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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcaatgtgggggcaaaactgcttgtgataagaccattgtgttgcagaatgctgactcaaaagagttgttgaccatttttttgcattgatttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCAGAAGGAACTTCCTTAAGCCAGGCTGCTACATTTTTTGCAAACTCAGACC

Basic information

species Zea mays
transcript GRMZM2G145376_T01
intron # 2
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|211288680|gb|FL312631.1|FL312631
EST:     TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTG                         GTATTGACAATGGAGACTTTTGAGCACCTTG-ATTTTCTAGTTCAGTTCTC
genomic: TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTT-CTAGTTCAGTTCTC
EST: gi|148945185|gb|EC890388.2|EC890388
EST:     TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTG                         GTATTTGACA-TGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCT
genomic: TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATT-GACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCT
EST: gi|211208734|gb|FL358266.1|FL358266
EST:     TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTG                         GTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
genomic: TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
EST: gi|211012394|gb|FL319255.1|FL319255
EST:     TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTG                         GTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
genomic: TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
EST: gi|78079827|gb|DV508239.1|DV508239
EST:     TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTG                         GTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
genomic: TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
EST: gi|211392160|gb|FL368046.1|FL368046
EST:     TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTG                         GTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
genomic: TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
EST: gi|211260626|gb|FL351803.1|FL351803
EST:     TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTG                         GTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
genomic: TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
EST: gi|211089442|gb|FL362867.1|FL362867
EST:     TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTG                         GTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
genomic: TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
EST: gi|148935831|gb|EC879879.2|EC879879
EST:     TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTG                         GTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
genomic: TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
EST: gi|211303808|gb|FL321303.1|FL321303
EST:     TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTG                         GTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGCTCAG
genomic: TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAG
EST: gi|76934101|gb|DV173728.1|DV173728
EST:     TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTG                         GTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCA
genomic: TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCA
EST: gi|89762105|gb|DY689855.1|DY689855
EST:     TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTG                         GTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
genomic: TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
EST: gi|148946192|gb|EC891487.2|EC891487
EST:     TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTG                         GTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCA
genomic: TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCA
EST: gi|211424273|gb|FL309087.1|FL309087
EST:     TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTG                         GTATTGACAATGGAGACTTTTGAGCACCTTGGATTTTCTAGTTCAGTTCTC
genomic: TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTT-CTAGTTCAGTTCTC
EST: gi|149011570|gb|EE042404.2|EE042404
EST:     TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTG                         GTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
genomic: TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
EST: gi|211316366|gb|FL341233.1|FL341233
EST:     TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTG                         GTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
genomic: TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
EST: gi|148978503|gb|EE026182.2|EE026182
EST:     TTCTTACTCTCTTGGCACATTCTGTTGAGGGTGAGGGTGACGATTCACTG                         GTATTGACAATGGAGACTTTTGAGCAGCTTGGATTTCTAGTTCTGTTCTCA
genomic: TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
EST: gi|211263174|gb|FL356041.1|FL356041
EST:     TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTG                         GTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
genomic: TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
EST: gi|211390755|gb|FL310442.1|FL310442
EST:     TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTG                         GNATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA
genomic: TTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCA

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), 48 (downstream exon)
Score: 135

TGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCAGAAGGAACTTCCTTAAGCCAGGCTGCTACATTTTTTGCAAACTCAGACC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 73

TGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCAGAAGGAACTTCCTTAAGCCAGGCTGCTACATTTTTTGCAAACTCAGACC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 70

TGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCAGAAGGAACTTCCTTAAGCCAGGCTGCTACATTTTTTGCAAACTCAGACC


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 169

TGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTCTCTTGGCAGATTCTGTTGAGGGTGAGGGTGACGATTCACTGgtatgccacc ... ttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCAGAAGGAACTTCCTTAAGCCAGGCTGCTACATTTTTTGCAAACTCAGACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaatgctgactcaaaagagttgttgaccatttttttgcattgatttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCAGAAGGAACTTCCTTAAGCCAGGCTGCTACATTTTTTGCAAACTCAGACC
                                            tttttac  CT-rich tract
                             atttttttgcattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcaatgtgggggcaaaactgcttgtgataagaccattgtgttgcagaatgctgactcaaaagagttgttgaccatttttttgcattgatttttacgcagGTATTGACAATGGAGACTTTTGAGCACCTTGGATTTCTAGTTCAGTTCTCAGAAGGAACTTCCTTAAGCCAGGCTGCTACATTTTTTGCAAACTCAGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- caatgtg
- - - - - - - - - -tgcttgt
- - - - - - - - - - - - - - - - - - - -tgttgca
- - - - - - - - - - - - - - - - - - - - - - - - -tgctgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaagag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgttga