Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGTGCACGGCAACATCTGCCTGGACATCCTCCAGGACAAGTGGTCCTCCGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAGgtaacggatcgctactgattgctagattccttcgtttgttcggtcggtccatggatctcgtgcgtcgccttcggttctcaccgacggattatgatttgttcag

Basic information

species Zea mays
transcript GRMZM2G007057_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|149100662|gb|EE186750.2|EE186750
EST:     CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAG                         AGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
genomic: CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAGgtaacggatc ... atttgttcagAGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
EST: gi|60350762|gb|DN217735.1|DN217735
EST:     CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAG                         AGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
genomic: CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAGgtaacggatc ... atttgttcagAGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
EST: gi|91873078|gb|EB403035.1|EB403035
EST:     CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAG                         AGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
genomic: CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAGgtaacggatc ... atttgttcagAGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
EST: gi|14242858|gb|BG840635.2|BG840635
EST:     CGCCTACGACGTGCGCACCATCCTCCTCTTCATNCAGAGCCTGCTCGGAG                         AGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCG
genomic: CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAGgtaacggatc ... atttgttcagAGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCG
EST: gi|18166640|gb|BM336479.1|BM336479
EST:     CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAG                         AGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
genomic: CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAGgtaacggatc ... atttgttcagAGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
EST: gi|60350951|gb|DN217924.1|DN217924
EST:     CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAG                         AGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
genomic: CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAGgtaacggatc ... atttgttcagAGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
EST: gi|14243313|gb|BG841009.2|BG841009
EST:     CGCCTACGACGTGCGCACCATCCTCCTCTTCATCCAGAGCCTGCTCGGAG                         AGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
genomic: CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAGgtaacggatc ... atttgttcagAGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
EST: gi|149090232|gb|EE179534.2|EE179534
EST:     CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAG                         AGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
genomic: CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAGgtaacggatc ... atttgttcagAGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
EST: gi|211335744|gb|FL462852.1|FL462852
EST:     CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAG                         AGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
genomic: CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAGgtaacggatc ... atttgttcagAGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
EST: gi|211175138|gb|FL206851.1|FL206851
EST:     CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAG                         AGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
genomic: CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAGgtaacggatc ... atttgttcagAGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
EST: gi|8930153|gb|BE224797.1|BE224797
EST:     CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAG                         AGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
genomic: CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAGgtaacggatc ... atttgttcagAGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
EST: gi|50323598|gb|CO518724.1|CO518724
EST:     CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAG                         AGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
genomic: CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAGgtaacggatc ... atttgttcagAGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
EST: gi|16927027|gb|BM080095.1|BM080095
EST:     GCCTACGACGTGCGCACCATCCTCCTCTCCATGCCAGAGCCTGCTCGGAG                         AGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
genomic: GCCTACGACGTGCGCACCATCCTCCTCTCCAT-CCAGAGCCTGCTCGGAGgtaacggatc ... atttgttcagAGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
EST: gi|60351551|gb|DN218524.1|DN218524
EST:     CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAG                         AGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
genomic: CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAGgtaacggatc ... atttgttcagAGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
EST: gi|18162022|gb|BM331861.1|BM331861
EST:     CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAG                         AGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA
genomic: CGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAGgtaacggatc ... atttgttcagAGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGA

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: 161

GACGTGCACGGCAACATCTGCCTGGACATCCTCCAGGACAAGTGGTCCTCCGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAGgtaacggatc ... atttgttcagAGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGAACCAGGAAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 6

GACGTGCACGGCAACATCTGCCTGGACATCCTCCAGGACAAGTGGTCCTCCGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAGgtaacggatc ... atttgttcagAGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGAACCAGGAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 28

GACGTGCACGGCAACATCTGCCTGGACATCCTCCAGGACAAGTGGTCCTCCGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAGgtaacggatc ... atttgttcagAGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGAACCAGGAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 45

GACGTGCACGGCAACATCTGCCTGGACATCCTCCAGGACAAGTGGTCCTCCGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAGgtaacggatc ... atttgttcagAGCCGAACAACGACTCGCCGCTCAACACGCAGGCGGCGGCGCTTTGGGCGAACCAGGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACGTGCACGGCAACATCTGCCTGGACATCCTCCAGGACAAGTGGTCCTCCGCCTACGACGTGCGCACCATCCTCCTCTCCATCCAGAGCCTGCTCGGAGgtaacggatcgctactgattgctagattccttcgtttgttcggtcggtccatggatctcgtgcgtcgccttcggttctcaccgacggattatgatttgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC