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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctactttagtttataccttggatttgtgtttgcttttgtcttaaaattattcaattattaaactgtgtagctaacgagctactgaaatgcaattccctagGTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACTATGTTCCCATACGAG

Basic information

species Zea mays
transcript GRMZM2G348578_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G348578_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g55380.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------------------------------------------ctact-ttagtttataccttggatttgtgtttgctt--ttgtct------taaaattattca------attattaaact---gtgtagctaacgagctactgaaatgcaattccctagGTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACTATGTTCCCATACGAG
                                                                             |  | ||  | |  ||   ||   |  || |||||  | | |       || ||| ||| |      || |||  ||     | ||||||| || ||| |||||||||| |    |||| || |||||||||||||||||||||||||| |||||||| |||||||| ||||||||||| |||
gtatgctcctacatttgcttgcattttgcctaacctatatttctcggttctagatgtcttgaagattgggctctttttgttatttatgtgaacagaggtgctaagtctgcttaatggaccactagatagaataatttaggttgaatgatttgacaagaatatagctaaggaactattgaaatgcaaattttcagGTCGCGTCTTTCTTGCTTTATCTCACGGATGTTGAAGAAGGCGGAGAAACCATGTTCCCATATGAG
















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|211499061|gb|FL037730.1|FL037730
EST:     ATTATGACGCATTTGACCCAGCTCAGTATGGTCCACNNNNNNNTCAAAGG                         GTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAG
genomic: ATTATGACGCATTTGACCCAGCTCAGTATGGTCCACAAAAAAATCAAAGGgtatgtagca ... aattccctagGTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAG
EST: gi|4776430|gb|AI665433.1|AI665433
EST:     ATTATGACGCATTTGACCCAGCTCAGTATGGTCCACNNNNNNNTCAAAGG                         GTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACT
genomic: ATTATGACGCATTTGACCCAGCTCAGTATGGTCCACAAAAAAATCAAAGGgtatgtagca ... aattccctagGTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACT
EST: gi|211364367|gb|FL430730.1|FL430730
EST:     TTATGACGCATTTGACCCAGCTCAGTATGGTCCACAAADAAAATCAAAGG                         GTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACT
genomic: TTATGACGCATTTGACCCAGCTCAGTATGGTCCACAAA-AAAATCAAAGGgtatgtagca ... aattccctagGTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACT
EST: gi|148950085|gb|EC895620.2|EC895620
EST:     ATTATGACGCATTTGACCCAGCTCAGTATGGTCCACNNNNNNNTCAAAGG                         GTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACT
genomic: ATTATGACGCATTTGACCCAGCTCAGTATGGTCCACAAAAAAATCAAAGGgtatgtagca ... aattccctagGTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACT
EST: gi|78027558|gb|DV495945.1|DV495945
EST:     ATTATGACGCATTTGACCCAGCTCAGTATGGTCCACNNNNNNNTCAAAGG                         GTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACT
genomic: ATTATGACGCATTTGACCCAGCTCAGTATGGTCCACAAAAAAATCAAAGGgtatgtagca ... aattccctagGTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACT
EST: gi|78110902|gb|DV529300.1|DV529300
EST:     ATTATGACGCATTTGACCCAGCTCAGTATGGTCCACNNNNNNNTCAAAGG                         GTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACT
genomic: ATTATGACGCATTTGACCCAGCTCAGTATGGTCCACAAAAAAATCAAAGGgtatgtagca ... aattccctagGTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACT
EST: gi|78080612|gb|DV509024.1|DV509024
EST:     ATTATGACGCATTTGACCCAGCTCAGTATGGTCCACNNNNNNNTCAAAGG                         GTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACT
genomic: ATTATGACGCATTTGACCCAGCTCAGTATGGTCCACAAAAAAATCAAAGGgtatgtagca ... aattccctagGTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACT
EST: gi|148941851|gb|EC886829.2|EC886829
EST:     ATTATGACGCATTTGACCCAGCTCAGTATGGTCCACNNNNNNNTCAAAGG                         GTGGCATCTTTCTTGCTTTTTCTCACGGATGTCGAAGAAGGGGGAGAAACT
genomic: ATTATGACGCATTTGACCCAGCTCAGTATGGTCCACAAAAAAATCAAAGGgtatgtagca ... aattccctagGTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACT
EST: gi|149009320|gb|EE041386.2|EE041386
EST:     ATTATGACGCATTTGACCCAGCTCAGTATGGTCCACNNNNNNNTCAAAGG                         GTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACT
genomic: ATTATGACGCATTTGACCCAGCTCAGTATGGTCCACAAAAAAATCAAAGGgtatgtagca ... aattccctagGTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACT

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: 47 (upstream exon), 47 (downstream exon)
Score: 36

CCATTTAATGTCCTGCGGTATAATATTGGACAAAGGTATGCTTCACATTATGACGCATTTGACCCAGCTCAGTATGGTCCACAAAAAAATCAAAGGgtatgtagca ... aattccctagGTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACTATGTTCCCATACGAG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 38

CCATTTAATGTCCTGCGGTATAATATTGGACAAAGGTATGCTTCACATTATGACGCATTTGACCCAGCTCAGTATGGTCCACAAAAAAATCAAAGGgtatgtagca ... aattccctagGTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACTATGTTCCCATACGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 83

CCATTTAATGTCCTGCGGTATAATATTGGACAAAGGTATGCTTCACATTATGACGCATTTGACCCAGCTCAGTATGGTCCACAAAAAAATCAAAGGgtatgtagca ... aattccctagGTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACTATGTTCCCATACGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 514

CCATTTAATGTCCTGCGGTATAATATTGGACAAAGGTATGCTTCACATTATGACGCATTTGACCCAGCTCAGTATGGTCCACAAAAAAATCAAAGGgtatgtagca ... aattccctagGTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACTATGTTCCCATACGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attattcaattattaaactgtgtagctaacgagctactgaaatgcaattccctagGTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACTATGTTCCCATACGAG
                       agctaac  putative branch site (score: 514)
                                               ttccct  putative PPT
     tcaattattaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctactttagtttataccttggatttgtgtttgcttttgtcttaaaattattcaattattaaactgtgtagctaacgagctactgaaatgcaattccctagGTGGCATCTTTCTTGCTTTATCTCACGGATGTCGAAGAAGGGGGAGAAACTATGTTCCCATACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctactg