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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTGGACGCGGCCAGCTTCCATCTCTCGGTCACCTCCCTCTACATCCCACGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacacggtatgcttctctgctcaggtttctagatgatattctgggtttagagattgggggttccaacgtgtaatcgtcttgtgttttattttcga...

Basic information

species Zea mays
transcript GRMZM5G824831_T03
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|71445140|gb|DR826190.1|DR826190
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGGTCTGCACACG               
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-C-CT-C----TC--CA-A-Ggtctgcacac ...
EST: gi|211156519|gb|FL164233.1|FL164233
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGGTCTGCACACG               
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-C-CT-C----TC--CA-A-Ggtctgcacac ...
EST: gi|211264908|gb|FL208724.1|FL208724
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-CTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
EST: gi|74241051|gb|DT648965.1|DT648965
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGGTCTGCACACG               
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-C-CT-C----TC--CA-A-Ggtctgcacac ...
EST: gi|211264911|gb|FL208727.1|FL208727
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-CTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
EST: gi|148956338|gb|EC902144.2|EC902144
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGGTCTGCACACGCAG            
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-----CC----TCT-C-CA---AGgtctgcacac .
EST: gi|211264912|gb|FL208728.1|FL208728
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-CTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
EST: gi|148931204|gb|EC873960.2|EC873960
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGCAG                       
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCC-A--AGgtctgcacac ... ttgccagc
EST: gi|211264909|gb|FL208725.1|FL208725
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
EST: gi|148952476|gb|EC898302.2|EC898302
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
EST: gi|211264913|gb|FL208729.1|FL208729
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
EST: gi|211264914|gb|FL208730.1|FL208730
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
EST: gi|149076954|gb|EE165611.2|EE165611
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
EST: gi|78112697|gb|DV531091.1|DV531091
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGGTCTGCACACGCAG            
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-----CC----TCT-C-CA---AGgtctgcacac .
EST: gi|211264910|gb|FL208726.1|FL208726
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
EST: gi|148987620|gb|EE031494.2|EE031494
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGGTCTGCACACGCAG            
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-----CC----TCT-C-CA---AGgtctgcacac .
EST: gi|91875485|gb|EB405442.1|EB405442
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGGTCTGCACACG               
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-C-CT-C----TC--CA-A-Ggtctgcacac ...
EST: gi|71447361|gb|DR828411.1|DR828411
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGGTCTGCACACG               
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGG-C-CT-C----TC--CA-A-Ggtctgcacac ...
EST: gi|211504926|gb|FL311934.1|FL311934
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
EST: gi|211264915|gb|FL208731.1|FL208731
EST:     CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAG                         GAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG
genomic: CGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAG

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: 1070

CATTGGACGCGGCCAGCTTCCATCTCTCGGTCACCTCCCTCTACATCCCACGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAGGTGACTCCCCACCGCGCCCATGGGTGACAGCCAGTACTCCTTCTCCCTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 770

CATTGGACGCGGCCAGCTTCCATCTCTCGGTCACCTCCCTCTACATCCCACGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAGGTGACTCCCCACCGCGCCCATGGGTGACAGCCAGTACTCCTTCTCCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 824

CATTGGACGCGGCCAGCTTCCATCTCTCGGTCACCTCCCTCTACATCCCACGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAGGTGACTCCCCACCGCGCCCATGGGTGACAGCCAGTACTCCTTCTCCCTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 642

CATTGGACGCGGCCAGCTTCCATCTCTCGGTCACCTCCCTCTACATCCCACGGCCGCTACCACCTTCCCTCTACCTCACACGGCCGCCGGCCTCTCCAAGgtctgcacac ... ttgccagcagGAAAAACCTTGCCACGAGTCGCCGACACTCCATCCCGGAAGAGCTAACGAGGTGACTCCCCACCGCGCCCATGGGTGACAGCCAGTACTCCTTCTCCCTC