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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgcttatgtcttcttgtttttgtcccaacgaatgcatttattggttactccatgctgattagcactttactttagtgtattgattgagacttg...

Basic information

species Zea mays
transcript GRMZM2G064988_T03
intron # 2
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|22819373|gb|BU499463.1|BU499463
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|74243422|gb|DT651336.1|DT651336
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|9028651|gb|BE238691.1|BE238691
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|211327564|gb|FL371063.1|FL371063
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCA-CAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|78544086|gb|DV621584.1|DV621584
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|26557837|gb|CA830072.1|CA830072
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|76284202|gb|DV023770.1|DV023770
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|60348995|gb|DN215968.1|DN215968
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|8665349|gb|BE186165.1|BE186165
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|28910088|gb|CB331256.1|CB331256
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|113701690|gb|EE679194.1|EE679194
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|33096101|gb|CF056095.1|CF056095
EST:     TGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: TGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|211199113|gb|FL383377.1|FL383377
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|8665340|gb|BE186156.1|BE186156
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|4885900|gb|AI677020.1|AI677020
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|60399890|gb|DN232700.1|DN232700
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|9028622|gb|BE238662.1|BE238662
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|22552497|gb|BU102336.1|BU102336
EST:     CGCGAGAAGACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: CGCGAGAAGACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|31558542|gb|CD527754.1|CD527754
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|15499296|gb|BI595809.1|BI595809
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|21843145|gb|BQ703726.1|BQ703726
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|20802464|gb|BQ293514.1|BQ293514
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|60291853|gb|DN190092.1|DN190092
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|86470083|gb|DY236453.1|DY236453
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|60347753|gb|DN214726.1|DN214726
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|31664335|gb|CD573060.1|CD573060
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|60343137|gb|DN210110.1|DN210110
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|26456052|gb|CA827635.1|CA827635
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|101396763|gb|EB820307.1|EB820307
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|18178204|gb|BM379414.1|BM379414
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|101396473|gb|EB820163.1|EB820163
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|30087735|gb|CB885941.1|CB885941
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|211045986|gb|FL421700.1|FL421700
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|211327957|gb|FL398348.1|FL398348
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAATGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|211126711|gb|FL428261.1|FL428261
EST:     ACCTGTCCTCTAGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCT-GCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
EST: gi|101396475|gb|EB820164.1|EB820164
EST:     ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG                         GTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA
genomic: ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCA

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: 402

ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCAAAGGATGAAGTTCAGATTTACACATGGAAGGATGCGACCCTCCGCGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 258

ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCAAAGGATGAAGTTCAGATTTACACATGGAAGGATGCGACCCTCCGCGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 266

ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCAAAGGATGAAGTTCAGATTTACACATGGAAGGATGCGACCCTCCGCGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgc ... ctgtttccagGTTGCTGGTCACCACCAAAATGAAGAGTTTGCAGTGAGAGGGAAGGAACCAAAGGATGAAGTTCAGATTTACACATGGAAGGATGCGACCCTCCGCGAGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGGgtaagcgtgcttatgtcttcttgtttttgtcccaacgaatgcatttattggttactccatgctgattagcactttactttagtgtattgattgagacttg

- - - - - TGCTGC
- - - - -  GCTGCT