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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCACGGCCTCCTGCCCTTCGCCCCCGCTGCCACGCCTACCCCGTCACGGTGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatctgatccccgcggggcccgtttccctgacgtcgtgctcgccgcctcgcgctggtcggatattgctcgctggcagcctcgagtctcagcggg...

Basic information

species Zea mays
transcript GRMZM5G825902_T02
intron # 1
splice site 5'
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|211172203|gb|FL341433.1|FL341433
EST:     GGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAG                         AATTTGTTGCCAATCTATCA
genomic: TGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCA
EST: gi|31351917|gb|CD436274.1|CD436274
EST:     GGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAG                         AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAAC
genomic: TGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAAC
EST: gi|26558566|gb|CA830801.1|CA830801
EST:     GGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAG                         AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAAC
genomic: TGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAAC
EST: gi|67035504|gb|CO464037.1|CO464037
EST:     GGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAG                         AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAAC
genomic: TGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAAC
EST: gi|31355619|gb|CD439976.1|CD439976
EST:     GGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAG                         AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAAC
genomic: TGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAAC
EST: gi|211033888|gb|FL356298.1|FL356298
EST:     GGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAG                         AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAAC
genomic: TGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAAC
EST: gi|8368912|gb|BE051857.1|BE051857
EST:     GGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAG                         AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAAC
genomic: TGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAAC
EST: gi|211133671|gb|FL369481.1|FL369481
EST:     GGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAG                         AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAAC
genomic: TGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAAC
EST: gi|211241644|gb|FL328623.1|FL328623
EST:     GGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAG                         AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAAC
genomic: TGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAAC
EST: gi|149100918|gb|EE187014.2|EE187014
EST:     GGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAG                         AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAAC
genomic: TGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAAC
EST: gi|87157787|gb|DY402576.1|DY402576
EST:     GGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAG                         AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAAC
genomic: TGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAAC
EST: gi|8516597|gb|BE123322.1|BE123322
EST:     GGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAG                         AATTTG-TGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAAC
genomic: TGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAAC
EST: gi|22545865|gb|BU098239.1|BU098239
EST:     GGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAG                         AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAAC
genomic: TGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAAC
EST: gi|149074678|gb|EE163096.2|EE163096
EST:     GGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAG                         AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAAC
genomic: TGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAAC
EST: gi|71447368|gb|DR828418.1|DR828418
EST:     GGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAG                         AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAAC
genomic: TGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAAC
EST: gi|6526657|gb|AW215948.1|AW215948
EST:     GGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAG                         AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAAC
genomic: TGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAAC
EST: gi|148999647|gb|EE036634.2|EE036634
EST:     GGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAG                         AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAAC
genomic: TGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAAC
EST: gi|31363719|gb|CD448076.1|CD448076
EST:     GGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAG                         AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAAC
genomic: TGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAAC
EST: gi|211502811|gb|FL321803.1|FL321803
EST:     GGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAG                         AATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGCTTCTTCAAC
genomic: TGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 222

ACCACGGCCTCCTGCCCTTCGCCCCCGCTGCCACGCCTACCCCGTCACGGTGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 336

ACCACGGCCTCCTGCCCTTCGCCCCCGCTGCCACGCCTACCCCGTCACGGTGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 656

ACCACGGCCTCCTGCCCTTCGCCCCCGCTGCCACGCCTACCCCGTCACGGTGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 292

ACCACGGCCTCCTGCCCTTCGCCCCCGCTGCCACGCCTACCCCGTCACGGTGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatc ... atcttcccagAATTTGTTGCCAATCTATCAACTCAGCTAATGTGTTGGGAGTTTCTTCAACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCACGGCCTCCTGCCCTTCGCCCCCGCTGCCACGCCTACCCCGTCACGGTGGCACCTGCGCTTCCGCGCCGCGCGCCCTCTGCCCCGCCCCGCCCGGAGgtgagcgatctgatccccgcggggcccgtttccctgacgtcgtgctcgccgcctcgcgctggtcggatattgctcgctggcagcctcgagtctcagcggg

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgccgcc