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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaattagattatttgggagtgaatgttcagtttgttgaaattgagctccaaccaggcaggtcatgaccatagtcttgactgttttatcttgaattgcagGTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTG

Basic information

species Zea mays
transcript GRMZM2G112609_T01
intron # 4
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|6601841|gb|AW256282.1|AW256282
EST:     ATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGG                         GTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTC
genomic: ATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGGgtaaatgttc ... tgaattgcagGTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTC
EST: gi|76917920|gb|DV167073.1|DV167073
EST:     ATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGG                         GTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTC
genomic: ATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGGgtaaatgttc ... tgaattgcagGTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTC
EST: gi|91048268|gb|EB158686.1|EB158686
EST:     ATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGG                         GTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTC
genomic: ATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGGgtaaatgttc ... tgaattgcagGTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTC
EST: gi|211076091|gb|FL368274.1|FL368274
EST:     ATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGG                         GTTCTTTNGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTC
genomic: ATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGGgtaaatgttc ... tgaattgcagGTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTC
EST: gi|50333879|gb|CO529005.1|CO529005
EST:     ATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGG                         GTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTC
genomic: ATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGGgtaaatgttc ... tgaattgcagGTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTC
EST: gi|56382233|gb|CV984902.1|CV984902
EST:     ATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGG                         GTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTC
genomic: ATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGGgtaaatgttc ... tgaattgcagGTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTC
EST: gi|76012317|gb|DT939487.1|DT939487
EST:     ATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGG                         GTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTC
genomic: ATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGGgtaaatgttc ... tgaattgcagGTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTC
EST: gi|91878613|gb|EB408570.1|EB408570
EST:     ATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGG                         GTTCTTTTGGGC
genomic: ATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGGgtaaatgttc ... tgaattgcagGTTCTTTTGGGC
EST: gi|148970116|gb|EE021054.2|EE021054
EST:     TATGAGCTTTCTGGGCCTGTTTACCTTTACCGGCTGCGTACTTACCATGG                         GTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTC
genomic: TATGAGCTTTCTGGGCCTGTTTACCTTTAC-GGCTGCGTACTTACCATGGgtaaatgttc ... tgaattgcagGTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTC
EST: gi|60342635|gb|DN209608.1|DN209608
EST:     ATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGG                         GTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTC
genomic: ATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGGgtaaatgttc ... tgaattgcagGTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTC

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: 48 (upstream exon), 49 (downstream exon)
Score: 135

GTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGGgtaaatgttc ... tgaattgcagGTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 136

GTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGGgtaaatgttc ... tgaattgcagGTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 93

GTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGGgtaaatgttc ... tgaattgcagGTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 163

GTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGGgtaaatgttc ... tgaattgcagGTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctccaaccaggcaggtcatgaccatagtcttgactgttttatcttgaattgcagGTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTG
                            tcttgac  putative branch site (score: 163)
                                     ttttatctt  putative PPT
                                     ttttatcttgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaattagattatttgggagtgaatgttcagtttgttgaaattgagctccaaccaggcaggtcatgaccatagtcttgactgttttatcttgaattgcagGTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - -gtgaatg
- - - - - - - - - - - - - - - -tttgttg
- - - - - - - - - - - - - - - - - - - - - - agctcca
- - - - - - - - - - - - - - - - - - - - - - - - - - ccaggca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgacc