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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcagtcaacgccgtatgctttcttccttttcagaaaaaaaaaactactcctttgtgctcatagcttgcctacatcctttccagATTACAGTTGACTGCATCGAAGGTTATCCACCGGTCAGTTTACTGCTAGGAAAGCACGTTTTCCTAAGTGCAGGGGATTTTTATCTGGCTAGTCGATCCT

Basic information

species Zea mays
transcript GRMZM2G158627_T02
intron # 13
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|71432888|gb|DR813938.1|DR813938
EST:     CAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATG                         ATTACAGTTGACTG
genomic: CAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATGgtaagcagtc ... tcctttccagATTACAGTTGACTG
EST: gi|60345148|gb|DN212121.1|DN212121
EST:     CAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATG                         ATTACAGTTGACTGCATCGAAGGTTATCCACCGGTCAGTTTACTGCTAGGA
genomic: CAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATGgtaagcagtc ... tcctttccagATTACAGTTGACTGCATCGAAGGTTATCCACCGGTCAGTTTACTGCTAGGA
EST: gi|78022271|gb|DV490658.1|DV490658
EST:     CAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATG                         ATTACAGTTGACTGCATCGAAGGTTATCCACCGGTCAGTTTACTGCTAGGA
genomic: CAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATGgtaagcagtc ... tcctttccagATTACAGTTGACTGCATCGAAGGTTATCCACCGGTCAGTTTACTGCTAGGA
EST: gi|74240586|gb|DT648500.1|DT648500
EST:     CAAGGTCTCTTTCCAGATTGA-GAAACAGTTCCAAGCTGGGAAGGGCATG                         ATTACAGTTGACTG
genomic: CAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATGgtaagcagtc ... tcctttccagATTACAGTTGACTG
EST: gi|45568479|gb|CK986083.1|CK986083
EST:     CAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATG                         ATTACAGTTGACTGCATCGAAGGTTATCCACCGGTCAGTTTACTGCTAGGA
genomic: CAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATGgtaagcagtc ... tcctttccagATTACAGTTGACTGCATCGAAGGTTATCCACCGGTCAGTTTACTGCTAGGA
EST: gi|113702485|gb|EE679989.1|EE679989
EST:     CAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATG                         ATTACAGTTGACTGCATCGAAGGTTATCCACCGGTCAGTTTACTGCTAGGA
genomic: CAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATGgtaagcagtc ... tcctttccagATTACAGTTGACTGCATCGAAGGTTATCCACCGGTCAGTTTACTGCTAGGA
EST: gi|78109267|gb|DV527683.1|DV527683
EST:     CAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATG                         ATTACAGTTGACTGCATCGAAGGTTATCCACCGGTCAGTTTACTGCTAGGA
genomic: CAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATGgtaagcagtc ... tcctttccagATTACAGTTGACTGCATCGAAGGTTATCCACCGGTCAGTTTACTGCTAGGA
EST: gi|37373885|gb|CF623267.1|CF623267
EST:     CAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATG                         ATTACAGTTGACTGCATCGAAGGTTATCCACCGGTCAGTTTACTGCTAGGA
genomic: CAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATGgtaagcagtc ... tcctttccagATTACAGTTGACTGCATCGAAGGTTATCCACCGGTCAGTTTACTGCTAGGA
EST: gi|60337676|gb|DN204649.1|DN204649
EST:     CAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATG                         ATTACAGTTGACTGCATCGAAGGTTATCCACCGGTCAGTTTACTGCTAGGA
genomic: CAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATGgtaagcagtc ... tcctttccagATTACAGTTGACTGCATCGAAGGTTATCCACCGGTCAGTTTACTGCTAGGA

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), 48 (downstream exon)
Score: 105

GCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATGgtaagcagtc ... tcctttccagATTACAGTTGACTGCATCGAAGGTTATCCACCGGTCAGTTTACTGCTAGGAAAGCACGTTTTCCTAAGTGCAGGGGATTTTTATCTGGCTAGTCGATCCT


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 46

GCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATGgtaagcagtc ... tcctttccagATTACAGTTGACTGCATCGAAGGTTATCCACCGGTCAGTTTACTGCTAGGAAAGCACGTTTTCCTAAGTGCAGGGGATTTTTATCTGGCTAGTCGATCCT


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 68

GCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATGgtaagcagtc ... tcctttccagATTACAGTTGACTGCATCGAAGGTTATCCACCGGTCAGTTTACTGCTAGGAAAGCACGTTTTCCTAAGTGCAGGGGATTTTTATCTGGCTAGTCGATCCT


Block sizes: 44 (upstream exon), 45 (downstream exon)
Score: 31

GCAAAAGCAATCATGTGGAGGCGTTGAGAGTATATCTTCTGTCAAGGTCTCTTTCCAGATTGAAGAACCAGTTCCAAGCTGGAAAGGGCATGgtaagcagtc ... tcctttccagATTACAGTTGACTGCATCGAAGGTTATCCACCGGTCAGTTTACTGCTAGGAAAGCACGTTTTCCTAAGTGCAGGGGATTTTTATCTGGCTAGTCGATCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagaaaaaaaaaactactcctttgtgctcatagcttgcctacatcctttccagATTACAGTTGACTGCATCGAAGGTTATCCACCGGTCAGTTTACTGCTAGGAAAGCACGTTTTCCTAAGTGCAGGGGATTTTTATCTGGCTAGTCGATCCT
                                       cctacatcctttcc  CT-rich tract
     aaaaaaaaaactact  TA-rich tract