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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgctgctccatttcatattttcagtgcctattgcatggattttggttttgccttatgtgaactcatggcagttatctaaatcgtgttcttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTACAGTACGAAGATTCGACAGTATCTGCTTGTGGTTCAAGCCGGGTTGAAC

Basic information

species Zea mays
transcript GRMZM5G886989_T02
intron # 4
splice site 3'
intron type U2

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|4646537|gb|AI491684.2|AI491684
EST:     CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|86470758|gb|DY237128.1|DY237128
EST:     CTTAGGAATTTGGTGTTCTGTCTCTGTTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|78086281|gb|DV514674.1|DV514674
EST:     CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|116818537|gb|EC861572.1|EC861572
EST:     CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|37379373|gb|CF626430.1|CF626430
EST:     CTTAGGAATTTCGTGTTCTTTCTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|60343078|gb|DN210051.1|DN210051
EST:     CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|60350952|gb|DN217925.1|DN217925
EST:     CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|32800423|gb|CD952659.1|CD952659
EST:     CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|88752115|gb|DY536256.1|DY536256
EST:     CTTAGGAATTTCGTGTTCTGTTTCTGTTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|211143815|gb|FL448466.1|FL448466
EST:     CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|32866946|gb|CF006628.1|CF006628
EST:     TTAGGAATTTCGTGTTCTGTCTCTGCTGACATGATCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: TTAGGAATTTCGTGTTCTGTCTCTGCTGACATG-TCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|32800662|gb|CD952898.1|CD952898
EST:     CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACGTGAACTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|60342045|gb|DN209018.1|DN209018
EST:     CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|60355961|gb|DN222934.1|DN222934
EST:     CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|8665604|gb|BE186420.1|BE186420
EST:     AGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: AGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|78075052|gb|DV503486.1|DV503486
EST:     CTTAGGAATTTCGTGTTCTGTTTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|89248854|gb|DY620640.1|DY620640
EST:     CTTAGGAATTTCGTGTTCTGTTTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|50334363|gb|CO529489.1|CO529489
EST:     CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|8665307|gb|BE186123.1|BE186123
EST:     CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|211253351|gb|FL463440.1|FL463440
EST:     CTCAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAAGGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|211101165|gb|FL105401.1|FL105401
EST:     CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGACCTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|32800833|gb|CD953069.1|CD953069
EST:     CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|60343072|gb|DN210045.1|DN210045
EST:     CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
EST: gi|60355163|gb|DN222136.1|DN222136
EST:     CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCAT                         GTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA
genomic: CTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTA

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), 47 (downstream exon)
Score: 31

ACCATGCTTCTGTATTTCCCATGCGGGTTGATAAGAGGTGCCTTGACCAACTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTACAGTACGAAGATTCGACAGTATCTGCTTGTGGTTCAAGCCGGGTTGAAC


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 27

ACCATGCTTCTGTATTTCCCATGCGGGTTGATAAGAGGTGCCTTGACCAACTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTACAGTACGAAGATTCGACAGTATCTGCTTGTGGTTCAAGCCGGGTTGAAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 31

ACCATGCTTCTGTATTTCCCATGCGGGTTGATAAGAGGTGCCTTGACCAACTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTACAGTACGAAGATTCGACAGTATCTGCTTGTGGTTCAAGCCGGGTTGAAC


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 17

ACCATGCTTCTGTATTTCCCATGCGGGTTGATAAGAGGTGCCTTGACCAACTTAGGAATTTCGTGTTCTGTCTCTGCTGACATGTCAAACCTTCCAGCATgtaagttcag ... ttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTACAGTACGAAGATTCGACAGTATCTGCTTGTGGTTCAAGCCGGGTTGAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttttgccttatgtgaactcatggcagttatctaaatcgtgttcttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTACAGTACGAAGATTCGACAGTATCTGCTTGTGGTTCAAGCCGGGTTGAAC
                                        tgttctt  CT-rich tract
                            ttatctaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgctgctccatttcatattttcagtgcctattgcatggattttggttttgccttatgtgaactcatggcagttatctaaatcgtgttcttgatgacagGTTCGTTTGTGGTGCGCATAAAGACATGAACTGTGAGGAATGATACAAGTACAGTACGAAGATTCGACAGTATCTGCTTGTGGTTCAAGCCGGGTTGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
gctgctg
- - - - - - -ttcatat
- - - - - - - - - - - - - - - - -tgcatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catggca