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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagaactcaattcagttcatccatgctagtaacctatgtctaccaaagaatgtgtattgtgtggctcaccggttgtaatttcttaatatgtttcagGGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCCGTCTCTACAATGATTTTAATACCCTGCCGCGCAGTAGTGCTTAGTTCCT

Basic information

species Zea mays
transcript GRMZM2G010085_T01
intron # 21
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|60394449|gb|DN227319.1|DN227319
EST:     GTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCTCG                         GGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCC
genomic: GTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCTCGgtaagagaac ... tatgtttcagGGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCC
EST: gi|60399555|gb|DN232366.1|DN232366
EST:     GTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCTCG                         GGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCC
genomic: GTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCTCGgtaagagaac ... tatgtttcagGGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCC
EST: gi|5901273|gb|AW042373.1|AW042373
EST:     GTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCTCG                         GGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCC
genomic: GTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCTCGgtaagagaac ... tatgtttcagGGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCC
EST: gi|61119150|gb|DN560111.1|DN560111
EST:     GTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCCCG                         GGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCC
genomic: GTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCTCGgtaagagaac ... tatgtttcagGGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCC
EST: gi|60342830|gb|DN209803.1|DN209803
EST:     GTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCTCG                         GGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCC
genomic: GTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCTCGgtaagagaac ... tatgtttcagGGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCC
EST: gi|60338945|gb|DN205918.1|DN205918
EST:     GTTCATTCAAGAGAAGACGGCAGTCCCTTATGGACGACTATGTGGGCTCG                         GGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCC
genomic: GTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCTCGgtaagagaac ... tatgtttcagGGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCC
EST: gi|78022398|gb|DV490785.1|DV490785
EST:     GTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCTCG                         GGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCC
genomic: GTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCTCGgtaagagaac ... tatgtttcagGGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCC
EST: gi|109179402|gb|EC379969.1|EC379969
EST:     GTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCTCG                         GGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCC
genomic: GTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCTCGgtaagagaac ... tatgtttcagGGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCC
EST: gi|5915179|gb|AW052820.1|AW052820
EST:     GTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCTCG                         GGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCC
genomic: GTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCTCGgtaagagaac ... tatgtttcagGGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCC

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: 256

AACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAATACTCCACCGAGTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCTCGgtaagagaac ... tatgtttcagGGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCCGTCTCTACAATGATTTTAATACCCTGCCGCGCAGTAGTGCTTAGTTCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 61

AACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAATACTCCACCGAGTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCTCGgtaagagaac ... tatgtttcagGGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCCGTCTCTACAATGATTTTAATACCCTGCCGCGCAGTAGTGCTTAGTTCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57

AACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAATACTCCACCGAGTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCTCGgtaagagaac ... tatgtttcagGGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCCGTCTCTACAATGATTTTAATACCCTGCCGCGCAGTAGTGCTTAGTTCCT


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 65

AACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAATACTCCACCGAGTTCATTCAAGAGACGACGGCAGTCCCTTATGGACGACTATGTGGGCTCGgtaagagaac ... tatgtttcagGGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCCGTCTCTACAATGATTTTAATACCCTGCCGCGCAGTAGTGCTTAGTTCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accaaagaatgtgtattgtgtggctcaccggttgtaatttcttaatatgtttcagGGAAAGCGTAAGAGAGGCTGACCACGTTTGGCATCCTCCCTTAGACATGCCGTCTCTACAATGATTTTAATACCCTGCCGCGCAGTAGTGCTTAGTTCCT
                                       tcttaat  putative branch site (score: 65)
                               ttgtaatttcttaata  TA-rich tract