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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatcccttgcagctgcaaaccatgtgtcatatgaaacatctaccttgccaatgcttcagatctcgctgccatttgcatctcctgtcaccgttccaagctgaccttgcaaaaactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACCGTGTGCTGATCGCGCGCGCCTGGGAAATGGAAGTCGAAGCGAGGGCCAC

Basic information

species Zea mays
transcript GRMZM2G037923_T02
intron # 16
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|78023792|gb|DV492179.1|DV492179
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|21432270|gb|BQ547760.1|BQ547760
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|22473314|gb|BU037794.1|BU037794
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|211493560|gb|FL280135.1|FL280135
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|101385454|gb|EB814773.1|EB814773
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|33096596|gb|CF056590.1|CF056590
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|211124333|gb|FL444269.1|FL444269
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTYTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|22713641|gb|BU197414.1|BU197414
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|211490684|gb|FL280131.1|FL280131
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|22545509|gb|BU097868.1|BU097868
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAAACTCTACATCGCTTCGATTTGCTTCGGGCGGA
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGA
EST: gi|4225592|gb|AI396045.1|AI396045
EST:     GACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: GACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|24770058|gb|CA405187.1|CA405187
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|61118390|gb|DN559351.1|DN559351
EST:     AGACACAGGAAACTCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|40303539|gb|CK347926.1|CK347926
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|32936218|gb|CF041030.1|CF041030
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|60353792|gb|DN220765.1|DN220765
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|32858553|gb|CD998234.1|CD998234
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|211490681|gb|FL280128.1|FL280128
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|21987385|gb|BQ778913.1|BQ778913
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|87156443|gb|DY401232.1|DY401232
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTA
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTA
EST: gi|78083128|gb|DV511521.1|DV511521
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|26559413|gb|CA831648.1|CA831648
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|67012040|gb|CO440789.1|CO440789
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|5058786|gb|AI737262.1|AI737262
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|31356845|gb|CD441202.1|CD441202
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|148933318|gb|EC876975.2|EC876975
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
EST: gi|31350536|gb|CD434893.1|CD434893
EST:     AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAG                         GAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC
genomic: AGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACC

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), 38 (downstream exon)
Score: 104

CGACCAAGCCGCTTTCATCCTGAGCATGCCGAAACGGAAGCCGATGGACGAGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACCGTGTGCTGATCGCGCGCGCCTGGGAAATGGAAGTCGAAGCGAGGGCCAC


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 43

CGACCAAGCCGCTTTCATCCTGAGCATGCCGAAACGGAAGCCGATGGACGAGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACCGTGTGCTGATCGCGCGCGCCTGGGAAATGGAAGTCGAAGCGAGGGCCAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 21

CGACCAAGCCGCTTTCATCCTGAGCATGCCGAAACGGAAGCCGATGGACGAGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACCGTGTGCTGATCGCGCGCGCCTGGGAAATGGAAGTCGAAGCGAGGGCCAC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 63

CGACCAAGCCGCTTTCATCCTGAGCATGCCGAAACGGAAGCCGATGGACGAGACACAGGAAACGCTGCGGACCTCCGCCTTCCCCAGCTCACACGTCAAGgtatatccct ... aactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACCGTGTGCTGATCGCGCGCGCCTGGGAAATGGAAGTCGAAGCGAGGGCCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgccatttgcatctcctgtcaccgttccaagctgaccttgcaaaaactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACCGTGTGCTGATCGCGCGCGCCTGGGAAATGGAAGTCGAAGCGAGGGCCAC
                              agctgac  putative branch site (score: 63)
                                          aaaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatcccttgcagctgcaaaccatgtgtcatatgaaacatctaccttgccaatgcttcagatctcgctgccatttgcatctcctgtcaccgttccaagctgaccttgcaaaaactccgtagGAGAAATGGGCCAAGAACCTCTACATCGCTTCGATTTGCTTCGGGCGGACCGTGTGCTGATCGCGCGCGCCTGGGAAATGGAAGTCGAAGCGAGGGCCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG