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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttcagaagtccttttacacttcgttaatatcctagattcatttttaggaacaccattctccatcaaattgatgttcagattcactgaccaattttcttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATAGTACTTGCAGCCTAAAAGCTTGGAAGGCAGCTGGGGTTCCGAAATCTGA

Basic information

species Zea mays
transcript GRMZM2G017329_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017329_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g15110.1 (Oryza sativa), 3'ss of exon 6
gtaatttcagaagtccttttacacttcgttaatatcctagattcatttttaggaacaccattctccatcaaattgatgttcagattcactgaccaattttcttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATAGTACTTGCAGCCTAAA----AGCTTGGAAGGCAGCTGGGGTTCCGAAATCTGA
            || |||||| ||| | |||  |  |   | |   ||| |    |||    || || ||  |  |   |    |||  |   ||  |||  || ||||||||||||||||||| ||||| ||||| ||||||||||||||||||||||| || || ||||||||      ||| ||||||  |  ||||  ||| | |||   
------------gtacttttagactcctttagcactcattaatatatttcactggcact-cacttcaacatgtgaaacattg--ttcgattctca--ttttatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATCGTCCTCGCAGCCTAGGCAGCAGCCTGGAAGA-ACATGGGACTCCTAGATC---
















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|37380366|gb|CF626991.1|CF626991
EST:     AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTG                         ATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATTATA
genomic: AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
EST: gi|18176906|gb|BM378116.1|BM378116
EST:     AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTG                         ATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
EST: gi|18166930|gb|BM336769.1|BM336769
EST:     AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTG                         ATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
EST: gi|101394622|gb|EB819246.1|EB819246
EST:     AAAACTCAGAAGTCGAACTCTTTTCTG                         ATATGCTTGTTGCTCGTTATTTTCGGAGTGGGTCCTGCTCATAGTGATAAT
genomic: AAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGT-GGTCCTGCTCATAGTGATAAT
EST: gi|78119338|gb|DV537722.1|DV537722
EST:     AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTTTG                         ATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
EST: gi|84980293|gb|DW530642.1|DW530642
EST:     AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTG                         ATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
EST: gi|78075157|gb|DV503591.1|DV503591
EST:     AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTTTTTG                         ATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
EST: gi|37380903|gb|CF627296.1|CF627296
EST:     AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTG                         ATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATTATA
genomic: AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
EST: gi|4609637|gb|AI600476.1|AI600476
EST:     AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTG                         ATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
EST: gi|6448408|gb|AW181174.1|AW181174
EST:     AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTTTCTG                         ATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
EST: gi|32868289|gb|CF007971.1|CF007971
EST:     AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTG                         ATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
EST: gi|15199008|gb|BI423606.1|BI423606
EST:     AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTG                         ATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
EST: gi|71760533|gb|DR958470.1|DR958470
EST:     AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTG                         ATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
EST: gi|67026173|gb|CO454922.1|CO454922
EST:     AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTG                         ATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
EST: gi|78083868|gb|DV512261.1|DV512261
EST:     AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTTTCTG                         ATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
EST: gi|71758925|gb|DR956862.1|DR956862
EST:     AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTTTTTG                         ATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
EST: gi|116820906|gb|EC864174.1|EC864174
EST:     AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTG                         ATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
EST: gi|16925613|gb|BM078681.1|BM078681
EST:     AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTG                         ATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
EST: gi|32941316|gb|CF046135.1|CF046135
EST:     AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTG                         ATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
EST: gi|211265555|gb|FL463513.1|FL463513
EST:     AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTG                         ATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA
genomic: AAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATA

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: 125

TGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTAAAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATAGTACTTGCAGCCTAAAAGCTTGGAAGGCAGCTGGGGTTCCGAAATCTGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 265

TGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTAAAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATAGTACTTGCAGCCTAAAAGCTTGGAAGGCAGCTGGGGTTCCGAAATCTGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 298

TGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTAAAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATAGTACTTGCAGCCTAAAAGCTTGGAAGGCAGCTGGGGTTCCGAAATCTGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 210

TGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTAAAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCTGgtaatttcag ... cttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATAGTACTTGCAGCCTAAAAGCTTGGAAGGCAGCTGGGGTTCCGAAATCTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccattctccatcaaattgatgttcagattcactgaccaattttcttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATAGTACTTGCAGCCTAAAAGCTTGGAAGGCAGCTGGGGTTCCGAAATCTGA
                               cactgac  putative branch site (score: 210)
                                         ttttcttgct  putative PPT
                                       aattttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttcagaagtccttttacacttcgttaatatcctagattcatttttaggaacaccattctccatcaaattgatgttcagattcactgaccaattttcttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATAGTACTTGCAGCCTAAAAGCTTGGAAGGCAGCTGGGGTTCCGAAATCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG