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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atattatggctactcatacttttttgtgcgatatgagctgaaagtcatggaaattaaaatacattgttacaagatctgatgaaaatgcaacattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATGGGCTGACACAATGAGTGATGTGAACAAGAAGCACCAGAAAGAATTTGAA

Basic information

species Zea mays
transcript GRMZM2G085670_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085670_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 6
atattatggctactcatacttttttgtg-cgatatgagctgaaagtcatggaaattaa----aatacattgttacaagatctgatgaaaatgcaacattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATGGGCTGACACAATGAGTGATGTGAACAAGAAGCACCAGAAAGAATTTGAA
 | |||   |    |||  | | |||   |  |||||| || | || |  |  |  ||    | |  |||| ||| |  ||  |||   ||| || ||||  |||| |||||||||| ||||   | |||||||| |||||||||||||| || |||||||| ||||||||||| ||||||||||||||||||||||| || |||
-ttttact-cggtccattttatgttgaaacattatgaggtgcatgttaacgggaccaatggaagtttattggtaccaactc--atgctgatgtaa-attgcacagGCTGGGAACATCGGATAATTTATTGCATCAGATTCAGGAGAAAATTAAGTGGGCTGATACAATGAGTGAAGTGAACAAGAAGCACCAGAAAGAGTTCGAA
















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|101398140|gb|EB820944.1|EB820944
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|93013201|gb|EB638721.1|EB638721
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|50325881|gb|CO521007.1|CO521007
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|101390708|gb|EB817288.1|EB817288
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|32927905|gb|CF032717.1|CF032717
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCC
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCC
EST: gi|86473889|gb|DY240259.1|DY240259
EST:     ACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: ACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|71330909|gb|DR802251.1|DR802251
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|71306428|gb|DR789361.1|DR789361
EST:     GATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|33092814|gb|CF052808.1|CF052808
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACCATCAGATATTCTGTTGCATCAAATTCAGGAGAAAATCAAAT
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAA-CATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAAT
EST: gi|74236689|gb|DT644603.1|DT644603
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|76936648|gb|DV174824.1|DV174824
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|211512612|gb|FL228205.1|FL228205
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|89247571|gb|DY619357.1|DY619357
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|32928013|gb|CF032825.1|CF032825
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGA-CATCAGATA
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATA
EST: gi|71423346|gb|DR806010.1|DR806010
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
EST: gi|60359667|gb|DN226640.1|DN226640
EST:     GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG                         GTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG
genomic: GATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTGgtttgtatgc ... cattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catggaaattaaaatacattgttacaagatctgatgaaaatgcaacattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATGGGCTGACACAATGAGTGATGTGAACAAGAAGCACCAGAAAGAATTTGAA
                            atctgat  putative branch site (score: 4)
     aaattaaaatacattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atattatggctactcatacttttttgtgcgatatgagctgaaagtcatggaaattaaaatacattgttacaagatctgatgaaaatgcaacattgttcagGTTGGGAACATCAGATAGCCTGTTGCATCAAATTCAGGAGAAAATCAAATGGGCTGACACAATGAGTGATGTGAACAAGAAGCACCAGAAAGAATTTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA