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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggacatttcattaacaatacgaacatgtttgtgataaatttgggtcactgcaaattcattagtatcttcctcacttggattggtgtgttattgtagcagGTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATCAAGGCGAAACAGCTTTAATTCTTTGTCTAAGGACCTAGACCTTCCTTCA

Basic information

species Zea mays
transcript GRMZM2G130230_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130230_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g40874.1 (Oryza sativa), 3'ss of exon 1
---------tggacatttcatt------aacaatacgaacatgtttgtgataaatttgggtcactgcaaattcattagtatcttcctcacttggattggtgtgttattgtagcagGTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATCAAGGCGAAACAGCTTTAATTCTTTGTCTAAGGACCTAGACCTTCCTTCA
         |  |  || ||||      |    || |||  |  ||    |   ||  | |      ||  |   | | || || ||||| |        || | ||||  | ||| ||||||| | |   | |||| |||||||||||||||||||||||   ||||| |||| ||||||||||||||| || |  || |              
agccaattgtaaatgttccatttcaatgagttgtatgaaatttcttagcctgtgttccgatagtcttaagattgattgcatttttctcaccttttcacagGTAT-ATTGCTGAAGGAAGAAGAGCACCAACCTATTTATCATGTCAGGAGGATCTTCACCAAGGTCAAGACGAAGCAGCTTTAATTCTTTATCAAGAGATC--------------
















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|211003557|gb|FK956136.1|FK956136
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGCAG                       
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCT---Ggtcagtgctc ... attgtagc
EST: gi|74237092|gb|DT645006.1|DT645006
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTG                         GTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGgtcagtgctc ... attgtagcagGTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
EST: gi|71449499|gb|DR830549.1|DR830549
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGCAG                       
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCT---Ggtcagtgctc ... attgtagc
EST: gi|211398371|gb|FK956119.1|FK956119
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAWATCTCGTCGCTGCAG                       
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCT---Ggtcagtgctc ... attgtagc
EST: gi|50339442|gb|CO534568.1|CO534568
EST:     CACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGCAG                       
genomic: CACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCT---Ggtcagtgctc ... attgtagc
EST: gi|71447340|gb|DR828390.1|DR828390
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTG                         GTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGgtcagtgctc ... attgtagcagGTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
EST: gi|89759526|gb|DY688327.1|DY688327
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTG                         GTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGgtcagtgctc ... attgtagcagGTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
EST: gi|211003554|gb|FK956133.1|FK956133
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAWATCTCGTCGCTG                         GTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGgtcagtgctc ... attgtagcagGTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
EST: gi|78083439|gb|DV511832.1|DV511832
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTG                         GTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGgtcagtgctc ... attgtagcagGTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
EST: gi|211398372|gb|FK956120.1|FK956120
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAWATCTCGTCGCTG                         GTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGgtcagtgctc ... attgtagcagGTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
EST: gi|211398375|gb|FK956123.1|FK956123
EST:     CTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCCAGAAATCTCGTCGCTGCAG                       
genomic: CTTCCCTCCCACACGCTCGGCGCTCTGTCCG-CCAGAAATCTCGTCGCT---Ggtcagtgctc ... attgtagc
EST: gi|211398373|gb|FK956121.1|FK956121
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGCAG                       
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCT---Ggtcagtgctc ... attgtagc
EST: gi|211003558|gb|FK956137.1|FK956137
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTG                         GTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGgtcagtgctc ... attgtagcagGTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
EST: gi|211003549|gb|FK956128.1|FK956128
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTG                         GTAGAAGAGAATCGTGGCCAATTTGGTCATGTCAGGAGGATCTTCACCATC
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGgtcagtgctc ... attgtagcagGTAGAAGAGAATCGT-GCC-ATTT-GTCATGTCAGGAGGATCTTCACCATC
EST: gi|211398378|gb|FK956126.1|FK956126
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGCAG                       
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCT---Ggtcagtgctc ... attgtagc
EST: gi|211003552|gb|FK956131.1|FK956131
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGCAG                       
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCT---Ggtcagtgctc ... attgtagc
EST: gi|211003559|gb|FK956138.1|FK956138
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTG                         GTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGgtcagtgctc ... attgtagcagGTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
EST: gi|71436592|gb|DR817642.1|DR817642
EST:     CCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTG                         GTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
genomic: CCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGgtcagtgctc ... attgtagcagGTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
EST: gi|211003548|gb|FK956127.1|FK956127
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGCAG                       
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCT---Ggtcagtgctc ... attgtagc
EST: gi|211003556|gb|FK956135.1|FK956135
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTG                         GTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGgtcagtgctc ... attgtagcagGTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
EST: gi|211003560|gb|FK956139.1|FK956139
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGCAG                       
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCT---Ggtcagtgctc ... attgtagc
EST: gi|211398377|gb|FK956125.1|FK956125
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTTCGCCAGAAATCTCGTCGCTG                         GTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGgtcagtgctc ... attgtagcagGTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
EST: gi|211398376|gb|FK956124.1|FK956124
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTG                         GTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGgtcagtgctc ... attgtagcagGTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
EST: gi|211003553|gb|FK956132.1|FK956132
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGCAG                       
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCT---Ggtcagtgctc ... attgtagc
EST: gi|93283386|gb|EB675650.1|EB675650
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGCAG                       
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCT---Ggtcagtgctc ... attgtagc
EST: gi|78109778|gb|DV528194.1|DV528194
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTG                         GTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGgtcagtgctc ... attgtagcagGTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
EST: gi|71449885|gb|DR830935.1|DR830935
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTG                         GTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGgtcagtgctc ... attgtagcagGTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
EST: gi|211398374|gb|FK956122.1|FK956122
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTG                         GTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGgtcagtgctc ... attgtagcagGTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATC
EST: gi|211003555|gb|FK956134.1|FK956134
EST:     TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCTGCAG                       
genomic: TCTTCCCTCCCACACGCTCGGCGCTCTGTCCGCCAGAAATCTCGTCGCT---Ggtcagtgctc ... attgtagc


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcactgcaaattcattagtatcttcctcacttggattggtgtgttattgtagcagGTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATCAAGGCGAAACAGCTTTAATTCTTTGTCTAAGGACCTAGACCTTCCTTCA
                       tcctcac  putative branch site (score: 2)
       aaattcattagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggacatttcattaacaatacgaacatgtttgtgataaatttgggtcactgcaaattcattagtatcttcctcacttggattggtgtgttattgtagcagGTAGAAGAGAATCGTGCCATTTGTCATGTCAGGAGGATCTTCACCATCATCAAGGCGAAACAGCTTTAATTCTTTGTCTAAGGACCTAGACCTTCCTTCA

- - - tttcatt
- - - - - - -aacaata
- - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - cactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtg