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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatgtgcagttccatttgtaatctgtgcggttctgtgatatacactgtaattatcaagctagtgaatgtattgactgaagttaatattcattgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG

Basic information

species Zea mays
transcript GRMZM2G130230_T03
intron # 2
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 2
lower sequence: LOC_Os04g40874.1 (Oryza sativa), 3'ss of exon 2
atatgtgcagttcc---atttgtaatctgtgcggttctgtgatatacactgtaattatcaagctagtgaatgtattgactgaagttaatattcat-tgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG
 || |  |   ||    | |  || ||| | |     ||  | ||    || | |  |  |  |      | ||| |  |||  || || | | | ||||||||||||| |||||||| || ||||| ||||||||||| ||||| |||||||| |||||||||||||||||||| ||||||||||||||
-tacgaaccactcataaaatcttagtctttacaagcatgcaaaatgtg-tgcagtgctataattcccaggt-tatcg-ttgatattcatgtccttgtgttacagGGATTTATACAATCAGGTGAAGTGCATATATTTGGGTATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG
















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|93283386|gb|EB675650.1|EB675650
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|71449499|gb|DR830549.1|DR830549
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|78083439|gb|DV511832.1|DV511832
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|71436592|gb|DR817642.1|DR817642
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|89757409|gb|DY687024.1|DY687024
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|71447340|gb|DR828390.1|DR828390
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|50339442|gb|CO534568.1|CO534568
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGTATAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|74237092|gb|DT645006.1|DT645006
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|71449885|gb|DR830935.1|DR830935
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|89759526|gb|DY688327.1|DY688327
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
EST: gi|78109778|gb|DV528194.1|DV528194
EST:     ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAG                         GGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT
genomic: ACCTTGCTAAGAAGAAAACATTCCCAGCCCTCTACCACCTCTTTGAGCAGgtatgaacta ... attgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtaattatcaagctagtgaatgtattgactgaagttaatattcattgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG
                                    ttaatattcattgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatgtgcagttccatttgtaatctgtgcggttctgtgatatacactgtaattatcaagctagtgaatgtattgactgaagttaatattcattgttacagGGATTCATACAATCTGGAGAAGTCCATATATTTGGTTATGCTAGATCAAATCTTTCTGATGATGGGTTAAGAGAACGCATTCGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA