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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgcgtcctactctaactcccagtcgccttcctcatctggctttcgattcggtccggtctgcgcccaacccgtgcgctgggcgaagcttccggaagcttcagggtttatcccggcatttcgttttcagcgacggcgcgcccggatcgcttgatctgacggagtttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCGGTGCCTCGGGTTCACGGCCAAATTCGCTGCTGCGTGGGGCTTTGGAGAT

Basic information

species Zea mays
transcript GRMZM2G492252_T01
intron # 1
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|211128948|gb|FL128226.1|FL128226
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|211128945|gb|FL128223.1|FL128223
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|149105940|gb|EE291566.2|EE291566
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|88758241|gb|DY542382.1|DY542382
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|71424496|gb|DR806334.1|DR806334
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|211129864|gb|FL128228.1|FL128228
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|211129863|gb|FL128227.1|FL128227
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|37417624|gb|CF646466.1|CF646466
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|50324565|gb|CO519691.1|CO519691
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|71774882|gb|DR972760.1|DR972760
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|91868647|gb|EB400100.1|EB400100
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|71426202|gb|DR807252.1|DR807252
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|211129866|gb|FL128230.1|FL128230
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|211128943|gb|FL128221.1|FL128221
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|211129865|gb|FL128229.1|FL128229
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|211039435|gb|FL384655.1|FL384655
EST:     ---T--CGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|211252415|gb|FL420141.1|FL420141
EST:     ---T--CGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|89760191|gb|DY688711.1|DY688711
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|211005956|gb|FL398095.1|FL398095
EST:     ---T--CGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|148971543|gb|EE022249.2|EE022249
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|93014828|gb|EB640348.1|EB640348
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|211045933|gb|FL419469.1|FL419469
EST:     ---T--CGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|211128939|gb|FL128217.1|FL128217
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|211128947|gb|FL128225.1|FL128225
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCAKTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|211128941|gb|FL128219.1|FL128219
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|211128940|gb|FL128218.1|FL128218
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
EST: gi|76936255|gb|DV174660.1|DV174660
EST:     CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAG                         GATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG
genomic: CGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCG

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: 47 (upstream exon), 48 (downstream exon)
Score: 145

TCCTGCAGGCTCCAGGCGCTGCTGCTCTCGTCCTCCGCTAGCGAGCGAATCGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCGGTGCCTCGGGTTCACGGCCAAATTCGCTGCTGCGTGGGGCTTTGGAGAT


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 25

TCCTGCAGGCTCCAGGCGCTGCTGCTCTCGTCCTCCGCTAGCGAGCGAATCGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCGGTGCCTCGGGTTCACGGCCAAATTCGCTGCTGCGTGGGGCTTTGGAGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

TCCTGCAGGCTCCAGGCGCTGCTGCTCTCGTCCTCCGCTAGCGAGCGAATCGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCGGTGCCTCGGGTTCACGGCCAAATTCGCTGCTGCGTGGGGCTTTGGAGAT


Block sizes: 48 (upstream exon), 37 (downstream exon)
Score: 56

TCCTGCAGGCTCCAGGCGCTGCTGCTCTCGTCCTCCGCTAGCGAGCGAATCGCTGACGCTGGCCCGACGCCGCGGCGGGAGGTATCTCGCTTTCGATCAGgtgcgcgtcc ... ttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCGGTGCCTCGGGTTCACGGCCAAATTCGCTGCTGCGTGGGGCTTTGGAGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgttttcagcgacggcgcgcccggatcgcttgatctgacggagtttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCGGTGCCTCGGGTTCACGGCCAAATTCGCTGCTGCGTGGGGCTTTGGAGAT
                                 atctgac  putative branch site (score: 56)
                                            tttctatct  putative PPT
                                            tttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgcgtcctactctaactcccagtcgccttcctcatctggctttcgattcggtccggtctgcgcccaacccgtgcgctgggcgaagcttccggaagcttcagggtttatcccggcatttcgttttcagcgacggcgcgcccggatcgcttgatctgacggagtttctatctagGATTTTGGTTGGGGCGTCGTTCTCCGGTGCTTATCTCATTTCTATTTATCGGTGCCTCGGGTTCACGGCCAAATTCGCTGCTGCGTGGGGCTTTGGAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT