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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctctcttttggctcaccggctgaagcccgttcaactgcaaccctcatgtgagatttctcgcatcaaagctcctttgcctaactttcgttgttgaacagATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAAGCATACTGTGCTTCCACGGAAACG

Basic information

species Zea mays
transcript GRMZM2G120578_T02
intron # 9
splice site 3'
intron type U2

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|148928250|gb|EE284812.2|EE284812
EST:     TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAG                         ATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
genomic: TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAGgtcagttttc ... tgttgaacagATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
EST: gi|37380776|gb|CF627223.1|CF627223
EST:     TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAG                         ATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
genomic: TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAGgtcagttttc ... tgttgaacagATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
EST: gi|6448423|gb|AW181189.1|AW181189
EST:     TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCANAG                         ATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
genomic: TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAGgtcagttttc ... tgttgaacagATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
EST: gi|32866078|gb|CF005760.1|CF005760
EST:     TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAG                         ATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
genomic: TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAGgtcagttttc ... tgttgaacagATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
EST: gi|211227788|gb|FL398706.1|FL398706
EST:     TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAG                         ATGCATATGGCAGC
genomic: TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAGgtcagttttc ... tgttgaacagATGCATATGGCAGC
EST: gi|113701473|gb|EE678977.1|EE678977
EST:     TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAG                         ATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
genomic: TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAGgtcagttttc ... tgttgaacagATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
EST: gi|161588702|gb|EY961924.1|EY961924
EST:     GAAGGAGCTACTAAAAGCGGGAAGGGAGATCTAGGTTTTATAATTCAGAG                         ATGCATATGGC
genomic: GAAGGAGCTACTAAA-GCGGGAAGGGAGATC-AGGTTTTATAATTCAGAGgtcagttttc ... tgttgaacagATGCATATGGC
EST: gi|78117804|gb|DV536191.1|DV536191
EST:     TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAG                         ATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
genomic: TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAGgtcagttttc ... tgttgaacagATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
EST: gi|4804277|gb|AI666143.1|AI666143
EST:     TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAG                         ATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
genomic: TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAGgtcagttttc ... tgttgaacagATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
EST: gi|78024870|gb|DV493257.1|DV493257
EST:     TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAG                         ATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
genomic: TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAGgtcagttttc ... tgttgaacagATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
EST: gi|113690734|gb|DW849290.1|DW849290
EST:     TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAG                         ATGCATATGGCAGCGTTTG
genomic: TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAGgtcagttttc ... tgttgaacagATGCATATGGCAGCGTTTG
EST: gi|12968943|gb|BG265784.1|BG265784
EST:     TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAG                         ATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
genomic: TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAGgtcagttttc ... tgttgaacagATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
EST: gi|110496613|gb|EE015080.1|EE015080
EST:     TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAG                         ATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
genomic: TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAGgtcagttttc ... tgttgaacagATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
EST: gi|211191319|gb|FL465409.1|FL465409
EST:     TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAG                         ATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
genomic: TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAGgtcagttttc ... tgttgaacagATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
EST: gi|89247054|gb|DY618840.1|DY618840
EST:     TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAG                         ATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
genomic: TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAGgtcagttttc ... tgttgaacagATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
EST: gi|37382012|gb|CF627919.1|CF627919
EST:     TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAG                         ATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
genomic: TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAGgtcagttttc ... tgttgaacagATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
EST: gi|211042510|gb|FL401130.1|FL401130
EST:     TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAG                         ATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA
genomic: TGGAAGGAGCTACTAAAGCGGGAAGGGAGATCAGGTTTTATAATTCAGAGgtcagttttc ... tgttgaacagATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgtgagatttctcgcatcaaagctcctttgcctaactttcgttgttgaacagATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAAGCATACTGTGCTTCCACGGAAACG
                                gcctaac  putative branch site (score: 2)
                                      ctttcgtt  CT-rich tract
                                   taacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctctcttttggctcaccggctgaagcccgttcaactgcaaccctcatgtgagatttctcgcatcaaagctcctttgcctaactttcgttgttgaacagATGCATATGGCAGCGTTTGTTCTTCCGACATTTGCCAAGAGGGAGCTAGAAGCATACTGTGCTTCCACGGAAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC