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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggaaacattctttaagatttatcgttggaataatcagttaatcactagcgcttagttaacaccggtcagtttggttagtttttctaatcagcattttatagaacttcgatccatggtgacctaattctccttgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA

Basic information

species Zea mays
transcript GRMZM2G029566_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029566_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g10310.1 (Oryza sativa), 3'ss of exon 9
gtgaggaaacattctttaagatttatcgttggaataatcagttaatcactagcgct-tagttaacaccggtcagtttggttagtttttctaatcagcattttatagaacttcgatccatggtgacctaattctccttgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA
                                     | ||    ||  |||   | ||||  | |   || |      ||    ||   ||||| |||||||| |  ||  |      | | |  ||| |  | |||| |  |||||||| || ||||| || |||||||| |||||||| ||| |||| || || ||||||||||| 
------------------------------------gtgagcatgtc-ttagtattatagtatata---gttaaccatattttccttgagaatcatcattttattgttctatg------gataaattaaattgctttgcgtggcagGAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGATATTCCTCTTGAG
















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|76920585|gb|DV168249.1|DV168249
EST:     TTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAG                         GAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
genomic: TTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAGgtgaggaaac ... tgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
EST: gi|31355627|gb|CD439984.1|CD439984
EST:     TTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAG                         GAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
genomic: TTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAGgtgaggaaac ... tgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
EST: gi|32851376|gb|CD991057.1|CD991057
EST:     TTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAG                         GAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
genomic: TTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAGgtgaggaaac ... tgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
EST: gi|211248919|gb|FL466732.1|FL466732
EST:     TTGTTACCCTAGATGC-TTGAAGCCTTTCATGTGTGATGCTCCTAAGCAG                         GAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
genomic: TTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAGgtgaggaaac ... tgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
EST: gi|71328227|gb|DR800747.1|DR800747
EST:     TTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAG                         GAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
genomic: TTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAGgtgaggaaac ... tgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
EST: gi|78124352|gb|DV542736.1|DV542736
EST:     TTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAG                         GAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
genomic: TTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAGgtgaggaaac ... tgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
EST: gi|60346412|gb|DN213385.1|DN213385
EST:     TTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAG                         GAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
genomic: TTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAGgtgaggaaac ... tgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
EST: gi|211059340|gb|FL474462.1|FL474462
EST:     GTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAG                         GAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
genomic: GTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAGgtgaggaaac ... tgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
EST: gi|91052882|gb|EB163300.1|EB163300
EST:     TGTTTCCCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAG                         GAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
genomic: TG-TTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAGgtgaggaaac ... tgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
EST: gi|149042086|gb|EE047064.2|EE047064
EST:     CCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAG                         GAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
genomic: CCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAGgtgaggaaac ... tgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
EST: gi|148946153|gb|EC891447.2|EC891447
EST:     TTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAG                         GAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
genomic: TTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAGgtgaggaaac ... tgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
EST: gi|86465953|gb|DY232326.1|DY232326
EST:     TTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAG                         GAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
genomic: TTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAGgtgaggaaac ... tgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
EST: gi|149076832|gb|EE165487.2|EE165487
EST:     GCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAG                         GAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC
genomic: GCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAGgtgaggaaac ... tgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGAC

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: 46 (upstream exon), 49 (downstream exon)
Score: 224

GTACCACGGTATCACCATGGATTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAGgtgaggaaac ... tgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 292

GTACCACGGTATCACCATGGATTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAGgtgaggaaac ... tgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 237

GTACCACGGTATCACCATGGATTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAGgtgaggaaac ... tgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1759

GTACCACGGTATCACCATGGATTGTTACCCTAGATGCTTTGAAGCCTTTCATGTGTGATGCTCCTAAGCAGgtgaggaaac ... tgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcagcattttatagaacttcgatccatggtgacctaattctccttgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA
                                      ttctccttgc  CT-rich tract
      attttatagaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggaaacattctttaagatttatcgttggaataatcagttaatcactagcgcttagttaacaccggtcagtttggttagtttttctaatcagcattttatagaacttcgatccatggtgacctaattctccttgcattacagGAACCCGAGCCTTTACCGTACTTAGCCGAAAAGAATCACATAAATTATGACATTCCTCTTGAA

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