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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgtttgtcaactactagttgtttaagtagcctcctgctcttatattttcgatatgctttggggggggggggggggggggggcgtttaagttgctt...

Basic information

species Zea mays
transcript GRMZM2G134582_T01
intron # 2
splice site 5'
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|211419497|gb|FK986932.1|FK986932
EST:     ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|211299931|gb|FL223399.1|FL223399
EST:     ATCTGAGATCGAGCG-A-MKAAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|211419502|gb|FK986937.1|FK986937
EST:     ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|211269909|gb|FK986924.1|FK986924
EST:     AAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: AAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|17930924|gb|BM267884.1|BM267884
EST:     ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|15053873|gb|BI359418.1|BI359418
EST:     ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|211269911|gb|FK986926.1|FK986926
EST:     ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|31354444|gb|CD438801.1|CD438801
EST:     ATCTCATATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|15209068|gb|BI430952.1|BI430952
EST:     CTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: CTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|50333934|gb|CO529060.1|CO529060
EST:     ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|211269910|gb|FK986925.1|FK986925
EST:     ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|211419500|gb|FK986935.1|FK986935
EST:     AAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: AAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|21891605|gb|BQ744818.1|BQ744818
EST:     ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGG-GCTT                         GTACTGCATGCTAACANG-GGTAACAAAAATGCATTCAAAACACTAATTGC
genomic: ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACA-GTGGTAACAAAAATGCATTCAAAACACTAATTGC
EST: gi|211244386|gb|FL238837.1|FL238837
EST:     ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|211269915|gb|FK986930.1|FK986930
EST:     ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|60398445|gb|DN231261.1|DN231261
EST:     ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|211512831|gb|FL354907.1|FL354907
EST:     ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|31354453|gb|CD438810.1|CD438810
EST:     ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|67020169|gb|CO448918.1|CO448918
EST:     ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|211269908|gb|FK986923.1|FK986923
EST:     AAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: AAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|60399613|gb|DN232423.1|DN232423
EST:     ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|6020992|gb|AW065920.1|AW065920
EST:     ATCTGAGATCGTGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
EST: gi|14529440|gb|BI096573.1|BI096573
EST:     CGATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTT                         GTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC
genomic: CGATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCC

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: 47 (upstream exon), 48 (downstream exon)
Score: 75

ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCCGCAGAATACAGCGGTGTCAAGGTTGAGTTGGTGAAGGACTTTCAAATGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 110

ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCCGCAGAATACAGCGGTGTCAAGGTTGAGTTGGTGAAGGACTTTCAAATGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 103

ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCCGCAGAATACAGCGGTGTCAAGGTTGAGTTGGTGAAGGACTTTCAAATGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 150

ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgttt ... cattgtgtagGTACTGCATGCTAACAGTGGTAACAAAAATGCATTCAAAACACTAATTGCCGCAGAATACAGCGGTGTCAAGGTTGAGTTGGTGAAGGACTTTCAAATGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTGAGATCGAGCGAAGCTAAGCTTTTTCATCGAGATGGTGCTTgtaagtgtttgtcaactactagttgtttaagtagcctcctgctcttatattttcgatatgctttggggggggggggggggggggggcgtttaagttgctt

- - GAGATC
- - - - - - - - - - - - - - - -  GAGATG