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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaacaaccttaacatcttttttgtcaacaaaagttcgcttaaactcattttttattgtacattatgcatcgcag

Basic information

species Zea mays
transcript GRMZM2G066051_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066051_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os07g39630.1 (Oryza sativa), 5'ss of exon 9
GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgt-ttaacaaccttaacatctttttt------gtcaacaaaagttcgcttaaactcattttttattgt-acatt----atgcatcgcag
||||| || |||||||||||||||||||||||||| |||||||||||  || |||| |  ||  | || | ||          ||    | |||   || ||||||  | | ||| | |||||    |   |  ||||
GATTCAAGCAAAAATATTCAAATTGAAGCATTTCATGTGTTCAAGgttagtattaatactctgcagatttattcccagtaaagcaggtgatgtttatttgaactcaggtatgattattacatttgctacatactgcag
















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|37401622|gb|CF638179.1|CF638179
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGGGGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTA
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|5597279|gb|AI891272.1|AI891272
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|148999213|gb|EE036132.2|EE036132
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|149082295|gb|EE171480.2|EE171480
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|111192096|gb|EE290232.1|EE290232
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|37386784|gb|CF630581.1|CF630581
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|5714302|gb|AI944287.1|AI944287
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACA-ACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|149041351|gb|EE046989.2|EE046989
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|78107218|gb|DV525636.1|DV525636
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|86475161|gb|DY241531.1|DY241531
EST:     GATTGGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|148931817|gb|EC877263.2|EC877263
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|33467028|gb|CF244077.1|CF244077
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCCCCTGAGGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|60354560|gb|DN221533.1|DN221533
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|16377803|gb|BI992125.1|BI992125
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|5895944|gb|AW037190.1|AW037190
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|14202201|gb|BG835878.1|BG835878
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAMGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|6056704|gb|AW091109.1|AW091109
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|6445388|gb|AW179351.1|AW179351
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCG
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCG
EST: gi|6056599|gb|AW091004.1|AW091004
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|3157331|gb|AA979953.1|AA979953
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|5525422|gb|AI861315.1|AI861315
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|110518192|gb|EE022779.1|EE022779
EST:     GATTGGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGGGAATAAAAACAAACCGCCGGAGGTGGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|24769447|gb|CA404576.1|CA404576
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|60350125|gb|DN217098.1|DN217098
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
EST: gi|211020659|gb|FL429513.1|FL429513
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGA
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGA
EST: gi|71328879|gb|DR801122.1|DR801122
EST:     GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAG                         CTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC
genomic: GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTC

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: 157

GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTCACCAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 195

GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTCACCAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTCACCAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 214

GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaa ... tgcatcgcagCTGTTTGCTGCGAATAAAAACAAACCGCCTGAGGTCGTGAACATACTGGTCACCAATAGAAGCAAGCTACTTCGGTTTTTTGCTGGATTCAAGATTGACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTCGAGTAAAAATATTCAAATTGAAGCATTTCACGTGTTCAAGgtatgtttaacaaccttaacatcttttttgtcaacaaaagttcgcttaaactcattttttattgtacattatgcatcgcag

- - - - - - - - - - - TTGAAG
- - - - - - - - - - -  TGAAGC