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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAAGGGTCCAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTAgtaagttctagattaatacataattgtattgcatttctagctttcttttgtcgttttgctctactcaactaaatcatgatttattaaggatcatcatgtaatttcaggtccccttgtatattttggatgtgccaatataaatatttttccattaaaatacacaaactaacatctgaccatacatttttcaaaag

Basic information

species Zea mays
transcript GRMZM2G157462_T01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 18
AAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAAGGGTCCAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTAgtaagttctagattaatacataattgtattgcatttctagctttctt-ttgtcgttttgctctactcaactaaatcatgatttattaaggatcatcatgtaatttcaggtccccttgtatattttggatgtgccaatataaatatttttccattaaaatacacaaactaacatctgaccatacatttttcaaaag
|||||||||    ||||| ||||| ||||||||||| || ||||||||||||| |||||| ||| |||| ||||| ||||||||||| ||||| ||| | |||  |||||| |  || |||     |  | |  || ||||  |||   | |  ||||   ||  ||||     |  | ||||       |  |   |  || ||                                                                                          
AAATAAGATACGGGCTGTAATTCAAAGCAAAGGGGGATCATTCAAGGGTCCAAATACTGATGGTGGTTCCATGAGACAAAGCAATTCCGATGGTGCTCTGgtagtttctagctatatccat-----tcctacgcttttagccctctggctctaattttctccttgtcaaactctttcttattttgatgttaagactgtaaaactt------------------------------------------------------------------------------------------
















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|12046697|gb|BF728836.1|BF728836
EST:     CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTA                         GATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
genomic: CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTAgtaagttcta ... ttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
EST: gi|78180891|gb|DV551264.1|DV551264
EST:     CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTA                         GATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
genomic: CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTAgtaagttcta ... ttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
EST: gi|26455909|gb|CA827492.1|CA827492
EST:     CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTA                         GATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
genomic: CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTAgtaagttcta ... ttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
EST: gi|31355296|gb|CD439653.1|CD439653
EST:     CAAGTACTGAGGGTAGTTCACTTAGGCAAAGCAATTCGGATGGCGCTTTA                         GATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTACATGGATG
genomic: CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTAgtaagttcta ... ttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
EST: gi|31353959|gb|CD438316.1|CD438316
EST:     CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTA                         GATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
genomic: CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTAgtaagttcta ... ttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
EST: gi|31357385|gb|CD441742.1|CD441742
EST:     CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTA                         GATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
genomic: CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTAgtaagttcta ... ttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
EST: gi|22491320|gb|BU051243.1|BU051243
EST:     CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTA                         GATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
genomic: CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTAgtaagttcta ... ttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
EST: gi|32940832|gb|CF045651.1|CF045651
EST:     ACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTA                         GATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
genomic: ACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTAgtaagttcta ... ttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
EST: gi|87151847|gb|DY396636.1|DY396636
EST:     CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTA                         GATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
genomic: CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTAgtaagttcta ... ttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
EST: gi|19437242|gb|BM953652.1|BM953652
EST:     CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTA                         GATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTT
genomic: CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTAgtaagttcta ... ttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTT
EST: gi|32857965|gb|CD997646.1|CD997646
EST:     CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTCTA                         GATACTATAGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGGTGGATG
genomic: CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTAgtaagttcta ... ttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATG
EST: gi|31354322|gb|CD438679.1|CD438679
EST:     CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTA                         GATACTATGGCAC
genomic: CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTAgtaagttcta ... ttttcaaaagGATACTATGGCAC
EST: gi|7031283|gb|AW461021.1|AW461021
EST:     CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTA                         GATACTATGGCACG
genomic: CAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTAgtaagttcta ... ttttcaaaagGATACTATGGCACG

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: 258

AAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAAGGGTCCAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTAgtaagttcta ... ttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 325

AAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAAGGGTCCAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTAgtaagttcta ... ttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 412

AAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAAGGGTCCAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTAgtaagttcta ... ttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 221

AAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAAGGGTCCAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTAgtaagttcta ... ttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATAAGATCAAAGCTGTTATTCAGAGCAAAGGGGGTTCTTTCAAGGGTCCAAGTACTGAGGGTAGTTCAATGAGGCAAAGCAATTCGGATGGCGCTTTAgtaagttctagattaatacataattgtattgcatttctagctttcttttgtcgttttgctctactcaactaaatcatgatttattaaggatcatcatgtaatttcaggtccccttgtatattttggatgtgccaatataaatatttttccattaaaatacacaaactaacatctgaccatacatttttcaaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA