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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGGTTCATTTGATGCTGAAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttcactggataactgttgttctgtcttgccctcattttattttacattatcaagtcatctatccctagagaagatagaccatgatatggaatat...

Basic information

species Zea mays
transcript GRMZM2G092152_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092152_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g48760.1 (Oryza sativa), 5'ss of exon 3
AAGGGTTCATTTGATGCTGAAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtact---gttcactggataactgttgttctgtcttgccctcattttattttacattatcaagtcatctatccctagagaagatagaccatgatatggaatat
|||||||| |||||||||||||||||||||||||| |||||||||||||| || ||||| ||||| ||||||||   ||||     | ||   |  | | |         || | |||  |    | |||| |   |||     |        | ||| ||   |  | |  
AAGGGTTCGTTTGATGCTGAAAAGAAAACAGTGACGCTCCAAAGCGAACTTGTGGGGAACGCATCCAAGgtacttttgttctgctcacaagaatattgcagatgaattaccaatctatagttttct-tcaaatgcactaatttaatttgcttaataccgtgcactacatt--
















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|5804510|gb|AI979480.1|AI979480
EST:     AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAG                         GTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
genomic: AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttca ... actttggcagGTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
EST: gi|78021667|gb|DV490054.1|DV490054
EST:     AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAG                         GTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
genomic: AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttca ... actttggcagGTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
EST: gi|60338639|gb|DN205612.1|DN205612
EST:     AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAG                         GTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
genomic: AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttca ... actttggcagGTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
EST: gi|32909568|gb|CF014380.1|CF014380
EST:     AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAG                         GTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
genomic: AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttca ... actttggcagGTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
EST: gi|211489357|gb|FL110823.1|FL110823
EST:     AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAG                         GTGAAGCAGWTCACGAGAACTTTTCAGGTGGCANATGGGGAGCTCTCGTAC
genomic: AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttca ... actttggcagGTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
EST: gi|9732493|gb|BE511245.1|BE511245
EST:     AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAG                         GTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
genomic: AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttca ... actttggcagGTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
EST: gi|211489363|gb|FL110829.1|FL110829
EST:     AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAG                         GTGAAGCARATCACGAGAACTTTTCAGGTGGCARATGGGGAGCTCTCGTAC
genomic: AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttca ... actttggcagGTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
EST: gi|211489356|gb|FL110822.1|FL110822
EST:     AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAG                         GTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
genomic: AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttca ... actttggcagGTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
EST: gi|211486489|gb|FL110821.1|FL110821
EST:     AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAG                         GTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCT
genomic: AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttca ... actttggcagGTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCT
EST: gi|32909569|gb|CF014381.1|CF014381
EST:     AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAG                         GTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCT
genomic: AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttca ... actttggcagGTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCT
EST: gi|17932025|gb|BM268985.1|BM268985
EST:     AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAG                         GTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
genomic: AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttca ... actttggcagGTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
EST: gi|211489362|gb|FL110828.1|FL110828
EST:     AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAG                         GTGAAGCAGATCACGAGAACTTTTCAGGTGGCA
genomic: AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttca ... actttggcagGTGAAGCAGATCACGAGAACTTTTCAGGTGGCA
EST: gi|9732494|gb|BE511246.1|BE511246
EST:     AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAG                         GTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
genomic: AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttca ... actttggcagGTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
EST: gi|211489359|gb|FL110825.1|FL110825
EST:     AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAG                         GTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
genomic: AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttca ... actttggcagGTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
EST: gi|14243770|gb|BG841433.2|BG841433
EST:     AAAAGAA--CAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAG                         GTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC
genomic: AAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttca ... actttggcagGTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTAC

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: 43 (upstream exon), 40 (downstream exon)
Score: 12

AAGGGTTCATTTGATGCTGAAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttca ... actttggcagGTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTACGTCGTTCAGATGGCAACGATCACAACTAGCCTACAGCCACATCTCAAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 31

AAGGGTTCATTTGATGCTGAAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttca ... actttggcagGTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTACGTCGTTCAGATGGCAACGATCACAACTAGCCTACAGCCACATCTCAAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 25

AAGGGTTCATTTGATGCTGAAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttca ... actttggcagGTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTACGTCGTTCAGATGGCAACGATCACAACTAGCCTACAGCCACATCTCAAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 36

AAGGGTTCATTTGATGCTGAAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttca ... actttggcagGTGAAGCAGATCACGAGAACTTTTCAGGTGGCAGATGGGGAGCTCTCGTACGTCGTTCAGATGGCAACGATCACAACTAGCCTACAGCCACATCTCAAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGGTTCATTTGATGCTGAAAAGAAAACAGTGACACTCCAAAGCGAACTCGTAGGGAATGCATCAAAGgtactgttcactggataactgttgttctgtcttgccctcattttattttacattatcaagtcatctatccctagagaagatagaccatgatatggaatat

- - - - - - - - - - AAAGAA
- - - - - - - - - -  AAGAAA