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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaatacaaatcacacgctccattattttttgttcgtgctgactcctgactagtaacgcacaatatctggttcttagTTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGGATACGGGCGCTACTGATTGATCTATTTCATAGTGCTCTAGACGACGATG

Basic information

species Zea mays
transcript GRMZM2G142553_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|149000476|gb|EE037652.2|EE037652
EST:     GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATG                         TTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGG
genomic: GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATGgtacaataca ... tggttcttagTTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGG
EST: gi|32945884|gb|CF050703.1|CF050703
EST:     GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATG                         TTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGG
genomic: GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATGgtacaataca ... tggttcttagTTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGG
EST: gi|193502411|gb|AM939258.1|AM939258
EST:     GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGAATG                         TTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAACGTTTCGGGGAGGG
genomic: GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATGgtacaataca ... tggttcttagTTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGG
EST: gi|93014963|gb|EB640483.1|EB640483
EST:     GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATG                         TTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGG
genomic: GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATGgtacaataca ... tggttcttagTTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGG
EST: gi|71305064|gb|DR788669.1|DR788669
EST:     GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATG                         TTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGG
genomic: GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATGgtacaataca ... tggttcttagTTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGG
EST: gi|193502468|gb|AM939287.1|AM939287
EST:     GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGG-ATG                         TTTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGG
genomic: GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATGgtacaataca ... tggttcttagTTT-GGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGG
EST: gi|86471376|gb|DY237746.1|DY237746
EST:     GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATG                         TTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGG
genomic: GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATGgtacaataca ... tggttcttagTTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGG
EST: gi|91048619|gb|EB159037.1|EB159037
EST:     GTTGACAAAAGAGGGCCTTGGCATG                         TTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGG
genomic: GTTGACAAAAGAGGGCCTTGGCATGgtacaataca ... tggttcttagTTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGG
EST: gi|148992843|gb|EE033670.2|EE033670
EST:     GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATG                         TTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGG
genomic: GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATGgtacaataca ... tggttcttagTTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGG
EST: gi|149000422|gb|EE037593.2|EE037593
EST:     GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATG                         TTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGG
genomic: GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATGgtacaataca ... tggttcttagTTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGG
EST: gi|110210546|gb|EC892443.1|EC892443
EST:     GGTTTATTCAAGATGCCCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATG                         TTTGGACGCAGATGGTTCACCCATGAAGAGGCTTCAGCGTTTCGGGGAGGG
genomic: GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATGgtacaataca ... tggttcttagTTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGG
EST: gi|71767171|gb|DR965108.1|DR965108
EST:     GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATG                         TTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGG
genomic: GGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATGgtacaataca ... tggttcttagTTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGG

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), 47 (downstream exon)
Score: 91

TCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTATATTGACAGGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATGgtacaataca ... tggttcttagTTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGGATACGGGCGCTACTGATTGATCTATTTCATAGTGCTCTAGACGACGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

TCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTATATTGACAGGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATGgtacaataca ... tggttcttagTTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGGATACGGGCGCTACTGATTGATCTATTTCATAGTGCTCTAGACGACGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 131

TCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTATATTGACAGGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATGgtacaataca ... tggttcttagTTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGGATACGGGCGCTACTGATTGATCTATTTCATAGTGCTCTAGACGACGATG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 59

TCAGCGTAACGAGTATGATTGTGGCCTCTTTATGCTTTACTATATTGACAGGTTTATTCAAGATGCGCCAGAGAGGTTGACAAAAGAGGGCCTTGGCATGgtacaataca ... tggttcttagTTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGGATACGGGCGCTACTGATTGATCTATTTCATAGTGCTCTAGACGACGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattttttgttcgtgctgactcctgactagtaacgcacaatatctggttcttagTTTGGACGCAGATGGTTCAACCATGAAGAGGCTTCAGCGTTTCGGGGAGGGATACGGGCGCTACTGATTGATCTATTTCATAGTGCTCTAGACGACGATG
                            tagtaac  putative branch site (score: 59)
                                                ttctt  putative PPT
     ttttgtt  TA-rich tract