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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatttgttgacgcacgttataaaatattcacattaatttgtcacatcctaatagtttctattctggctcacatgtatgagagtctgtcatctcattgcagGAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTATATCTGTCTTGTCGCG

Basic information

species Zea mays
transcript GRMZM2G136389_T03
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|89247752|gb|DY619538.1|DY619538
EST:     CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG                         GAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
genomic: CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAGgtacttgtgt ... ctcattgcagGAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
EST: gi|78114509|gb|DV532898.1|DV532898
EST:     CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG                         GAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
genomic: CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAGgtacttgtgt ... ctcattgcagGAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
EST: gi|76291396|gb|DV030964.1|DV030964
EST:     CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG                         GAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
genomic: CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAGgtacttgtgt ... ctcattgcagGAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
EST: gi|89758710|gb|DY687791.1|DY687791
EST:     CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG                         GAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
genomic: CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAGgtacttgtgt ... ctcattgcagGAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
EST: gi|50323554|gb|CO518680.1|CO518680
EST:     CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG                         GAATTCCATGCATTTAAGAAGAGGATGCA-CACACAACATAGAGAGAAGTA
genomic: CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAGgtacttgtgt ... ctcattgcagGAATTCCATGCATTAAAGAAGAG-ATGCAACACACAACATAGAGAGAAGTA
EST: gi|18963822|gb|BM660649.1|BM660649
EST:     CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG                         GAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
genomic: CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAGgtacttgtgt ... ctcattgcagGAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
EST: gi|71431215|gb|DR812265.1|DR812265
EST:     CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG                         GAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
genomic: CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAGgtacttgtgt ... ctcattgcagGAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
EST: gi|101382964|gb|EB813535.1|EB813535
EST:     CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG                         GAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
genomic: CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAGgtacttgtgt ... ctcattgcagGAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
EST: gi|91876453|gb|EB406410.1|EB406410
EST:     CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG                         GAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
genomic: CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAGgtacttgtgt ... ctcattgcagGAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
EST: gi|94472235|gb|EB701193.1|EB701193
EST:     CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG                         GAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
genomic: CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAGgtacttgtgt ... ctcattgcagGAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
EST: gi|87153075|gb|DY397864.1|DY397864
EST:     CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG                         GAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
genomic: CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAGgtacttgtgt ... ctcattgcagGAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
EST: gi|71429124|gb|DR810174.1|DR810174
EST:     CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG                         GAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
genomic: CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAGgtacttgtgt ... ctcattgcagGAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
EST: gi|71307824|gb|DR790133.1|DR790133
EST:     CTATGGTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG                         GAATTCCCTGCCTTAGAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
genomic: CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAGgtacttgtgt ... ctcattgcagGAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
EST: gi|149009815|gb|EE041700.2|EE041700
EST:     CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG                         GAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT
genomic: CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAGgtacttgtgt ... ctcattgcagGAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTAT

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: 48 (upstream exon), 40 (downstream exon)
Score: 58

CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAGgtacttgtgt ... ctcattgcagGAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTATATCTGTCTTGTCGCG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 110

CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAGgtacttgtgt ... ctcattgcagGAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTATATCTGTCTTGTCGCG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 97

CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAGgtacttgtgt ... ctcattgcagGAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTATATCTGTCTTGTCGCG


Block sizes: 48 (upstream exon), 37 (downstream exon)
Score: 95

CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAGgtacttgtgt ... ctcattgcagGAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTATATCTGTCTTGTCGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctaatagtttctattctggctcacatgtatgagagtctgtcatctcattgcagGAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTATATCTGTCTTGTCGCG
                                         tcatctc  CT-rich tract
         tttctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatttgttgacgcacgttataaaatattcacattaatttgtcacatcctaatagtttctattctggctcacatgtatgagagtctgtcatctcattgcagGAATTCCATGCATTAAAGAAGAGATGCAACACACAACATAGAGAGAAGTATATCTGTCTTGTCGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- tttgttg
- - - - - - - - - - - - - - - - - - - - -cacatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgtatg