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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagttggtggtcatgaatccaacctatagtaaagtcaaaggacttgttagtatttggtataaacattggtgggatgtttacatgtactattgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGCTTTCAATTATTGCTTTCAAGAATAAGGACAACCTTGGAGGAGATAAGCT

Basic information

species Zea mays
transcript GRMZM2G109383_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109383_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 13
tgagttggtggtcatgaatccaacctatagtaaagtcaaaggacttgttagtatttgg-tataaaca--ttggtgggatgtttacatgtactattgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGCTTTCAATTATTGCTTTCAAGAATAAGGACAACCTTGGAGGAGATAAGCT
    |   ||   || ||    | | | | | || | |   | |    |    |  || ||| |  |  |     ||||| ||| |  ||||||  ||   ||| ||||| |||||||||||||| ||||| || |||||||| || |||||| | || ||| ||||||||||||| ||||||||||||||||| ||||||||
--catcaatgaaaatcaagtggatc-acatttaaataatgagtcacactgcagtcaggatatgactagctcaccaggatgcttatacctactatgttgtttagGTTCTGATCACATTCGTGAGAAAGATGGTATTTGGGCTGTTCTAGCATGGTTATCTATTCTTGCTTTCAAGAACAAGGACAACCTTGGAGGCGATAAGCT

upper sequence: GRMZM2G109383_T02 (Zea mays), 3'ss of exon 13
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 14
tgagttggtggtcatgaatccaacctatagtaaagtcaaaggacttgttagtatttggtataaacattggtggg---atgtttacatgtactat---tgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGCTTTCAATTATTGCTTTCAAGAATAAGGACAACCTTGGAGGAGATAAGCT
              |   |   |  | | ||  |    ||     ||||| | | ||  ||| ||||  ||      || |||  || |  | |   |  || |||| || ||||||||||||||||| ||||| |||||||||||  | || |||||||| ||| | ||||   | |||||||| |||||||| ||||  |||||
-------------gtaggtttcatattttgtgta--tgaaatttctgttaat-tatgacatacacatatgtaaagcaatattttgatctgttgtatctacggacagGTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGCTTTCTATTCTCGCTTATGAAAATAAGGAAAACCTTGGTGGAGCAAAGCT
















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|31363628|gb|CD447985.1|CD447985
EST:     GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG                         GGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
genomic: GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
EST: gi|211190027|gb|FL186117.1|FL186117
EST:     GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG                         GGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
genomic: GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
EST: gi|32915471|gb|CF020283.1|CF020283
EST:     GATGGATGCTGGAATGTGCTCAATCTGTGGCGAAGAAAGCTTTGGCACTG                         GGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
genomic: GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
EST: gi|211541124|gb|FL006425.1|FL006425
EST:     GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG                         GGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
genomic: GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
EST: gi|120480298|gb|EH210799.1|EH210799
EST:     GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG                         GGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
genomic: GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
EST: gi|149109220|gb|EE293196.2|EE293196
EST:     GTGGTGAAGAAAGCTTTGGCACTG                         GGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
genomic: GTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
EST: gi|32910896|gb|CF015708.1|CF015708
EST:     GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG                         GGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
genomic: GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
EST: gi|18167299|gb|BM337138.1|BM337138
EST:     ATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG                         GGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
genomic: ATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
EST: gi|67024904|gb|CO453653.1|CO453653
EST:     GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAA-GCTTTGGCACTG                         NGTCTGACCACATTCGTGAGAAAGATGGCATCTGGGCTGTGCTTGCATGGC
genomic: GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
EST: gi|20508129|gb|BQ279907.1|BQ279907
EST:     GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG                         GGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
genomic: GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
EST: gi|67025110|gb|CO453859.1|CO453859
EST:     GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG                         GGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
genomic: GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
EST: gi|213170007|gb|FM188153.1|FM188153
EST:     GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG                         GGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
genomic: GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
EST: gi|31354675|gb|CD439032.1|CD439032
EST:     GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG                         GGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
genomic: GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
EST: gi|31353391|gb|CD437748.1|CD437748
EST:     GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG                         GGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
genomic: GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
EST: gi|67022599|gb|CO451348.1|CO451348
EST:     GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG                         GGTCTGACCACATTCGTGAGAAGGATGGCAT-TGGGCTGTGCTT-CATGGC
genomic: GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
EST: gi|67018536|gb|CO447285.1|CO447285
EST:     GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG                         GGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
genomic: GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
EST: gi|67014425|gb|CO443174.1|CO443174
EST:     GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG                         GGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
genomic: GATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
EST: gi|26456763|gb|CA828346.1|CA828346
EST:     GAAGAAAGCTTTGGCACTG                         GGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC
genomic: GAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGC

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), 48 (downstream exon)
Score: 274

GTGCCTACTGGATGGAAGTTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGCTTTCAATTATTGCTTTCAAGAATAAGGACAACCTTGGAGGAGATAAGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 367

GTGCCTACTGGATGGAAGTTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGCTTTCAATTATTGCTTTCAAGAATAAGGACAACCTTGGAGGAGATAAGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

GTGCCTACTGGATGGAAGTTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGCTTTCAATTATTGCTTTCAAGAATAAGGACAACCTTGGAGGAGATAAGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 640

GTGCCTACTGGATGGAAGTTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatg ... ttgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGCTTTCAATTATTGCTTTCAAGAATAAGGACAACCTTGGAGGAGATAAGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttagtatttggtataaacattggtgggatgtttacatgtactattgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGCTTTCAATTATTGCTTTCAAGAATAAGGACAACCTTGGAGGAGATAAGCT
             tataaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagttggtggtcatgaatccaacctatagtaaagtcaaaggacttgttagtatttggtataaacattggtgggatgtttacatgtactattgtggccagGGTCTGACCACATTCGTGAGAAGGATGGCATCTGGGCTGTGCTTGCATGGCTTTCAATTATTGCTTTCAAGAATAAGGACAACCTTGGAGGAGATAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- -gttggtg
- - - - - - catgaat
- - - - - - - - - -ccaacct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtac