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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttatctcccaattcaagcttgctgcagcctctggtgtcgattcctgcatattttgcagcactgtgatgtaactaactgataagctttaaatccttctgacctgatgcagGTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTG

Basic information

species Zea mays
transcript GRMZM2G080375_T02
intron # 7
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|116813643|gb|EC856113.1|EC856113
EST:     AAGTGCGGAGAACGGCATCGGTGTCGTGAAGCTTATGGGCCGCAACAGCG                         GTTTTATCGCGATGTACGCAACTCTAGCTAGCCGTGATGTG
genomic: AAGTGCGGAGAACGGCATCGGTGTCGTGAAGCTTATGGGCCGCAACAGTGgtatgtttat ... cctgatgcagGTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTG
EST: gi|33099629|gb|CF059589.1|CF059589
EST:     AAGTGCGGAGAACGGCATCGGTGTCGTGAAGCTTATGGGCCGCAACAGCG                         GTTTTATCGCGATGTAC
genomic: AAGTGCGGAGAACGGCATCGGTGTCGTGAAGCTTATGGGCCGCAACAGTGgtatgtttat ... cctgatgcagGTTTTATCGCGATGTAC
EST: gi|211450005|gb|FL281917.1|FL281917
EST:     AAGTGCGGAGAACGGCATCGGTGTCGTGAAGCTTATGGGCCGCAACAGCG                         GTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTG
genomic: AAGTGCGGAGAACGGCATCGGTGTCGTGAAGCTTATGGGCCGCAACAGTGgtatgtttat ... cctgatgcagGTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTG
EST: gi|211450006|gb|FL281918.1|FL281918
EST:     AAGTGCGGAGAACGGCATCGGTGTCGTGAAGCTTATGGGCCGCAACAGCG                         GTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTG
genomic: AAGTGCGGAGAACGGCATCGGTGTCGTGAAGCTTATGGGCCGCAACAGTGgtatgtttat ... cctgatgcagGTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTG

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), 40 (downstream exon)
Score: 32

GCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCGGTGTCGTGAAGCTTATGGGCCGCAACAGTGgtatgtttat ... cctgatgcagGTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 316

GCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCGGTGTCGTGAAGCTTATGGGCCGCAACAGTGgtatgtttat ... cctgatgcagGTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 217

GCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCGGTGTCGTGAAGCTTATGGGCCGCAACAGTGgtatgtttat ... cctgatgcagGTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 82

GCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCGGTGTCGTGAAGCTTATGGGCCGCAACAGTGgtatgtttat ... cctgatgcagGTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagcactgtgatgtaactaactgataagctttaaatccttctgacctgatgcagGTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTG
                              tttaaat  TA-rich tract