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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taataatatggatacaaatatacaatgctaggcatatgaatgagtgccaatctttctactttttcactaattctatgtgtactgtttgtgctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG

Basic information

species Zea mays
transcript GRMZM2G022777_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 5
--taataatatggatacaaatataca--atgctaggcatatgaatgagtgccaatctttctactttttcactaattctatgtgtactgtttgtgctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG
  ||    |||   | ||||| ||||  ||        | |||   |  |  ||||  || |  | |    || |  ||    || |  |||  || ||| ||||||||||||||||||| | || |||||||||||||| ||||||||||| |||||||| || || |||
tctagctctatat-tgcaaatgtacaaaatatgttttgtgtgacatacagataatcaatcaatctatcagttattcataatcatatt--ttggactattt-cagATACTTCACTGGTCTCTTGTCACCATGGAAAGGCATTTTACTTTTTGGTCCCCCAGGAACTGGGAAG

upper sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 5
taataatatggatacaaatatac-aatgctaggcatatgaatgagtgccaatctttc-tactttttcactaattctatgtgtactgtttgtgctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG
   |  ||    | || || | | |||   |||    |  |  |||    || |    |    | |   | ||  |     || | ||| |  ||| |  || ||||||||||||||  | || |||||||| || ||| | ||||||||||| || ||||||||||||
--tttctagacttgcatatgtgctaataaaaggttactagagaagtagagatatagagtggaatctttttcatgatcaagctaatctttctcatgtgtctagGTACTTCACTGGTCTGTTATCACCATGGAAGGGTATCCTCCTTTTTGGCCCACCGGGGACAGGAAAG

upper sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G26100.1 (Glycine max), 3'ss of exon 5
taataatatggatacaaatatacaatgctaggcatatgaatgagtgccaatctttctactttttcactaattctatgtgtactgtttgtgctgttt--tcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG
  ||  ||| ||     ||||    |  ||   |  | | |        |    | ||   |   |    ||  |||   |   | | |    |||    || ||||||||||||||  | || |||||||| |||||| | ||||||||||| || ||||||||||||
-gattttatagacttgcatatgtgctaataaa-aggttactagagaagtagagatatagagtgaaatctttttcatggtcaagatctttctcatttgtctagGTACTTCACTGGTCTGTTATCACCATGGAAGGGCATCCTCCTTTTTGGCCCACCGGGGACAGGAAAG

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|148995361|gb|EE034575.2|EE034575
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
EST: gi|91876817|gb|EB406774.1|EB406774
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
EST: gi|148933119|gb|EC876754.2|EC876754
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGG
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGG
EST: gi|31355560|gb|CD439917.1|CD439917
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
EST: gi|76933170|gb|DV173349.1|DV173349
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
EST: gi|211165539|gb|FL456882.1|FL456882
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
EST: gi|78109695|gb|DV528111.1|DV528111
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
EST: gi|149080059|gb|EE169077.2|EE169077
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
EST: gi|76280583|gb|DV020151.1|DV020151
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
EST: gi|211131749|gb|FL468282.1|FL468282
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
EST: gi|149106054|gb|EE291707.2|EE291707
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTTC-CTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGG
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTT-CACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGG
EST: gi|71297616|gb|DR784759.1|DR784759
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
EST: gi|148963213|gb|EE014191.2|EE014191
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
EST: gi|78121929|gb|DV540313.1|DV540313
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
EST: gi|78106806|gb|DV525224.1|DV525224
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
EST: gi|76281419|gb|DV020987.1|DV020987
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
EST: gi|67021064|gb|CO449813.1|CO449813
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
EST: gi|149035101|gb|EE155087.2|EE155087
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
EST: gi|8367772|gb|BE050717.1|BE050717
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
EST: gi|148963079|gb|EE014036.2|EE014036
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
EST: gi|30307202|gb|CD001875.1|CD001875
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
EST: gi|22472534|gb|BU037014.1|BU037014
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
EST: gi|31355569|gb|CD439926.1|CD439926
EST:     GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAA                         ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC
genomic: GCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCC

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), 49 (downstream exon)
Score: 217

TTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACTGGAAAATGCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

TTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACTGGAAAATGCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197

TTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACTGGAAAATGCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

TTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACTGGAAAATGCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAGTACCCAAAgtaagttagt ... ctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccaatctttctactttttcactaattctatgtgtactgtttgtgctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG
                   cactaat  putative branch site (score: 169)
                                             ctgttttc  putative PPT
                      taattctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taataatatggatacaaatatacaatgctaggcatatgaatgagtgccaatctttctactttttcactaattctatgtgtactgtttgtgctgttttcagATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - -atacaaa
- - - - - - - - - - - caatgct
- - - - - - - - - - - - - - - - - -atgaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgt