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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgtttattgctactctggatgttttgatgattatatgggcatattttccctcatcctaacactttttatttctttcagAATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG

Basic information

species Zea mays
transcript GRMZM2G089259_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G089259_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA01G37000.1 (Glycine max), 3'ss of exon 11
----gtgatgtt-tattgctactctggatgttttgatgattatatgggcatattttccctcatcctaacactttttatttctttcagAATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG
    || || || | || | | | ||    |||   || | ||||     |   || |||  |||      |||||||  |||||||||||| |||||  ||||||||||||||||||| |||
gtaagtaatattgtgtttccattttg--cttttcattgctgatatacttcttaatttccttttcccttttttttttat--ctttcagAATGCATTTGAAATGGCAACATTCTTATGGTCCCTG
















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|71428022|gb|DR809072.1|DR809072
EST:     TTTCATTTCAG                         AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG
genomic: TTTCATTTCAGgtgatgttta ... tttctttcagAATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG
EST: gi|76012906|gb|DT940076.1|DT940076
EST:     TTGGAAAGCCTCGGGTACTCTGGTGGCTTATACAGTTCATTTCATTTCAG                         AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG
genomic: TTGGAAAGCCTCGGGTACTCTGGTGGCTTATACAGTTCATTTCATTTCAGgtgatgttta ... tttctttcagAATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG
EST: gi|50336815|gb|CO531941.1|CO531941
EST:     GGTGGCTTATACAGTTCATTTCATTTCAG                         AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG
genomic: GGTGGCTTATACAGTTCATTTCATTTCAGgtgatgttta ... tttctttcagAATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG
EST: gi|148994787|gb|EE034232.2|EE034232
EST:     TTGGAAAGCCTCGGGTACTCTGGTGGCTTATACAGTTCATTTCATTTCAG                         AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG
genomic: TTGGAAAGCCTCGGGTACTCTGGTGGCTTATACAGTTCATTTCATTTCAGgtgatgttta ... tttctttcagAATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG
EST: gi|60356662|gb|DN223635.1|DN223635
EST:     TTGGAAAGCCTCGGGTACTCTGGTGGCTTATACAGTTCATTTCATTTCAG                         AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG
genomic: TTGGAAAGCCTCGGGTACTCTGGTGGCTTATACAGTTCATTTCATTTCAGgtgatgttta ... tttctttcagAATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG
EST: gi|71329463|gb|DR801452.1|DR801452
EST:     TTGGAAAGCCTCGGGTACTCTGGTGGCTTATACAGTTCATTTCATTTCAG                         AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG
genomic: TTGGAAAGCCTCGGGTACTCTGGTGGCTTATACAGTTCATTTCATTTCAGgtgatgttta ... tttctttcagAATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG
EST: gi|29129794|gb|CB380498.1|CB380498
EST:     TTGGAAAGCCTCGGGTACTCTGGTGGCTTATACAGTTCATTTCATTTCAG                         AATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG
genomic: TTGGAAAGCCTCGGGTACTCTGGTGGCTTATACAGTTCATTTCATTTCAGgtgatgttta ... tttctttcagAATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG
EST: gi|71321199|gb|DR797301.1|DR797301
EST:     TTGGAAAGCCTCGGGTACTCTGGTGGCTTATACAGTTCATTTCATTTCAG                         AATGCTTTTGAGCTGGCAACATTCTTATGGTCTTTG
genomic: TTGGAAAGCCTCGGGTACTCTGGTGGCTTATACAGTTCATTTCATTTCAGgtgatgttta ... tttctttcagAATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG

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), 45 (downstream exon)
Score: 209

AGCGCCTTATGTTGGCTCACAACTTAAACTGCGTGATGATCTATTTTGGTTTGGAAAGCCTCGGGTACTCTGGTGGCTTATACAGTTCATTTCATTTCAGgtgatgttta ... tttctttcagAATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG


Block sizes: 48 (upstream exon), 36 (downstream exon)
Score: 40

AGCGCCTTATGTTGGCTCACAACTTAAACTGCGTGATGATCTATTTTGGTTTGGAAAGCCTCGGGTACTCTGGTGGCTTATACAGTTCATTTCATTTCAGgtgatgttta ... tttctttcagAATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG


Block sizes: 41 (upstream exon), 36 (downstream exon)
Score: 21

AGCGCCTTATGTTGGCTCACAACTTAAACTGCGTGATGATCTATTTTGGTTTGGAAAGCCTCGGGTACTCTGGTGGCTTATACAGTTCATTTCATTTCAGgtgatgttta ... tttctttcagAATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG


Block sizes: 48 (upstream exon), 36 (downstream exon)
Score: 103

AGCGCCTTATGTTGGCTCACAACTTAAACTGCGTGATGATCTATTTTGGTTTGGAAAGCCTCGGGTACTCTGGTGGCTTATACAGTTCATTTCATTTCAGgtgatgttta ... tttctttcagAATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatgattatatgggcatattttccctcatcctaacactttttatttctttcagAATGCTTTTGAGCTGGCAACATTCTTATGGTCTCTG
                              tcctaac  putative branch site (score: 103)
                                    cactttttatttcttt  CT-rich tract
                                 taacactttttattt  TA-rich tract