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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaggctctactggttaaaataggattttattttttctgtcattgaaagtggtgtggcgtcaaggtgaataatatttggctctgatactggtacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG

Basic information

species Zea mays
transcript GRMZM2G344476_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G344476_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g47120.1 (Oryza sativa), 3'ss of exon 2
aaggctctactggttaaaataggattttatttt--ttctgtcattgaaagtggtgt------ggcgtcaaggtgaata-atatttg---gctctgatactg---gtacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG
               |   | |  | || ||||  | |||  | |||| ||||| |      ||  ||||| ||| || || | ||   | | |||||||    | |  |||||||||||||||  || || ||||| |||||||| |||||  ||||||||||||||||| ||||||| |||
---------------agtgttgtttctttttttggtactgaaagtgaatgtggtttcaagttggaatcaagctgattacatgtctgttcgttgtgatacttttcgaattttgcagAACCTGGTGGTTACGTTGCTCGTGAAGGTGACCCTGTAGATGGCCTTTACATCATATTGGATGGGCAG
















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|50337659|gb|CO532785.1|CO532785
EST:     GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG                         AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
genomic: GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACGgtacgtacct ... tacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
EST: gi|148956464|gb|EC902291.2|EC902291
EST:     GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG                         AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
genomic: GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACGgtacgtacct ... tacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
EST: gi|74238643|gb|DT646557.1|DT646557
EST:     GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG                         AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
genomic: GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACGgtacgtacct ... tacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
EST: gi|211119071|gb|FL021982.1|FL021982
EST:     GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG                         AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
genomic: GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACGgtacgtacct ... tacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
EST: gi|149104205|gb|EE289638.2|EE289638
EST:     GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG                         AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
genomic: GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACGgtacgtacct ... tacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
EST: gi|148936448|gb|EC880552.2|EC880552
EST:     GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG                         AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
genomic: GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACGgtacgtacct ... tacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
EST: gi|149112589|gb|EE191373.2|EE191373
EST:     GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG                         AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
genomic: GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACGgtacgtacct ... tacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
EST: gi|91872284|gb|EB402241.1|EB402241
EST:     GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG                         AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
genomic: GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACGgtacgtacct ... tacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
EST: gi|71315516|gb|DR794364.1|DR794364
EST:     GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG                         AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
genomic: GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACGgtacgtacct ... tacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
EST: gi|50331303|gb|CO526429.1|CO526429
EST:     GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG                         AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
genomic: GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACGgtacgtacct ... tacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
EST: gi|148958992|gb|EE010517.2|EE010517
EST:     GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG                         AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
genomic: GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACGgtacgtacct ... tacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
EST: gi|148944150|gb|EC889238.2|EC889238
EST:     GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG                         AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
genomic: GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACGgtacgtacct ... tacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
EST: gi|4730512|gb|AI649678.1|AI649678
EST:     GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG                         AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
genomic: GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACGgtacgtacct ... tacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
EST: gi|71315960|gb|DR794668.1|DR794668
EST:     GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG                         AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
genomic: GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACGgtacgtacct ... tacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
EST: gi|91875931|gb|EB405888.1|EB405888
EST:     GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACG                         AACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA
genomic: GGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACGgtacgtacct ... tacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACA

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), 45 (downstream exon)
Score: 39

TGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACGgtacgtacct ... tacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 67

TGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACGgtacgtacct ... tacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 57

TGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACGgtacgtacct ... tacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 43

TGACCGAATTCCTGGGCCAGGTGCCCCTCCTGCAGTGCCTCCCGGGTTCCTCTATCCGCAGAATCGCGGAGGCCGTCCAGGTCAAGAACTACGgtacgtacct ... tacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtggtgtggcgtcaaggtgaataatatttggctctgatactggtacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG
                                 ctctgat  putative branch site (score: 43)
                   tgaataatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaggctctactggttaaaataggattttattttttctgtcattgaaagtggtgtggcgtcaaggtgaataatatttggctctgatactggtacgttgcagAACCTGGTGACTATGTCGCTCGCGAAGGTGAACCTGTCAATGGCCTTTACATCATAGTGGATGGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - ctactgg
- - - - - - - -aaaatagg
- - - - - - - - - - - - - - - -ttttctg
- - - - - - - - - - - - - - - - - - - - - - - - tggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatactg