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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCTGTGGCGTGCGCGGAGAGGGCGACTAACGACATGCTGATCGGCCCGGATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccgaagtctcccccccctatctactatgtgaatgtataatttgtctgttctttgatatgtctgggtcggtattgttgccgaacagtgtaaaaaa...

Basic information

species Zea mays
transcript GRMZM2G151050_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151050_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g09329.2 (Oryza sativa), 5'ss of exon 2
CGGCTGTGGCGTGCGCGGAGAGGGCGACTAACGACATGCTGATCGGCCCGGATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccgaagtctcccccccctatctactatgtgaatgtataatttgtctgttctttgatatgtctg-ggtcggtattgttgccgaacagtgtaaaaaa-
|||| ||||||||||||||||||||||| | ||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||| |     |||| |     |  ||    |    |  | |  |||    |||||||||| ||| ||   | | ||||| |  |  |  ||   |   | 
CGGCCGTGGCGTGCGCGGAGAGGGCGACGAGCGACATGCTGATCGGGCCGGATTGGGCGGTGAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctggcttctctctctcgatgatgcctctgttcgagactttttgtttag--gttctttgatttgtttgtaattgttattgctatcatatggtaggatggag

upper sequence: GRMZM2G151050_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G21380.1 (Arabidopsis thaliana), 5'ss of exon 2
CGGCTGTGGCGTGCGCGGAGAGGGCGACTAACGACATGCTGATCGGCCCGGATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgac----cgaagtctcccccccctatctactatgtgaatgtataatttgtctgttctttgatatgtctgggtcggtattgttgccgaacagtgtaaaaaa
  || |  || || || |||||||| || ||||| ||||||||||| || ||||||||  ||||||| || || || ||||| ||||||||||| ||  |||  | |      | | ||           ||  ||| ||| ||  |  |  |   |     |   |||  |       |    |||            |    
ATGCGGCTGCTTGTGCTGAGAGGGCTACAAACGATATGCTGATCGGTCCAGATTGGGCTATCAACATTGAACTGTGTGACATTATCAACATGGAACCAAGgtaagtcgttttaatgactatagagatctactgatatttgattgagtc-taggctaggagcctaggatgcttaaagttttgaccttgttttgtttctctag---
















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|148962190|gb|EE013005.2|EE013005
EST:     GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGG                         ACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
genomic: GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccga ... tgaagtgcagACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
EST: gi|93012296|gb|EB637816.1|EB637816
EST:     GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGG                         ACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
genomic: GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccga ... tgaagtgcagACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
EST: gi|74233431|gb|DT641345.1|DT641345
EST:     GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGG                         ACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
genomic: GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccga ... tgaagtgcagACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
EST: gi|91876199|gb|EB406156.1|EB406156
EST:     GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGG                         ACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
genomic: GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccga ... tgaagtgcagACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
EST: gi|148954553|gb|EC899991.2|EC899991
EST:     GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGG                         ACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
genomic: GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccga ... tgaagtgcagACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
EST: gi|89247370|gb|DY619156.1|DY619156
EST:     GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGG                         ACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
genomic: GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccga ... tgaagtgcagACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
EST: gi|29168003|gb|CB411263.1|CB411263
EST:     GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGG                         ACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
genomic: GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccga ... tgaagtgcagACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
EST: gi|149106511|gb|EE188403.2|EE188403
EST:     GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGG                         ACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
genomic: GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccga ... tgaagtgcagACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
EST: gi|91871540|gb|EB401497.1|EB401497
EST:     GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGG                         ACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
genomic: GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccga ... tgaagtgcagACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
EST: gi|33942576|gb|CF349176.1|CF349176
EST:     GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGG                         ACAAGCAAAGGATACACTCAAGCTCCTAAAGAAACGTCTTGCAAGCAAGAA
genomic: GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccga ... tgaagtgcagACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
EST: gi|211038878|gb|FL017021.1|FL017021
EST:     GATTGGGCGGTCAACATCGAGCTCTGTGACATCATCAACATGGATCCCGG                         ACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
genomic: GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccga ... tgaagtgcagACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
EST: gi|149100088|gb|EE186140.2|EE186140
EST:     GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGG                         ACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
genomic: GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccga ... tgaagtgcagACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
EST: gi|28873357|gb|CB329357.1|CB329357
EST:     GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGG                         ACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
genomic: GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccga ... tgaagtgcagACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
EST: gi|93013764|gb|EB639284.1|EB639284
EST:     GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGG                         ACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
genomic: GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccga ... tgaagtgcagACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
EST: gi|31909129|gb|CD650764.1|CD650764
EST:     GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGG                         ACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
genomic: GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccga ... tgaagtgcagACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
EST: gi|71449169|gb|DR830219.1|DR830219
EST:     GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGG                         ACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA
genomic: GATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccga ... tgaagtgcagACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAA

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: 90

CGGCTGTGGCGTGCGCGGAGAGGGCGACTAACGACATGCTGATCGGCCCGGATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccga ... tgaagtgcagACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAATACGAAAGTGCAAATTCTAACACTTTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 102

CGGCTGTGGCGTGCGCGGAGAGGGCGACTAACGACATGCTGATCGGCCCGGATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccga ... tgaagtgcagACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAATACGAAAGTGCAAATTCTAACACTTTAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 92

CGGCTGTGGCGTGCGCGGAGAGGGCGACTAACGACATGCTGATCGGCCCGGATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccga ... tgaagtgcagACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAATACGAAAGTGCAAATTCTAACACTTTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

CGGCTGTGGCGTGCGCGGAGAGGGCGACTAACGACATGCTGATCGGCCCGGATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccga ... tgaagtgcagACAAGCAAAGGATACACTCAAACTCCTAAAGAAACGTCTTGCAAGCAAGAATACGAAAGTGCAAATTCTAACACTTTAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCTGTGGCGTGCGCGGAGAGGGCGACTAACGACATGCTGATCGGCCCGGATTGGGCGGTCAACATCGAGCTCTGCGACATCATCAACATGGATCCCGGgtctgaccgaagtctcccccccctatctactatgtgaatgtataatttgtctgttctttgatatgtctgggtcggtattgttgccgaacagtgtaaaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccccc