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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttgcactgagctgtgtggccttaatgtccttgggaaaaaataaaaaatgagaacgcaggagctgatgaacgaccgggaactcctgacccttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCGGGTGAACCACGTGAGGCAGACGCACGAGTTCGTGGCGCGGATGCGGGCG

Basic information

species Zea mays
transcript GRMZM2G126900_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126900_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g36560.1 (Oryza sativa), 3'ss of exon 2
----ccttgcactgagctgtgtggccttaatgtccttgggaaaaaataaaaaatgagaacgcaggagctgatgaacgaccgggaactcctgacccttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCGGGTGAACCACGTGAGGCAGACGCACGAGTTCGTGGCGCGGATGCGGGCG
    |     | |||  | | |  |     ||    |   | | | |    ||  | || | |  | | |    |  |  | ||  |  | |  ||     |||| | || || || ||||| ||| ||||| ||||||| ||||||||||||||||| |||||| | |  |||||  | || |||                  
taatctagaaattgaaatctttttcaacggtggtagtaaaagatatttcttaaaaaaaaggaattaaccggaataatatggtgatgttttaaatctc----cagGAATTATGAGGCCGAGTCTGAGAGGAAGGAGACGGTGGAGGAGTTCTACCGGGTCAACCACATCAACCAGACATATGATTTC------------------
















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|148942392|gb|EC887411.2|EC887411
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAG                         GGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|19057958|gb|BM736625.1|BM736625
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAG                         GGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|211533476|gb|FL294724.1|FL294724
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTT-AG                         GAACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|211530464|gb|FL294704.1|FL294704
EST:     ACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTCTNAG                         GAACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGATTTCTACC
genomic: ACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCT-TCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACC
EST: gi|37424596|gb|CF650031.1|CF650031
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAG                         GGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|78086722|gb|DV515115.1|DV515115
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAG                         GGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|19821829|gb|BQ047853.1|BQ047853
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAG                         GGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|211530473|gb|FL294713.1|FL294713
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAG                         GAACTACGACGCGGA
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGA
EST: gi|18964769|gb|BM661199.1|BM661199
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAG                         GGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|211533475|gb|FL294723.1|FL294723
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAG                         GAACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|148939596|gb|EC884223.2|EC884223
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAG                         GGACTACCACGCGGAGTCCGAGCGGAAGCAGAAGGGAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|211533468|gb|FL294716.1|FL294716
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAG                         GAACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGATTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|211414693|gb|FL109921.1|FL109921
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGSAATACCTTCAG                         GAACTACGACGCGGAGT
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGT
EST: gi|211530472|gb|FL294712.1|FL294712
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAG                         GAACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|20300192|gb|BQ163135.1|BQ163135
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAG                         GGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|211530465|gb|FL294705.1|FL294705
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAG                         GAACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|211530467|gb|FL294707.1|FL294707
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTYNAG                         GAACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|211533473|gb|FL294721.1|FL294721
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAG                         GAACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGATTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|211530463|gb|FL294703.1|FL294703
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTYNAG                         GAACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGATTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|211533477|gb|FL294725.1|FL294725
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTYNAG                         GAACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|211533471|gb|FL294719.1|FL294719
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAG                         GAACTACGACGCGGAGT
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGT
EST: gi|15005365|gb|BI325432.1|BI325432
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAG                         GGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|211530466|gb|FL294706.1|FL294706
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAG                         GAACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|148962202|gb|EE013017.2|EE013017
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAG                         GGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|211530461|gb|FL294701.1|FL294701
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTYNAG                         GAACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGATTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|211530469|gb|FL294709.1|FL294709
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAG                         GAACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|211530474|gb|FL294714.1|FL294714
EST:     ACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCT-CTAG                         GAACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACC
genomic: ACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTC-AGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACC
EST: gi|211533478|gb|FL294726.1|FL294726
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTYYAG                         GAACTACGACGCGGAGTCSGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|211533469|gb|FL294717.1|FL294717
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTYNAG                         GAACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|211533474|gb|FL294722.1|FL294722
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGSAATACCTTCAG                         GAACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|211533470|gb|FL294718.1|FL294718
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTYNAG                         GAACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
EST: gi|15177491|gb|BI398430.1|BI398430
EST:     GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAG                         GGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG
genomic: GACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCG

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: 34 (upstream exon), 27 (downstream exon)
Score: 9

TGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGGTGCTCGACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCGGGTGAACCACGTGAGGCAGACGCACGAGTTCGTGGCGCGGATGCGGGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1024

TGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGGTGCTCGACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCGGGTGAACCACGTGAGGCAGACGCACGAGTTCGTGGCGCGGATGCGGGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 405

TGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGGTGCTCGACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCGGGTGAACCACGTGAGGCAGACGCACGAGTTCGTGGCGCGGATGCGGGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 446

TGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGGTGCTCGACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATACCTTCAGgtgaaacagc ... cttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCGGGTGAACCACGTGAGGCAGACGCACGAGTTCGTGGCGCGGATGCGGGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatgagaacgcaggagctgatgaacgaccgggaactcctgacccttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCGGGTGAACCACGTGAGGCAGACGCACGAGTTCGTGGCGCGGATGCGGGCG
                                     tcctgac  putative branch site (score: 446)
                                           ccctt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttgcactgagctgtgtggccttaatgtccttgggaaaaaataaaaaatgagaacgcaggagctgatgaacgaccgggaactcctgacccttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCGGGTGAACCACGTGAGGCAGACGCACGAGTTCGTGGCGCGGATGCGGGCG

-cttgcac
- - - - tgagctg
- - - - - - - - - - - - - -gtccttg
- - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgatg