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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaccttgcaattgcaaatacatacgactactgaatttactagtaataaaatgctagaattgagtaaggaagggataacataaaatcattttcccaaatcttacatttttttttcctttctgctctcctcacagCATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCATTCCATCTACGGCCAGTGACAATACGGG

Basic information

species Zea mays
transcript AC233960.1_FGT003
intron # 3
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|211234363|gb|FK958991.1|FK958991
EST:     GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGG                         CATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
genomic: GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGGgtatgtacct ... ctcctcacagCATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
EST: gi|211234353|gb|FK958981.1|FK958981
EST:     GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGG                         CATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
genomic: GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGGgtatgtacct ... ctcctcacagCATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
EST: gi|211339302|gb|FK958992.1|FK958992
EST:     GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGG                         CATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
genomic: GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGGgtatgtacct ... ctcctcacagCATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
EST: gi|211234359|gb|FK958987.1|FK958987
EST:     GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGG                         CATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
genomic: GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGGgtatgtacct ... ctcctcacagCATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
EST: gi|211234358|gb|FK958986.1|FK958986
EST:     GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGG                         CATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
genomic: GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGGgtatgtacct ... ctcctcacagCATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
EST: gi|211234356|gb|FK958984.1|FK958984
EST:     GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGG                         CATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
genomic: GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGGgtatgtacct ... ctcctcacagCATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
EST: gi|211234362|gb|FK958990.1|FK958990
EST:     GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGG                         CATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
genomic: GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGGgtatgtacct ... ctcctcacagCATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
EST: gi|211234357|gb|FK958985.1|FK958985
EST:     GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGG                         CATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
genomic: GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGGgtatgtacct ... ctcctcacagCATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
EST: gi|211234355|gb|FK958983.1|FK958983
EST:     GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGG                         CATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
genomic: GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGGgtatgtacct ... ctcctcacagCATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
EST: gi|211234361|gb|FK958989.1|FK958989
EST:     GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGG                         CATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
genomic: GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGGgtatgtacct ... ctcctcacagCATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
EST: gi|211234354|gb|FK958982.1|FK958982
EST:     GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGG                         CATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA
genomic: GCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGGgtatgtacct ... ctcctcacagCATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCA

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: 42 (upstream exon), 49 (downstream exon)
Score: 6

AAATACAGGCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGGgtatgtacct ... ctcctcacagCATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCATTCCATCTACGGCCAGTGACAATACGGG


Block sizes: 40 (upstream exon), 47 (downstream exon)
Score: 30

AAATACAGGCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGGgtatgtacct ... ctcctcacagCATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCATTCCATCTACGGCCAGTGACAATACGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 25

AAATACAGGCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGGgtatgtacct ... ctcctcacagCATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCATTCCATCTACGGCCAGTGACAATACGGG


Block sizes: 38 (upstream exon), 47 (downstream exon)
Score: 10

AAATACAGGCTTGGAAAGCAGACCAAGAAAGACACGGGTTTGGACGCCGGCAGAGGGGgtatgtacct ... ctcctcacagCATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCATTCCATCTACGGCCAGTGACAATACGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaaatcattttcccaaatcttacatttttttttcctttctgctctcctcacagCATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCATTCCATCTACGGCCAGTGACAATACGGG
                  atcttac  putative branch site (score: 10)
                   tcttacattttttttt  CT-rich tract
                aaatcttacatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtaccttgcaattgcaaatacatacgactactgaatttactagtaataaaatgctagaattgagtaaggaagggataacataaaatcattttcccaaatcttacatttttttttcctttctgctctcctcacagCATTCGCGGCGCAGGGCATCAATTTCTCCACACCAGTACCTCCTCCTAGCATTCCATCTACGGCCAGTGACAATACGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC