | ||| ||||||| ||||||||||| |||||||||||  | |||| | ||||||||||||||||||||||||| || || ||||
---tttcttcaaggcatgataattactg-gaaatagaatttgatgtgtatttatgttaatgtttcgattaactgaagtttgcataaccttcctatgcttttcagGATATTTCAGATTATTTAAAGGGTTGTAGATTTCTTCCAAAGCTTAACAATGAGTTACCAGGTGAAAGAAATGCCACCTACAAGGAAAGGTTTAGCAGCT

upper sequence: GRMZM2G374779_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA01G41570.1 (Glycine max), 3'ss of exon 9
--ttgattattagtacaattaaatttgt-catgtaatatagtttcatagtatatgagaatgtttctggtgcacgaagtttgtctaactaaaagtatgtatcagGATATGGCAGATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAATGAAATTCCAGATAAAAGAAATGCCACCTACAAGGAAAGATTCAGTAGCT
   ||   | |  |  ||| |    | | ||||||   |||||    | |   |   ||| |        |    |  |||   |  ||||| |   | |||||  ||  | |||||| || |||  ||||| |||||||||   |||||||||||||| |||||||| |||||| | || |||||||||||||| |||||||
cactgtgcaattatgtaataatccctattcatgtatcttagttattcatttgctttcaatatgctcaaaaccttgacattg---atataaaatttgatttcagGCCATACCTGATTATTTGGAGAACTGTAGATTTCTTCCAGTGCTTAACAATGAAATACCAGATAAGAGAAATTCTACTTACAAGGAAAGATTTAGTAGCT
















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|32854010|gb|CD993691.1|CD993691
EST:     GGAACATCTTGCACCTAGTGGCTACCTCAAAATCCCAACT                         GATATGGCAGATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAAT
genomic: GGAACATCTTGCACCTAGTGGCTACCTCAAAATCCCAACTgtgagtataa ... tatgtatcagGATATGGCAGATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAAT
EST: gi|60353728|gb|DN220701.1|DN220701
EST:     GAACATCTTGCACCTAGTGGCTACCTCAAAATCCCAACT                         GATATGGCAGATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAAT
genomic: GAACATCTTGCACCTAGTGGCTACCTCAAAATCCCAACTgtgagtataa ... tatgtatcagGATATGGCAGATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAAT
EST: gi|18175059|gb|BM350447.1|BM350447
EST:     TCAAAATCCCAACT                         GATATGGCAGATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAAT
genomic: TCAAAATCCCAACTgtgagtataa ... tatgtatcagGATATGGCAGATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAAT
EST: gi|91871940|gb|EB401897.1|EB401897
EST:     AAATCCCAACT                         GATATGGCAGATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAAT
genomic: AAATCCCAACTgtgagtataa ... tatgtatcagGATATGGCAGATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAAT
EST: gi|71331117|gb|DR802384.1|DR802384
EST:     GGAACATCTTGCACCTAGTGGCTACCTCAAAATCCCAACT                         GATATGGCAGATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAAT
genomic: GGAACATCTTGCACCTAGTGGCTACCTCAAAATCCCAACTgtgagtataa ... tatgtatcagGATATGGCAGATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatatgagaatgtttctggtgcacgaagtttgtctaactaaaagtatgtatcagGATATGGCAGATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAATGAAATTCCAGATAAAAGAAATGCCACCTACAAGGAAAGATTCAGTAGCT
                                    aactaaa  putative branch site (score: 2)
                                   taactaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgattattagtacaattaaatttgtcatgtaatatagtttcatagtatatgagaatgtttctggtgcacgaagtttgtctaactaaaagtatgtatcagGATATGGCAGATTATCTGAAGAGTTGTAGGTTTCTTCCAAAACTTAACAATGAAATTCCAGATAAAAGAAATGCCACCTACAAGGAAAGATTCAGTAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA