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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgacgtgcaactccacagcattaggttagattttgcttgcgtccagaggaatgtgaatgctgactaatcctaccggtaacattttctcttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG

Basic information

species Zea mays
transcript GRMZM2G064988_T03
intron # 1
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|22819373|gb|BU499463.1|BU499463
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|74243422|gb|DT651336.1|DT651336
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|9028651|gb|BE238691.1|BE238691
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|211327564|gb|FL371063.1|FL371063
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|78544086|gb|DV621584.1|DV621584
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|26557837|gb|CA830072.1|CA830072
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|76284202|gb|DV023770.1|DV023770
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|60348995|gb|DN215968.1|DN215968
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|8665349|gb|BE186165.1|BE186165
EST:     CCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: CCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|28910088|gb|CB331256.1|CB331256
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|113701690|gb|EE679194.1|EE679194
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|211199113|gb|FL383377.1|FL383377
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|8665340|gb|BE186156.1|BE186156
EST:     CCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: CCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|4885900|gb|AI677020.1|AI677020
EST:     CCCCGATGGCGCGCCTCCGCCCCGAACCAATCGCCCCCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: CCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|60399890|gb|DN232700.1|DN232700
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|9028622|gb|BE238662.1|BE238662
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|31558542|gb|CD527754.1|CD527754
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|15499296|gb|BI595809.1|BI595809
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|21843145|gb|BQ703726.1|BQ703726
EST:     GTCCGCCCCCGA-GGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|20802464|gb|BQ293514.1|BQ293514
EST:     ACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: ACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|60291853|gb|DN190092.1|DN190092
EST:     GTCCGCCCCCGATGGCGCGCATCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|86470083|gb|DY236453.1|DY236453
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|60347753|gb|DN214726.1|DN214726
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|31664335|gb|CD573060.1|CD573060
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|60343137|gb|DN210110.1|DN210110
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|26456052|gb|CA827635.1|CA827635
EST:     CCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: CCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|101396763|gb|EB820307.1|EB820307
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|18178204|gb|BM379414.1|BM379414
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|101396473|gb|EB820163.1|EB820163
EST:     CGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: CGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|30087735|gb|CB885941.1|CB885941
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|211045986|gb|FL421700.1|FL421700
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|211327957|gb|FL398348.1|FL398348
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
EST: gi|211126711|gb|FL428261.1|FL428261
EST:     GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTAGCTGCTCAGGGTTTTCACAAGG
genomic: GTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCT-GCTGCTCAGGGTTTTCACAAGG
EST: gi|101396475|gb|EB820164.1|EB820164
EST:     CGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAG                         ACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
genomic: CGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG

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: 392

CGATATGCCGATGAGGCCTGCGCGGCCGGGCCCGCCGATGCAGCACCGTGGTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 236

CGATATGCCGATGAGGCCTGCGCGGCCGGGCCCGCCGATGCAGCACCGTGGTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 314

CGATATGCCGATGAGGCCTGCGCGGCCGGGCCCGCCGATGCAGCACCGTGGTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 178

CGATATGCCGATGAGGCCTGCGCGGCCGGGCCCGCCGATGCAGCACCGTGGTCCGCCCCCGATGGCGCGCCTCCGCCCCGAACCAATCGACCGCGAGAAGgtcagttctt ... ttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagaggaatgtgaatgctgactaatcctaccggtaacattttctcttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG
                                    cattttctctt  CT-rich tract
                                 taacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgacgtgcaactccacagcattaggttagattttgcttgcgtccagaggaatgtgaatgctgactaatcctaccggtaacattttctcttgtgtgcagACCTGTCCTCTGCTGCTCAGGGTTTTCACAAGG

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