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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagttataatcatgtttgccatttttgtttacctactttttttttgccctcaattgattatctgataattggtgaaatgatgttttctttccttgtatagGGCTTAAGGGGCAGTCAAACCGAAGGTTAATTTCTTTGGAAGAGGTTAAGCAGCACAAAGCAGGAGATTGTATTTGGACAGTTCTCAAAGGCCGCGTGTA

Basic information

species Zea mays
transcript GRMZM2G152438_T05
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152438_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g12830.1 (Oryza sativa), 3'ss of exon 3
tagttataatcatgtttgccatttttgtttacctactttttttttgccctcaattgattatctgataattggtgaaatgatgttttcttt---ccttgtatagGGCTTAAGGGGCAGTCAAACCGAAGGTTAATTTCTTTGGAAGAGGTTAAGCAGCACAAAGCAGGAGATTGTATTTGGACAGTTCTCAAAGGCCGCGTGTA
|  || || || | |||   |  | ||| |  ||  |  |   |||   |    || | |  | |||   | |    |    |||  | |     || ||||||||| |||||||||| |||||||||||| |||||| | ||||| ||||| ||||| ||| |||||||| |||||||||| ||| | ||||| || |||||
ttattttactccttttt--taactgtgtgttacttgtaatgaattgatgtttgctggtgaaataata-ccgatttcctttcatttggtgtggcatttttatagGGCTCAAGGGGCAGTTAAACCGAAGGTTGATTTCTCTAGAAGAAGTTAAACAGCATAAAACAGGAGATAGTATTTGGACTGTTTTGAAAGGTCGTGTGTA
















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|149078224|gb|EE166978.2|EE166978
EST:     TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTG                         GGCTTAAGGGGCAGTCAAACCGAAGGTTAATTTCTTTGGAAGAGGTTAAGC
genomic: TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTGgtaagttgtt ... ccttgtatagGGCTTAAGGGGCAGTCAAACCGAAGGTTAATTTCTTTGGAAGAGGTTAAGC
EST: gi|78081711|gb|DV510123.1|DV510123
EST:     TAGTCCAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTG                         GGCTTAAGGGGCAGTCCAACCCGA-GGTTAATTTTCTTTGGAAGAGGTTA
genomic: TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTGgtaagttgtt ... ccttgtatagGGCTTAAGGGGCAGTCAAACC-GAAGGTTAATTT-CTTTGGAAGAGGTTA
EST: gi|89761685|gb|DY689600.1|DY689600
EST:     TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTG                         GGCTTAAGGGGCAG
genomic: TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTGgtaagttgtt ... ccttgtatagGGCTTAAGGGGCAG
EST: gi|71333030|gb|DR803544.1|DR803544
EST:     TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTG                         GGCTTAAGGGGCAGTCAAACCGAAGGTTAATTTCTTTG
genomic: TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTGgtaagttgtt ... ccttgtatagGGCTTAAGGGGCAGTCAAACCGAAGGTTAATTTCTTTG
EST: gi|71772486|gb|DR970418.1|DR970418
EST:     TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTG                         GGCTTAAGGGGCAGTCAAACCGAAGGTTAATTTCTTTGGAAGAGGTTAAGC
genomic: TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTGgtaagttgtt ... ccttgtatagGGCTTAAGGGGCAGTCAAACCGAAGGTTAATTTCTTTGGAAGAGGTTAAGC
EST: gi|71439167|gb|DR820217.1|DR820217
EST:     TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTG                         GGCTTAAGGGGCAGTCAAACCGAAAGGT-AATTTCTTTGGAAGAGG
genomic: TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTGgtaagttgtt ... ccttgtatagGGCTTAAGGGGCAGTCAAACCGAA-GGTTAATTTCTTTGGAAGAGG
EST: gi|93015732|gb|EB641252.1|EB641252
EST:     TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTG                         GGCTTAAGGGGCAGTCAAACCGAAGGTTAATTTCTTTGGAAGAGGTTAAGC
genomic: TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTGgtaagttgtt ... ccttgtatagGGCTTAAGGGGCAGTCAAACCGAAGGTTAATTTCTTTGGAAGAGGTTAAGC
EST: gi|71431621|gb|DR812671.1|DR812671
EST:     TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTG                         GGCTTAAGGGGCAGTCAAACCGAAAGGT-AATTTCTTTGGA
genomic: TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTGgtaagttgtt ... ccttgtatagGGCTTAAGGGGCAGTCAAACCGAA-GGTTAATTTCTTTGGA
EST: gi|149088304|gb|EE177398.2|EE177398
EST:     TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTG                         GGCTTAAGGGGCAGTC
genomic: TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTGgtaagttgtt ... ccttgtatagGGCTTAAGGGGCAGTC
EST: gi|71433873|gb|DR814923.1|DR814923
EST:     TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTG                         GGCTTAAGGGGCAGTCA
genomic: TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTGgtaagttgtt ... ccttgtatagGGCTTAAGGGGCAGTCA
EST: gi|71422888|gb|DR805891.1|DR805891
EST:     TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTG                         GGCTTAAGGGGCAGTCAAACCGAAGGTTAATTTCTTTGGGAGAGGTTAAGC
genomic: TAGTCAAATGGATTGGCTAAAACTGACACAAACACATCCTGATCTAGCTGgtaagttgtt ... ccttgtatagGGCTTAAGGGGCAGTCAAACCGAAGGTTAATTTCTTTGGAAGAGGTTAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccctcaattgattatctgataattggtgaaatgatgttttctttccttgtatagGGCTTAAGGGGCAGTCAAACCGAAGGTTAATTTCTTTGGAAGAGGTTAAGCAGCACAAAGCAGGAGATTGTATTTGGACAGTTCTCAAAGGCCGCGTGTA
              atctgat  putative branch site (score: 4)
                                   tgttttctttccttgt  putative PPT
           attatctgataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagttataatcatgtttgccatttttgtttacctactttttttttgccctcaattgattatctgataattggtgaaatgatgttttctttccttgtatagGGCTTAAGGGGCAGTCAAACCGAAGGTTAATTTCTTTGGAAGAGGTTAAGCAGCACAAAGCAGGAGATTGTATTTGGACAGTTCTCAAAGGCCGCGTGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT