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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttttctgagccttgccagctactgcacgcttttgttgaagtttcgtttcgacaccgccgccattcttgtcaagttagtgaccgcgtcgtctatatatggtgccgacgtagGTGCTGAGCATGCAGCAACTGTACCGGATCAGCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAA

Basic information

species Zea mays
transcript GRMZM5G852338_T02
intron # 4
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|76289318|gb|DV028886.1|DV028886
EST:     ACGACAAGCATAGCCGGAGTCTCGCGGAGATCACAGACGACTTCTGCCCA                         GTGCTGAGCATGCAGCAACTGTACCGGATCAGCACGATGTACTGCGACGAC
genomic: ACGACAAGCATAGCCGGAGTCTCGCGGAGATCACAGACGACTTCTGCCCAgtgagttttc ... gccgacgtagGTGCTGAGCATGCAGCAACTGTACCGGATCAGCACGATGTACTGCGACGAC
EST: gi|211128089|gb|FL016621.1|FL016621
EST:     ACGACAAGCATAGCCGGAGTCTCGCGGAGATCACAGACGACTTCTGCCCA                         GTGCTGAGCATGCAGCAACTGTACCGGATCAGCACGATGTACTGCGACGAC
genomic: ACGACAAGCATAGCCGGAGTCTCGCGGAGATCACAGACGACTTCTGCCCAgtgagttttc ... gccgacgtagGTGCTGAGCATGCAGCAACTGTACCGGATCAGCACGATGTACTGCGACGAC
EST: gi|88750549|gb|DY534690.1|DY534690
EST:     AAGCATAGCCGGAGTCTCGCGGAGATCACAGACGACTTCTGCCCA                         GTGCTGAGCATGCAGCAACTGTACCGGATCAGCACGATGTACTGCGACGAC
genomic: AAGCATAGCCGGAGTCTCGCGGAGATCACAGACGACTTCTGCCCAgtgagttttc ... gccgacgtagGTGCTGAGCATGCAGCAACTGTACCGGATCAGCACGATGTACTGCGACGAC
EST: gi|16925511|gb|BM078579.1|BM078579
EST:     ACGACAAGCATAGCCGGAGTCTCGCGGAGATCACAGACGACTTCTGCCCA                         GTGCTGAGCATGCAGCAACTGTACCGGATCAGCACGATGTACTGCGACGAC
genomic: ACGACAAGCATAGCCGGAGTCTCGCGGAGATCACAGACGACTTCTGCCCAgtgagttttc ... gccgacgtagGTGCTGAGCATGCAGCAACTGTACCGGATCAGCACGATGTACTGCGACGAC

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: 42 (upstream exon), 48 (downstream exon)
Score: 24

ATGGGACGAGCTGAAGCATATCAGGCAGGCAGTTACCCTCTTGATACTTGACGACAAGCATAGCCGGAGTCTCGCGGAGATCACAGACGACTTCTGCCCAgtgagttttc ... gccgacgtagGTGCTGAGCATGCAGCAACTGTACCGGATCAGCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 187

ATGGGACGAGCTGAAGCATATCAGGCAGGCAGTTACCCTCTTGATACTTGACGACAAGCATAGCCGGAGTCTCGCGGAGATCACAGACGACTTCTGCCCAgtgagttttc ... gccgacgtagGTGCTGAGCATGCAGCAACTGTACCGGATCAGCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 288

ATGGGACGAGCTGAAGCATATCAGGCAGGCAGTTACCCTCTTGATACTTGACGACAAGCATAGCCGGAGTCTCGCGGAGATCACAGACGACTTCTGCCCAgtgagttttc ... gccgacgtagGTGCTGAGCATGCAGCAACTGTACCGGATCAGCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

ATGGGACGAGCTGAAGCATATCAGGCAGGCAGTTACCCTCTTGATACTTGACGACAAGCATAGCCGGAGTCTCGCGGAGATCACAGACGACTTCTGCCCAgtgagttttc ... gccgacgtagGTGCTGAGCATGCAGCAACTGTACCGGATCAGCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccgccattcttgtcaagttagtgaccgcgtcgtctatatatggtgccgacgtagGTGCTGAGCATGCAGCAACTGTACCGGATCAGCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAA
                                 tctatatat  TA-rich tract