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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaaactattgactgatgcattctcatgttgagtcaccagaacaaacctgttggattttgacatgcattgtgtaatgtatgtctccttgttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATATTTCACTGTGCACCCCGTTATGGCCAGACAAACATCGTGGTGTATGTGGG

Basic information

species Zea mays
transcript GRMZM2G097421_T01
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|78118379|gb|DV536765.1|DV536765
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|101399470|gb|EB821607.1|EB821607
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|149012854|gb|EE042696.2|EE042696
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|91048854|gb|EB159272.1|EB159272
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACACCCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCA
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCA
EST: gi|74236901|gb|DT644815.1|DT644815
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|149101364|gb|EE187481.2|EE187481
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|148951157|gb|EC896836.2|EC896836
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|40334623|gb|CK368693.1|CK368693
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|148947645|gb|EC893125.2|EC893125
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|74244190|gb|DT652104.1|DT652104
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|148942011|gb|EC887002.2|EC887002
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|71416856|gb|DR803834.1|DR803834
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|148972078|gb|EE022933.2|EE022933
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|149005298|gb|EE039847.2|EE039847
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|149070089|gb|EE158489.2|EE158489
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|91050129|gb|EB160547.1|EB160547
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|211193191|gb|FK988936.1|FK988936
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         G
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcag-
EST: gi|211193191|gb|FK988936.1|FK988936
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         G
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcag-
EST: gi|149013793|gb|EE043260.2|EE043260
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|148948891|gb|EC894305.2|EC894305
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|94477226|gb|EB706184.1|EB706184
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|33285537|gb|CF075332.1|CF075332
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|78079716|gb|DV508128.1|DV508128
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|71446399|gb|DR827449.1|DR827449
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|76012865|gb|DT940035.1|DT940035
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
EST: gi|50323304|gb|CO518430.1|CO518430
EST:     AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTG                         CCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT
genomic: AGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATAT

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), 46 (downstream exon)
Score: 178

GTGCTCTGTATAATCGGGTCAACCATAATCATCCTCCATGCACCTGAAGAAGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATATTTCACTGTGCACCCCGTTATGGCCAGACAAACATCGTGGTGTATGTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 263

GTGCTCTGTATAATCGGGTCAACCATAATCATCCTCCATGCACCTGAAGAAGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATATTTCACTGTGCACCCCGTTATGGCCAGACAAACATCGTGGTGTATGTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 232

GTGCTCTGTATAATCGGGTCAACCATAATCATCCTCCATGCACCTGAAGAAGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATATTTCACTGTGCACCCCGTTATGGCCAGACAAACATCGTGGTGTATGTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

GTGCTCTGTATAATCGGGTCAACCATAATCATCCTCCATGCACCTGAAGAAGAGACACCAAGCTCAGTGACACAGATCTGGCAGTTGGCAACACAACCTGgtatgcccta ... ttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATATTTCACTGTGCACCCCGTTATGGCCAGACAAACATCGTGGTGTATGTGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacctgttggattttgacatgcattgtgtaatgtatgtctccttgttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATATTTCACTGTGCACCCCGTTATGGCCAGACAAACATCGTGGTGTATGTGGG
           ttttgac  putative branch site (score: 161)
                                   tgtctccttgttttct  putative PPT
                            taatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaaactattgactgatgcattctcatgttgagtcaccagaacaaacctgttggattttgacatgcattgtgtaatgtatgtctccttgttttctgcagCCTTTCTTTGTTATGCGGCTTCTGCATTGACTATCTCACTGATCTTGATATTTCACTGTGCACCCCGTTATGGCCAGACAAACATCGTGGTGTATGTGGG

- - - - - - -ctgatgc
- - - - - - - - - - - - - atgttga
- - - - - - - - - - - - - - - - -gtcacca
- - - - - - - - - - - - - - - - - - - - gaacaaa
- - - - - - - - - - - - - - - - - - - - - - - -cctgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgca