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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgcacctttctatttttttaaagatgaagaaagtatcacttttttgcttcgtacaaatagggacgcacacatccatctacatctttctatagactgaatatactgcagacttgcatcatggaaaatgcaatctcacttctatcttttattctctttcgcagACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG

Basic information

species Zea mays
transcript GRMZM2G070315_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070315_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g10650.1 (Oryza sativa), 3'ss of exon 3
gtactgcacctttctatttttttaaagatgaagaaagtatcacttttttgcttcgtacaaatagggacgcacacatccatctacatctttctatagactgaatatactgcagacttgcatcatggaaaatgcaatctcacttctatcttttattctcttt--cgcagACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
                                                                                || ||  | |||| |  ||    | |  |||  |||||||||    |  |   | |||  |     || ||  | |  ||    |||||  || |||||||||||||||||| || |||||||||||||||
-----------------------------------------------------------------------------gtactgcaattatcta-actctcctcacatcgcacgcttgcatcacaacatttcagacctctttaactcctgttgcttttcttgatacagACGTAAAAAACCAACCTCTGCTTATTCACTGCAAGAGAGGCAAG
















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|32925414|gb|CF030226.1|CF030226
EST:     TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG                         ACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
genomic: TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tctttcgcagACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
EST: gi|149028367|gb|EE286122.2|EE286122
EST:     TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG                         ACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
genomic: TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tctttcgcagACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
EST: gi|148939874|gb|EC884586.2|EC884586
EST:     TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG                         ACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
genomic: TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tctttcgcagACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
EST: gi|88755665|gb|DY539806.1|DY539806
EST:     TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG                         ACCCAAGAAACCAACCTCTGCTTATCCA
genomic: TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tctttcgcagACCCAAGAAACCAACCTCTGCTTATCCA
EST: gi|89758678|gb|DY687773.1|DY687773
EST:     TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG                         ACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
genomic: TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tctttcgcagACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
EST: gi|211209829|gb|FK949987.1|FK949987
EST:     TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG                         ACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
genomic: TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tctttcgcagACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
EST: gi|148937447|gb|EC881628.2|EC881628
EST:     TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG                         ACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
genomic: TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tctttcgcagACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
EST: gi|148940906|gb|EC885740.2|EC885740
EST:     TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG                         ACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
genomic: TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tctttcgcagACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
EST: gi|149028366|gb|EE154635.2|EE154635
EST:     TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG                         ACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
genomic: TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tctttcgcagACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
EST: gi|89249010|gb|DY620796.1|DY620796
EST:     TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG                         ACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
genomic: TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tctttcgcagACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
EST: gi|149083277|gb|EE172563.2|EE172563
EST:     TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG                         ACCCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
genomic: TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tctttcgcagACCC-AAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
EST: gi|76290784|gb|DV030352.1|DV030352
EST:     TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAG                         ACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
genomic: TGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tctttcgcagACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 3

GAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tctttcgcagACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 30

GAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tctttcgcagACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 67

GAACCATTTGTCAACATACCCGACGACAAAATAAGGGAGGCGCTCAAAGTTGTCTTAGgtactgcacc ... tctttcgcagACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacttgcatcatggaaaatgcaatctcacttctatcttttattctctttcgcagACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG
                       atctcac  putative branch site (score: 67)
                        tctcacttctatcttt  CT-rich tract
                              ttctatcttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgcacctttctatttttttaaagatgaagaaagtatcacttttttgcttcgtacaaatagggacgcacacatccatctacatctttctatagactgaatatactgcagacttgcatcatggaaaatgcaatctcacttctatcttttattctctttcgcagACCCAAGAAACCAACCTCTGCTTATCCATTGCAAGAGAGGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG