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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgaagttgatagttacaccgttgcttgcataaagttgaatgctcgtatactacgaaaaaatatcaacctgtgttgtttggttccctttttaccataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGAGTAATAATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAG

Basic information

species Zea mays
transcript GRMZM2G044011_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044011_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g56480.1 (Oryza sativa), 3'ss of exon 9
cgaagttgatagttacaccgttgcttgcataaagttgaatgctcgtatactacgaaaaaatatcaacctgtgttgtttggttcc----------ctttttaccataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGAGTAATAATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAG
     ||  | | |     | | ||| || ||      ||||| ||||   |   |||||||||||| | ||   ||   |||           |||  || | |||||||| ||||||||||||||| ||  ||||||||||||||||||||| |||||| |||||||||||||||| || ||| ||||||| || |||||| | ||||
----atttgttgctgt--tggtactttcagaacc----atgcttgtatgacaaacaaaaatatcaacttatgcaattctcttcttgtactttctcttcatatcttaacagGATCAGTTCCGCGATTATATGCATCTTGAAGCTGCACGGCGAGACTTAAGATTAATAATTGAGAACAAACAGCGCATTGTTCTTGCACATGCACCTTCAG
















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|67018605|gb|CO447354.1|CO447354
EST:     ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAG                         GACCAGTTCCGTGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
genomic: ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
EST: gi|67024357|gb|CO453106.1|CO453106
EST:     ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAG                         GACCAGTTCCGTGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
genomic: ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
EST: gi|71763506|gb|DR961443.1|DR961443
EST:     ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAG                         GACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
genomic: ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
EST: gi|74236267|gb|DT644181.1|DT644181
EST:     CCAGGTTTTACGAAG                         GACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
genomic: CCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
EST: gi|71442136|gb|DR823186.1|DR823186
EST:     ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAG                         GACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
genomic: ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
EST: gi|50333168|gb|CO528294.1|CO528294
EST:     ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAG                         GACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
genomic: ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
EST: gi|32825337|gb|CD965059.1|CD965059
EST:     ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAG                         GACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATT
genomic: ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATT
EST: gi|71302744|gb|DR787484.1|DR787484
EST:     TTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCCAGGTTTTACGAAG                         GACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
genomic: TTTGAAGTTGTCCAGTGTACTGTAATTGCAAG-CCCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
EST: gi|76016282|gb|DT943452.1|DT943452
EST:     ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAG                         GACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA
genomic: ATTTTGAAGTTGTCCAGTGTACTGTAATTGCAAGCCCAGGTTTTACGAAGgtaatcctca ... accataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatactacgaaaaaatatcaacctgtgttgtttggttccctttttaccataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGAGTAATAATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAG
                                   ttccctttttaccat  CT-rich tract
         aaaaaatatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgaagttgatagttacaccgttgcttgcataaagttgaatgctcgtatactacgaaaaaatatcaacctgtgttgtttggttccctttttaccataacagGACCAGTTCCGCGATTATTTGTTTCTTGAAGCTGCACGGCGAGATTTAAGAGTAATAATTGAGAACAAGCAACGCCTTGTTCTGGCGCATGCAACATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA