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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtctgaccgggcgcgacctcatggggcgcttgctggcgcggtttgctgatcaaaatggggtctttctcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTTCGGGGCATTCGTCGGTTTGTCTGTCGGTGACGGTGGTGCTGCGTTTCGA

Basic information

species Zea mays
transcript GRMZM2G063511_T01
intron # 1
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|211307063|gb|FL384792.1|FL384792
EST:     TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAATCCGACCGCA-GAGC-                         GTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
genomic: TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCGgtaggtctga ... tcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
EST: gi|78113976|gb|DV532365.1|DV532365
EST:     TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCG                         GTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
genomic: TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCGgtaggtctga ... tcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
EST: gi|211294862|gb|FL410180.1|FL410180
EST:     TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAATCCGACCGCAGGAGCG                         GTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
genomic: TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCGgtaggtctga ... tcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
EST: gi|211509433|gb|FL413814.1|FL413814
EST:     TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAATCCGACCGCAGGAGCG                         GTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
genomic: TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCGgtaggtctga ... tcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
EST: gi|211425863|gb|FL372097.1|FL372097
EST:     TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAATCCGACCGCAGGAGCG                         GTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGT
genomic: TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCGgtaggtctga ... tcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGT
EST: gi|148991668|gb|EE033210.2|EE033210
EST:     TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCG                         GTGCACCGCGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
genomic: TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCGgtaggtctga ... tcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
EST: gi|211321010|gb|FL370064.1|FL370064
EST:     TCGCTCATATCTGATAGCGGCTCTGATTTTCCAATCCGACCGCAGGAGCG                         GTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
genomic: TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCGgtaggtctga ... tcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
EST: gi|71303455|gb|DR787837.1|DR787837
EST:     TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCG                         GTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
genomic: TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCGgtaggtctga ... tcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
EST: gi|211425870|gb|FL372104.1|FL372104
EST:     TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAATCCGACCGCAGGAGCG                         GTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
genomic: TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCGgtaggtctga ... tcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
EST: gi|148934066|gb|EC878080.2|EC878080
EST:     TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCG                         GTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
genomic: TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCGgtaggtctga ... tcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
EST: gi|74238674|gb|DT646588.1|DT646588
EST:     TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCG                         GTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
genomic: TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCGgtaggtctga ... tcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
EST: gi|211209581|gb|FL394646.1|FL394646
EST:     TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAATCCGACCGCAGGAGCG                         GTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
genomic: TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCGgtaggtctga ... tcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
EST: gi|76281072|gb|DV020640.1|DV020640
EST:     TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCG                         GTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
genomic: TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCGgtaggtctga ... tcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
EST: gi|71770743|gb|DR968680.1|DR968680
EST:     TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCG                         GTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
genomic: TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCGgtaggtctga ... tcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
EST: gi|71444391|gb|DR825441.1|DR825441
EST:     TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCG                         GTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT
genomic: TCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCGgtaggtctga ... tcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTT

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), 49 (downstream exon)
Score: 69

CCCAGATCTCGTCTCCATTAAAGCCGACCTTGCCCAGATTCGCGCCCTCCTCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCGgtaggtctga ... tcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTTCGGGGCATTCGTCGGTTTGTCTGTCGGTGACGGTGGTGCTGCGTTTCGA


Block sizes: 42 (upstream exon), 42 (downstream exon)
Score: 21

CCCAGATCTCGTCTCCATTAAAGCCGACCTTGCCCAGATTCGCGCCCTCCTCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCGgtaggtctga ... tcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTTCGGGGCATTCGTCGGTTTGTCTGTCGGTGACGGTGGTGCTGCGTTTCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 35

CCCAGATCTCGTCTCCATTAAAGCCGACCTTGCCCAGATTCGCGCCCTCCTCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCGgtaggtctga ... tcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTTCGGGGCATTCGTCGGTTTGTCTGTCGGTGACGGTGGTGCTGCGTTTCGA


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

CCCAGATCTCGTCTCCATTAAAGCCGACCTTGCCCAGATTCGCGCCCTCCTCGCTCATATCTGAAAGCGGCTCTGATTTTCCAAGCCGACCGCAGGAGCGgtaggtctga ... tcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTTCGGGGCATTCGTCGGTTTGTCTGTCGGTGACGGTGGTGCTGCGTTTCGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggggcgcttgctggcgcggtttgctgatcaaaatggggtctttctcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTTCGGGGCATTCGTCGGTTTGTCTGTCGGTGACGGTGGTGCTGCGTTTCGA
                      tgctgat  putative branch site (score: 110)
                                       tctttctc  putative PPT
                           atcaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtctgaccgggcgcgacctcatggggcgcttgctggcgcggtttgctgatcaaaatggggtctttctcggctgcagGTGCACCGGGCCGCGTGATTCCGGCGGCTTGATTTGGAATTTGTGATCTTTCGGGGCATTCGTCGGTTTGTCTGTCGGTGACGGTGGTGCTGCGTTTCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC