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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCTGGACGCTGTTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttgcatttcgcgttgcttgcaagtcgttcgtttgtttgtgtcgttcgtttgtttgtgttgacgactaagggcctgtttagttcctttagtcta...

Basic information

species Zea mays
transcript GRMZM2G013890_T01
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013890_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os02g58020.1 (Oryza sativa), 5'ss of exon 17
GATCTGGACGCTGTTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttgcat--ttcgcgttgct-tgcaagtcgttcgtttgtttgtgtcgttcgtttgtttgtgttgacgactaagggcctgtttagttcctttagtcta
|||||||| ||||| |||||||| ||||||||||||||| |||| |||||||| ||||| ||||||  | |   ||  |||   ||| | |  |||  | |   |||   |  || |||   |  ||     |     |  | | ||  |||  |  |  ||    
GATCTGGATGCTGTGGAGGCGCTGATCCAGGGTTTACTCGTTTTCCAGGGAGGAGTGCTAATGgtaaaactaagatcgttcattttggtgtaaaagctgatgacttg---gcatcattc---taattacaa-gctatatgggtgacttgttatcttttacag----
















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|211429010|gb|FL174619.1|FL174619
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCG
EST: gi|24769470|gb|CA404599.1|CA404599
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|113810056|gb|DW932154.1|DW932154
EST:     CAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: CAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|92088048|gb|EB484279.1|EB484279
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|71307301|gb|DR789831.1|DR789831
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|45567942|gb|CK985824.1|CK985824
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|32836532|gb|CD976210.1|CD976210
EST:     TTGAGGCGCTCATCCAGGG-TTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|7216688|gb|AW562810.1|AW562810
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|60341793|gb|DN208766.1|DN208766
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|211142472|gb|FL453924.1|FL453924
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|12970170|gb|BG266849.1|BG266849
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACAATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|7227521|gb|AW566162.1|AW566162
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|22552549|gb|BU102388.1|BU102388
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|60352803|gb|DN219776.1|DN219776
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|5069942|gb|AI737907.1|AI737907
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|76914779|gb|DV165687.1|DV165687
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|67015572|gb|CO444321.1|CO444321
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|78544243|gb|DV621741.1|DV621741
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|84980921|gb|DW531270.1|DW531270
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|5108202|gb|AI739915.1|AI739915
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|7162610|gb|AW520232.1|AW520232
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCNCTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|40336236|gb|CK370306.1|CK370306
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAAGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|211429006|gb|FL174615.1|FL174615
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|93011869|gb|EB637389.1|EB637389
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|6859953|gb|AW355947.1|AW355947
EST:     ATGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGCGCTGATG                         GCGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|211429007|gb|FL174616.1|FL174616
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|86472924|gb|DY239294.1|DY239294
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGGTGATG                         GTGAGTCACGATGAGCATCTTATCACCGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|37390519|gb|CF632491.1|CF632491
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|32943068|gb|CF047887.1|CF047887
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|20802514|gb|BQ293564.1|BQ293564
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATAAAAACACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|213187661|gb|FM193141.1|FM193141
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|37377213|gb|CF625190.1|CF625190
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
EST: gi|7304451|gb|AW600390.1|AW600390
EST:     TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATG                         GTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG
genomic: TTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTG

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: 239

GATCTGGACGCTGTTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTGGTGTCGGAAGGCAGGGTGACCCCGTTCTCGGGCACTTTCAAGGACTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 259

GATCTGGACGCTGTTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTGGTGTCGGAAGGCAGGGTGACCCCGTTCTCGGGCACTTTCAAGGACTACA


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

GATCTGGACGCTGTTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTGGTGTCGGAAGGCAGGGTGACCCCGTTCTCGGGCACTTTCAAGGACTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

GATCTGGACGCTGTTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttg ... tgcattgcagGTGAGTCACGATGAGCATCTTATCACTGGAAGCGTGGACGAGCTTTGGGTGGTGTCGGAAGGCAGGGTGACCCCGTTCTCGGGCACTTTCAAGGACTACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCTGGACGCTGTTGAGGCGCTCATCCAGGGTTTACTCATTTTTCAGGGAGGGGTGCTGATGgtatgatttgcatttcgcgttgcttgcaagtcgttcgtttgtttgtgtcgttcgtttgtttgtgttgacgactaagggcctgtttagttcctttagtcta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT