Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgagttgtggttgcaatcttgttgcttttagtcagtatgatttgaacagtacattgctgaatttgcgcctgaccttactgcactatgtattcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTGTTGGTCATGGCTGCGCTGACCTTGCAGCACTGCTGGCGAGTGGCATGCC

Basic information

species Zea mays
transcript GRMZM2G102021_T01
intron # 6
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|33285553|gb|CF075348.1|CF075348
EST:     AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATG                         ACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
genomic: AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
EST: gi|67020084|gb|CO448833.1|CO448833
EST:     AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATG                         ACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
genomic: AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
EST: gi|50328020|gb|CO523146.1|CO523146
EST:     AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATG                         ACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
genomic: AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
EST: gi|86468508|gb|DY234878.1|DY234878
EST:     AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATG                         ACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
genomic: AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
EST: gi|211072382|gb|FL433877.1|FL433877
EST:     AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATG                         ACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
genomic: AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
EST: gi|166698820|gb|EG068824.1|EG068824
EST:     AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATG                         ACACTTGTTAACCTCGCCCCAGGAGG
genomic: AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGG
EST: gi|22818907|gb|BU498997.1|BU498997
EST:     AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATG                         ACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
genomic: AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
EST: gi|211105116|gb|FL057782.1|FL057782
EST:     AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATG                         ACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
genomic: AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
EST: gi|149048871|gb|EE048372.2|EE048372
EST:     AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATG                         ACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
genomic: AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
EST: gi|87155707|gb|DY400496.1|DY400496
EST:     AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATG                         ACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
genomic: AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
EST: gi|148946111|gb|EC891405.2|EC891405
EST:     AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATG                         ACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
genomic: AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
EST: gi|91876597|gb|EB406554.1|EB406554
EST:     AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATG                         ACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
genomic: AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
EST: gi|113607274|gb|DW776952.1|DW776952
EST:     ATTTGGCTGCTGCTGCGATG                         ACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
genomic: ATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
EST: gi|113703076|gb|EE680580.1|EE680580
EST:     AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATG                         ACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
genomic: AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
EST: gi|37395770|gb|CF635168.1|CF635168
EST:     AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATG                         ACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
genomic: AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
EST: gi|33091816|gb|CF051810.1|CF051810
EST:     AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATG                         ACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
genomic: AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
EST: gi|211503758|gb|FL479708.1|FL479708
EST:     AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATG                         ACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
genomic: AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
EST: gi|40336955|gb|CK371025.1|CK371025
EST:     AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATG                         ACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
genomic: AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
EST: gi|148946112|gb|EC891406.2|EC891406
EST:     AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATG                         ACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG
genomic: AAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTG

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: 182

CCATACATTCTCAATGATTATTGCTTTTAATGCATATGACGAGGGAAAGAAAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTGTTGGTCATGGCTGCGCTGACCTTGCAGCACTGCTGGCGAGTGGCATGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

CCATACATTCTCAATGATTATTGCTTTTAATGCATATGACGAGGGAAAGAAAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTGTTGGTCATGGCTGCGCTGACCTTGCAGCACTGCTGGCGAGTGGCATGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

CCATACATTCTCAATGATTATTGCTTTTAATGCATATGACGAGGGAAAGAAAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTGTTGGTCATGGCTGCGCTGACCTTGCAGCACTGCTGGCGAGTGGCATGCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 113

CCATACATTCTCAATGATTATTGCTTTTAATGCATATGACGAGGGAAAGAAAAGTGATCAAGTCTTTGTTCCAGTAATTCATTTGGCTGCTGCTGCGATGgtaagaacca ... ttcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTGTTGGTCATGGCTGCGCTGACCTTGCAGCACTGCTGGCGAGTGGCATGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacagtacattgctgaatttgcgcctgaccttactgcactatgtattcatttcagACACTTGTTAACCTCGCCCCAGGAGGCTGTCTCATTGGTACCCCGCTGTTGTTGGTCATGGCTGCGCTGACCTTGCAGCACTGCTGGCGAGTGGCATGCC
                           accttac  putative branch site (score: 113)
                                             ttcatttc  putative PPT
                                           tattcattt  TA-rich tract