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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttggttttgtacactgtttgcacctgattatctgactgaaagcgtgggattaatgttgttgtgctattgtggtcattcgtttcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTTCTATGATTGGCTGAGTGAAGATTTTGGCTGATTATTTGTCGTCCCATAT

Basic information

species Zea mays
transcript GRMZM2G119169_T04
intron # 5
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|37390893|gb|CF632684.1|CF632684
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|5847620|gb|AW000699.1|AW000699
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|67011457|gb|CO440206.1|CO440206
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|4885932|gb|AI677052.1|AI677052
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|9952004|gb|BE638587.1|BE638587
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|60345876|gb|DN212849.1|DN212849
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|32848019|gb|CD987700.1|CD987700
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|30704734|gb|CD058588.1|CD058588
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|33097211|gb|CF057171.1|CF057171
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|50335900|gb|CO531026.1|CO531026
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|113801487|gb|DW924047.1|DW924047
EST:     AGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: AGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|101386822|gb|EB815428.1|EB815428
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|211381023|gb|FL000683.1|FL000683
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGA-CATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|13178113|gb|BG349371.1|BG349371
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|5525695|gb|AI861588.1|AI861588
EST:     GCCCCATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|60349795|gb|DN216768.1|DN216768
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|32837215|gb|CD976893.1|CD976893
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|213173920|gb|FM195799.1|FM195799
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|60356912|gb|DN223885.1|DN223885
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|14701011|gb|BI233429.1|BI233429
EST:     CCACATC-AAGCTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: CCACATCGAA-CTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|32945522|gb|CF050341.1|CF050341
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCCCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTC
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|32934714|gb|CF039526.1|CF039526
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|29544312|gb|CB604692.1|CB604692
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|211140525|gb|FL058263.1|FL058263
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|67011073|gb|CO439822.1|CO439822
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
EST: gi|211372347|gb|FL430779.1|FL430779
EST:     GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAG                         GCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT
genomic: GCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTT

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: 41 (upstream exon), 43 (downstream exon)
Score: 250

CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTTCTATGATTGGCTGAGTGAAGATTTTGGCTGATTATTTGTCGTCCCATAT


Block sizes: 47 (upstream exon), 37 (downstream exon)
Score: 141

CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTTCTATGATTGGCTGAGTGAAGATTTTGGCTGATTATTTGTCGTCCCATAT


Block sizes: 48 (upstream exon), 41 (downstream exon)
Score: 115

CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTTCTATGATTGGCTGAGTGAAGATTTTGGCTGATTATTTGTCGTCCCATAT


Block sizes: 41 (upstream exon), 37 (downstream exon)
Score: 129

CTTACATGTCCTCCCCGTGCCACATCGAACTCATCTTGTCAGAGAAGGAAGAGCCCGTGAAGAAAGAGgtatttggtt ... tcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTTCTATGATTGGCTGAGTGAAGATTTTGGCTGATTATTTGTCGTCCCATAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaagcgtgggattaatgttgttgtgctattgtggtcattcgtttcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTTCTATGATTGGCTGAGTGAAGATTTTGGCTGATTATTTGTCGTCCCATAT
           gattaat  putative branch site (score: 129)
                                    tcattcgtttcctc  putative PPT
            attaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttggttttgtacactgtttgcacctgattatctgactgaaagcgtgggattaatgttgttgtgctattgtggtcattcgtttcctcgtcagGCTGAGTCTCAGATCGCAACCAGGAATGCTTAGAGAATGGGAACATACCTTCTATGATTGGCTGAGTGAAGATTTTGGCTGATTATTTGTCGTCCCATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT