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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgcttcacgagagccactactgaaacagtggctttattcagactgcagtttattattcattacataagactaacttttatggttccacaactgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAATTGTTGGGTACACAGACAGTCAGTGCCATCTGGCAT

Basic information

species Zea mays
transcript GRMZM2G481755_T02
intron # 4
splice site 3'
intron type U2

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|18384036|gb|BM417236.1|BM417236
EST:     TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|32832587|gb|CD972265.1|CD972265
EST:     TCTATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|86473156|gb|DY239526.1|DY239526
EST:     TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|32835654|gb|CD975332.1|CD975332
EST:     TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|76293935|gb|DV033503.1|DV033503
EST:     CAAATGCCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGGAAGAAACCAGGTTTCCTTCAAT
genomic: CAATTG-CCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|60355006|gb|DN221979.1|DN221979
EST:     TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|93283191|gb|EB675455.1|EB675455
EST:     GAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: GAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|148929470|gb|EC875572.2|EC875572
EST:     TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|211507831|gb|FL109994.1|FL109994
EST:     TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTT
genomic: TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTT
EST: gi|148999994|gb|EE037082.2|EE037082
EST:     TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|149002181|gb|EE038858.2|EE038858
EST:     TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|149070161|gb|EE158564.2|EE158564
EST:     TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|32848785|gb|CD988466.1|CD988466
EST:     TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|86470375|gb|DY236745.1|DY236745
EST:     GAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: GAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|37375476|gb|CF624176.1|CF624176
EST:     CAA-TGNCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: CAATTG-CCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|78092900|gb|DV521274.1|DV521274
EST:     TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|40334619|gb|CK368689.1|CK368689
EST:     TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|149069158|gb|EE157887.2|EE157887
EST:     TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|149103580|gb|EE288980.2|EE288980
EST:     TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|148980799|gb|EE027355.2|EE027355
EST:     TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|32836088|gb|CD975766.1|CD975766
EST:     TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|32834684|gb|CD974362.1|CD974362
EST:     TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
EST: gi|78026847|gb|DV495234.1|DV495234
EST:     TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTGCGATACT                         ATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT
genomic: TCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAAT

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: 46 (upstream exon), 48 (downstream exon)
Score: 107

CGTGCAAAAAATGTTGATGTATTAGGTGTTGAATTAGCTGGAAGTTCAGTTCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAATTGTTGGGTACACAGACAGTCAGTGCCATCTGGCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 343

CGTGCAAAAAATGTTGATGTATTAGGTGTTGAATTAGCTGGAAGTTCAGTTCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAATTGTTGGGTACACAGACAGTCAGTGCCATCTGGCAT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 299

CGTGCAAAAAATGTTGATGTATTAGGTGTTGAATTAGCTGGAAGTTCAGTTCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAATTGTTGGGTACACAGACAGTCAGTGCCATCTGGCAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 414

CGTGCAAAAAATGTTGATGTATTAGGTGTTGAATTAGCTGGAAGTTCAGTTCAATTGCCCCTTGTGTGGAATATTCAAGTGAGCACATGGCTACGATACTgtaagttccg ... actgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAATTGTTGGGTACACAGACAGTCAGTGCCATCTGGCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagtttattattcattacataagactaacttttatggttccacaactgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAATTGTTGGGTACACAGACAGTCAGTGCCATCTGGCAT
                       gactaac  putative branch site (score: 414)
                                              ctgtttc  putative PPT
     ttattattcattacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcttcacgagagccactactgaaacagtggctttattcagactgcagtttattattcattacataagactaacttttatggttccacaactgtttcagATGTCTATGAGAGGTTAATTCAGAAAGGAAAGAAACCAGGTTTCCTTCAATTGTTGGGTACACAGACAGTCAGTGCCATCTGGCAT

gtgcttc
- - - - - - - ccactac
- - - - - - - - - - - - - - - - - - - - - actgcag