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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTGTACTCAGCCCGCTGCTTCTCAGTCCACTTCATCCACAGCTCCTCTTCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTGgtaagcaatcatatccgagcttgcttggatgcctggattccctagtccaaagggctttgttgccaatcgaaccctaaaatccttcttctgcttcgttcag...

Basic information

species Zea mays
transcript GRMZM2G017254_T01
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|149101979|gb|EE287486.2|EE287486
EST:     TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTG                         GCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACT
genomic: TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTGgtaagcaatc ... tgtctaatagGCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACT
EST: gi|93012276|gb|EB637796.1|EB637796
EST:     TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTG                         GCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACT
genomic: TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTGgtaagcaatc ... tgtctaatagGCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACT
EST: gi|211083302|gb|FL091158.1|FL091158
EST:     TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTGG                         GCACAACGAAC-ATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTAC
genomic: TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTT-Ggtaagcaatc ... tgtctaatagGCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTAC
EST: gi|88752415|gb|DY536556.1|DY536556
EST:     TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTG                         GCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACT
genomic: TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTGgtaagcaatc ... tgtctaatagGCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACT
EST: gi|71303979|gb|DR788111.1|DR788111
EST:     TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTG                         GCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACT
genomic: TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTGgtaagcaatc ... tgtctaatagGCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACT
EST: gi|71308449|gb|DR790459.1|DR790459
EST:     TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTG                         GCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACT
genomic: TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTGgtaagcaatc ... tgtctaatagGCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACT
EST: gi|211083301|gb|FL091157.1|FL091157
EST:     TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTGG                         GCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTAC
genomic: TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTT-Ggtaagcaatc ... tgtctaatagGCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTAC
EST: gi|148939370|gb|EC883899.2|EC883899
EST:     TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTG                         GCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACT
genomic: TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTGgtaagcaatc ... tgtctaatagGCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACT
EST: gi|211083304|gb|FL091160.1|FL091160
EST:     TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTGG                         GCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTAC
genomic: TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTT-Ggtaagcaatc ... tgtctaatagGCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTAC
EST: gi|149108502|gb|EE292810.2|EE292810
EST:     TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTG                         GCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACT
genomic: TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTGgtaagcaatc ... tgtctaatagGCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACT
EST: gi|78089523|gb|DV517897.1|DV517897
EST:     TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTG                         GCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACT
genomic: TCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTGgtaagcaatc ... tgtctaatagGCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACT
EST: gi|60348333|gb|DN215306.1|DN215306
EST:     CGTCCGGGCACGGTAGTCTCGCCTTCGTTTTG                         GCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACT
genomic: CGTCCGGGCACGGTAGTCTCGCCTTCGTTTTGgtaagcaatc ... tgtctaatagGCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACT

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: 49 (upstream exon), 49 (downstream exon)
Score: 76

GCCTGTACTCAGCCCGCTGCTTCTCAGTCCACTTCATCCACAGCTCCTCTTCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTGgtaagcaatc ... tgtctaatagGCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACTCTCTGTAACAATCTTACCAATTACCATTCTTGAGAAGAGGTACATCTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 75

GCCTGTACTCAGCCCGCTGCTTCTCAGTCCACTTCATCCACAGCTCCTCTTCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTGgtaagcaatc ... tgtctaatagGCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACTCTCTGTAACAATCTTACCAATTACCATTCTTGAGAAGAGGTACATCTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

GCCTGTACTCAGCCCGCTGCTTCTCAGTCCACTTCATCCACAGCTCCTCTTCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTGgtaagcaatc ... tgtctaatagGCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACTCTCTGTAACAATCTTACCAATTACCATTCTTGAGAAGAGGTACATCTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

GCCTGTACTCAGCCCGCTGCTTCTCAGTCCACTTCATCCACAGCTCCTCTTCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTGgtaagcaatc ... tgtctaatagGCACAACGAACAATTACTCTAGAAGAGTTGTACTCTTTGGTGTGCCGTACTCTCTGTAACAATCTTACCAATTACCATTCTTGAGAAGAGGTACATCTGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTGTACTCAGCCCGCTGCTTCTCAGTCCACTTCATCCACAGCTCCTCTTCTCTCGGTCTAGAGATCCGTCCGGGCACGGTAGTCTCGCCTTCGTTTTGgtaagcaatcatatccgagcttgcttggatgcctggattccctagtccaaagggctttgttgccaatcgaaccctaaaatccttcttctgcttcgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC