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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgatcttacatttgtgaattattatggggatggacacattgcatcttgttggtttgtacagacactgaattttttacctttcttttctctttttacagAGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTCCTTGGGAATGGCTTAATTGCCATTGTGTCTGGGCTATTCGCGAACCTTC

Basic information

species Zea mays
transcript GRMZM2G077669_T01
intron # 3
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|78179671|gb|DV550044.1|DV550044
EST:     CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAG                         AGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC
genomic: CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC
EST: gi|32803871|gb|CD956107.1|CD956107
EST:     CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGGGCACAACAAG                         AGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC
genomic: CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC
EST: gi|211181672|gb|FL010880.1|FL010880
EST:     CGCTGCTCTTCTCCGGCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAG                         AGAGGCTTTGACC
genomic: CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACC
EST: gi|149009314|gb|EE041383.2|EE041383
EST:     CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAG                         AGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC
genomic: CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC
EST: gi|211344699|gb|FL214759.1|FL214759
EST:     CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCCGAGCACAACAAG                         AGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTC
genomic: CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTC
EST: gi|211184075|gb|FL010888.1|FL010888
EST:     CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAG                         AGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTTCAAAGCCATCTTC
genomic: CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC
EST: gi|50336619|gb|CO531745.1|CO531745
EST:     CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAG                         AGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC
genomic: CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC
EST: gi|211184079|gb|FL010892.1|FL010892
EST:     CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAG                         AGAGGCTTTGACCCGCAGTGGCTGTC
genomic: CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACCCGCAGTGGCTGTC
EST: gi|149016972|gb|EE154301.2|EE154301
EST:     CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAG                         AGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC
genomic: CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC
EST: gi|211184070|gb|FL010883.1|FL010883
EST:     CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAG                         AGAAGCTTTGACCCGCAGTGGCTG
genomic: CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACCCGCAGTGGCTG
EST: gi|211184080|gb|FL010893.1|FL010893
EST:     CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAG                         AGAGGCTTTGACCCGCAGTGGCTGTCCA
genomic: CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACCCGCAGTGGCTGTCCA
EST: gi|31354966|gb|CD439323.1|CD439323
EST:     CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAG                         AGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC
genomic: CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC
EST: gi|8577312|gb|BE129949.1|BE129949
EST:     CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAG                         AGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC
genomic: CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC
EST: gi|211184071|gb|FL010884.1|FL010884
EST:     CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAG                         AGAGGCTTTGACCCGCAG
genomic: CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACCCGCAG
EST: gi|74236381|gb|DT644295.1|DT644295
EST:     CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAG                         AGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC
genomic: CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC
EST: gi|149030377|gb|EE286314.2|EE286314
EST:     CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAG                         AGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC
genomic: CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC
EST: gi|78110935|gb|DV529333.1|DV529333
EST:     CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAG                         AGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC
genomic: CGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTC

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), 46 (downstream exon)
Score: 39

CGAGTACAGGGTCCTCATGATCGGCCGCATCCTCGGAGGCATCGCCACCTCGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTCCTTGGGAATGGCTTAATTGCCATTGTGTCTGGGCTATTCGCGAACCTTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 53

CGAGTACAGGGTCCTCATGATCGGCCGCATCCTCGGAGGCATCGCCACCTCGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTCCTTGGGAATGGCTTAATTGCCATTGTGTCTGGGCTATTCGCGAACCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 115

CGAGTACAGGGTCCTCATGATCGGCCGCATCCTCGGAGGCATCGCCACCTCGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTCCTTGGGAATGGCTTAATTGCCATTGTGTCTGGGCTATTCGCGAACCTTC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 87

CGAGTACAGGGTCCTCATGATCGGCCGCATCCTCGGAGGCATCGCCACCTCGCTGCTCTTCTCCGCCTTCGAGTCCTGGCTCGTCGCAGAGCACAACAAGgtacagtaac ... ctttttacagAGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTCCTTGGGAATGGCTTAATTGCCATTGTGTCTGGGCTATTCGCGAACCTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgttggtttgtacagacactgaattttttacctttcttttctctttttacagAGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTCCTTGGGAATGGCTTAATTGCCATTGTGTCTGGGCTATTCGCGAACCTTC
                     ctgaattttttacctt  CT-rich tract
                        aattttttaccttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgatcttacatttgtgaattattatggggatggacacattgcatcttgttggtttgtacagacactgaattttttacctttcttttctctttttacagAGAGGCTTTGACCCGCAGTGGCTGTCCATAACATTCTCCAAAGCCATCTTCCTTGGGAATGGCTTAATTGCCATTGTGTCTGGGCTATTCGCGAACCTTC

catgatc
- - - - tacattt
- - - - - - - - - - - - - - - gatggac
- - - - - - - - - - - - - - - - - - - cattgca
- - - - - - - - - - - - - - - - - - - - - - - - tgttggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactgaa