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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatactgcatccctttcttgttatctttccctagctaccgcgctctgagttctcttcaatttggttcttccatgtatgaattcatgtctgcaattaaccacaaaattgaacagTGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACTGTCAAAAGGATTAGAGGAGCGACCTGCAGCTTACAATTGCTATGACCCT

Basic information

species Zea mays
transcript GRMZM2G083749_T05
intron # 1
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|211051350|gb|FK945215.1|FK945215
EST:     CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCT                         TGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
genomic: CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCTgtaaatactg ... aattgaacagTGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
EST: gi|211077489|gb|FL419989.1|FL419989
EST:     CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCT                         TGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
genomic: CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCTgtaaatactg ... aattgaacagTGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
EST: gi|149055404|gb|EE156323.2|EE156323
EST:     CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCT                         TGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
genomic: CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCTgtaaatactg ... aattgaacagTGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
EST: gi|78115486|gb|DV533874.1|DV533874
EST:     CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCT                         TGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
genomic: CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCTgtaaatactg ... aattgaacagTGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
EST: gi|211434382|gb|FL408927.1|FL408927
EST:     CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCT                         TGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
genomic: CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCTgtaaatactg ... aattgaacagTGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
EST: gi|211084381|gb|FL369930.1|FL369930
EST:     CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCT                         TGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
genomic: CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCTgtaaatactg ... aattgaacagTGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
EST: gi|149095094|gb|EE180702.2|EE180702
EST:     CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCT                         TGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
genomic: CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCTgtaaatactg ... aattgaacagTGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
EST: gi|91874519|gb|EB404476.1|EB404476
EST:     CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCT                         TGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
genomic: CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCTgtaaatactg ... aattgaacagTGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
EST: gi|148981124|gb|EE027442.2|EE027442
EST:     CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCT                         TGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
genomic: CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCTgtaaatactg ... aattgaacagTGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
EST: gi|50339291|gb|CO534417.1|CO534417
EST:     CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCT                         TGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
genomic: CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCTgtaaatactg ... aattgaacagTGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
EST: gi|101386436|gb|EB815235.1|EB815235
EST:     CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCT                         TGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
genomic: CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCTgtaaatactg ... aattgaacagTGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
EST: gi|94472188|gb|EB701146.1|EB701146
EST:     CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCT                         TGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
genomic: CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCTgtaaatactg ... aattgaacagTGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
EST: gi|148932563|gb|EC876392.2|EC876392
EST:     CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCT                         TGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT
genomic: CATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCTgtaaatactg ... aattgaacagTGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACT

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: 48 (upstream exon), 38 (downstream exon)
Score: 25

TGCCTCTGCCTCCTGAGGTGCTGAACGACAGCTCTGCTACTTCTGATCTGCATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCTgtaaatactg ... aattgaacagTGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACTGTCAAAAGGATTAGAGGAGCGACCTGCAGCTTACAATTGCTATGACCCT


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 76

TGCCTCTGCCTCCTGAGGTGCTGAACGACAGCTCTGCTACTTCTGATCTGCATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCTgtaaatactg ... aattgaacagTGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACTGTCAAAAGGATTAGAGGAGCGACCTGCAGCTTACAATTGCTATGACCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

TGCCTCTGCCTCCTGAGGTGCTGAACGACAGCTCTGCTACTTCTGATCTGCATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCTgtaaatactg ... aattgaacagTGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACTGTCAAAAGGATTAGAGGAGCGACCTGCAGCTTACAATTGCTATGACCCT


Block sizes: 47 (upstream exon), 29 (downstream exon)
Score: 20

TGCCTCTGCCTCCTGAGGTGCTGAACGACAGCTCTGCTACTTCTGATCTGCATGATGGCCGGGAAAGCAGCATGCCGGAGTCATGGAGCCAGCTGCTTCTgtaaatactg ... aattgaacagTGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACTGTCAAAAGGATTAGAGGAGCGACCTGCAGCTTACAATTGCTATGACCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttggttcttccatgtatgaattcatgtctgcaattaaccacaaaattgaacagTGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACTGTCAAAAGGATTAGAGGAGCGACCTGCAGCTTACAATTGCTATGACCCT
                                 aattaac  putative branch site (score: 20)
                                           aaaattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatactgcatccctttcttgttatctttccctagctaccgcgctctgagttctcttcaatttggttcttccatgtatgaattcatgtctgcaattaaccacaaaattgaacagTGGGGGATTAGTCGGAGATCACGAGAGATACAACGCTGCCACAGCTTTACTGTCAAAAGGATTAGAGGAGCGACCTGCAGCTTACAATTGCTATGACCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT