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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattattagatgcatgtcccattttggttcttacctatgcttttgtacttggtgaaaatgatgatcacttgatgttgcagCGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAG

Basic information

species Zea mays
transcript GRMZM2G138125_T03
intron # 10
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|28873896|gb|CB329825.1|CB329825
EST:     AAGTTGGTCAGGATGTCTCATGCAAGCTATCATTCATCATGTCCTTGTTG                         CGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGT
genomic: AAGTTGGTCAGGATGTCTCATGCAAGCTATCATTCATCATGTCCTTGTTGgtaagtatta ... gatgttgcagCGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGT
EST: gi|67035224|gb|CO463757.1|CO463757
EST:     AAGTTGGTCAGGATGTCTCATGCAAGCTATCATTCATCATGTCCTTGTTG                         CGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGT
genomic: AAGTTGGTCAGGATGTCTCATGCAAGCTATCATTCATCATGTCCTTGTTGgtaagtatta ... gatgttgcagCGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGT
EST: gi|28987103|gb|CB351465.1|CB351465
EST:     AAGTTGGTCAGGATGTCTCATGCAAGCTATCATTCATCATGTCCTTGTTG                         CGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGT
genomic: AAGTTGGTCAGGATGTCTCATGCAAGCTATCATTCATCATGTCCTTGTTGgtaagtatta ... gatgttgcagCGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGT
EST: gi|31909131|gb|CD650765.1|CD650765
EST:     AAGTTGGTCAGGATGTCTCATGCAAGCTATCATTCATCATGTCCTTGTTG                         CGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGT
genomic: AAGTTGGTCAGGATGTCTCATGCAAGCTATCATTCATCATGTCCTTGTTGgtaagtatta ... gatgttgcagCGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGT
EST: gi|28930971|gb|CB334332.1|CB334332
EST:     AAGTTGGTCAGGATGTCTCATGCAAGCTATCATTCATCATGTCCTTGTTG                         CGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGT
genomic: AAGTTGGTCAGGATGTCTCATGCAAGCTATCATTCATCATGTCCTTGTTGgtaagtatta ... gatgttgcagCGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGT

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: 47 (upstream exon), 49 (downstream exon)
Score: 206

AAAAATGGCCATGAACCTTGCAGATATGGCTCATGATGATAATGCACTGGAAGTTGGTCAGGATGTCTCATGCAAGCTATCATTCATCATGTCCTTGTTGgtaagtatta ... gatgttgcagCGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 36

AAAAATGGCCATGAACCTTGCAGATATGGCTCATGATGATAATGCACTGGAAGTTGGTCAGGATGTCTCATGCAAGCTATCATTCATCATGTCCTTGTTGgtaagtatta ... gatgttgcagCGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 33

AAAAATGGCCATGAACCTTGCAGATATGGCTCATGATGATAATGCACTGGAAGTTGGTCAGGATGTCTCATGCAAGCTATCATTCATCATGTCCTTGTTGgtaagtatta ... gatgttgcagCGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 42

AAAAATGGCCATGAACCTTGCAGATATGGCTCATGATGATAATGCACTGGAAGTTGGTCAGGATGTCTCATGCAAGCTATCATTCATCATGTCCTTGTTGgtaagtatta ... gatgttgcagCGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttcttacctatgcttttgtacttggtgaaaatgatgatcacttgatgttgcagCGGAACCTTGTTGGAGAGGGGCATCATGTTTTAATATTTTCACAGACTCGTAAAATGCTAAACCTTATTCAG
                             aaaatgat  TA-rich tract