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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAAGGGCAGAAGGACTCTGCCCAGGAAGGCTTCAATGCTGGGTTCAGGCAATCTGTAAACGCTGGCTACAAGTGGGGCCTTGTTCGCGGGGTTGCCAGgtgtatatccttccaagaactgatctcttgtattgccattctcctctagtcttgccctccgattttgatttcctttcctatctgtcgtcattccaaag

Basic information

species Zea mays
transcript GRMZM5G833593_T05
intron # 4
splice site 5'
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|71443400|gb|DR824450.1|DR824450
EST:     CAATCTGTAAACGCTGGCTACAAGTGGGGCCTTGTTCGCGGGGTTGCCAG                         T-G--CGCTAGCCAATCTTCCAGACAGCTTGAAAGAGAAACTGGTGCCGGA
genomic: CAATCTGTAAACGCTGGCTACAAGTGGGGCCTTGTTCGCGGGGTTGCCAGgtgtatatcc ... cattccaaagTAGTGCGCTAGCCAATCTTCCAGACAGCTTGAAAGAGAAACTGGTGCCGGA
EST: gi|71327087|gb|DR800190.1|DR800190
EST:     CAATCTGTAAACGCTGGCTACAAGTGGGGCCTTGTTCGCGGGGTTGCC--                         -AGTGCGCTAGCCAATCTTCCAGACAGCTTGAAAGAGAAACTGGTGCCGGA
genomic: CAATCTGTAAACGCTGGCTACAAGTGGGGCCTTGTTCGCGGGGTTGCCAGgtgtatatcc ... cattccaaagTAGTGCGCTAGCCAATCTTCCAGACAGCTTGAAAGAGAAACTGGTGCCGGA
EST: gi|71448668|gb|DR829718.1|DR829718
EST:     CAATCTGTAAACGCTGGCTACAAGTGGGGCCTTGTTCGCGGGGTTGCCAG                         TAGTGCGCTAGCCAATCTTCCAGACAGCTTGAAAGAGAAACTGGTGCCGGA
genomic: CAATCTGTAAACGCTGGCTACAAGTGGGGCCTTGTTCGCGGGGTTGCCAGgtgtatatcc ... cattccaaagTAGTGCGCTAGCCAATCTTCCAGACAGCTTGAAAGAGAAACTGGTGCCGGA
EST: gi|76929776|gb|DV172157.1|DV172157
EST:     CAATCTGTAAACGCTGGCTACAAGTGGGGCCTTGTTCGCGGGGTTGCCAG                         T-G--CGCTTGCCAATCTTCCAGACAGCTTGAAAGAGAAACTGGGGCCGGA
genomic: CAATCTGTAAACGCTGGCTACAAGTGGGGCCTTGTTCGCGGGGTTGCCAGgtgtatatcc ... cattccaaagTAGTGCGCTAGCCAATCTTCCAGACAGCTTGAAAGAGAAACTGGTGCCGGA
EST: gi|76934920|gb|DV174088.1|DV174088
EST:     CAATCTGTAAACGCTGGCTACAAGTGGGGCCTTGTTCGCGGGGTTGCCAG                         T-G--CGCTAGCCAATCTTCCAGACAGCTTGAAAGAGAAACTGGTGCCGGA
genomic: CAATCTGTAAACGCTGGCTACAAGTGGGGCCTTGTTCGCGGGGTTGCCAGgtgtatatcc ... cattccaaagTAGTGCGCTAGCCAATCTTCCAGACAGCTTGAAAGAGAAACTGGTGCCGGA
EST: gi|71771514|gb|DR969451.1|DR969451
EST:     CAATCTGTAAACGCTGGCTACAAGTGGGGCCTTGTTCGCGGGGTTGCCAG                         T-G--CGCTAGCCAATCTTCCAGACAGCTTGAAAGAGAAACTGGTGCCGGA
genomic: CAATCTGTAAACGCTGGCTACAAGTGGGGCCTTGTTCGCGGGGTTGCCAGgtgtatatcc ... cattccaaagTAGTGCGCTAGCCAATCTTCCAGACAGCTTGAAAGAGAAACTGGTGCCGGA
EST: gi|74234252|gb|DT642166.1|DT642166
EST:     CAATCTGTAAACGCTGGCTACAAGTGGGGCCTTGTTCGCGGGGTTGCCAG                         T-G--CGCTAGCCAATCTTCCAGACAGCTTGAAAGAGAAACTGGTGCCGGA
genomic: CAATCTGTAAACGCTGGCTACAAGTGGGGCCTTGTTCGCGGGGTTGCCAGgtgtatatcc ... cattccaaagTAGTGCGCTAGCCAATCTTCCAGACAGCTTGAAAGAGAAACTGGTGCCGGA
EST: gi|71774208|gb|DR972086.1|DR972086
EST:     CAATCTGTAAACGCTGGCTACAAGTGGGGCCTTGTTCGCGGGGTTGCCAG                         T-G--CGCTAGCCAATCTTCCAGACAGCTTGAAAGAGAAACTGGTGCCGGA
genomic: CAATCTGTAAACGCTGGCTACAAGTGGGGCCTTGTTCGCGGGGTTGCCAGgtgtatatcc ... cattccaaagTAGTGCGCTAGCCAATCTTCCAGACAGCTTGAAAGAGAAACTGGTGCCGGA

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 3 RNA-Seq libraries.


Block sizes: 14 (upstream exon), 36 (downstream exon)
Score: 1

CACAAGGGCAGAAGGACTCTGCCCAGGAAGGCTTCAATGCTGGGTTCAGGCAATCTGTAAACGCTGGCTACAAGTGGGGCCTTGTTCGCGGGGTTGCCAGgtgtatatcc ... cattccaaagTAGTGCGCTAGCCAATCTTCCAGACAGCTTGAAAGAGAAACTGGTGCCGGACGTCCAGTGCAGAGGGAAACTACAGGATCTGCACAGCTCCGTGCGAGAA


Block sizes: 23 (upstream exon), 27 (downstream exon)
Score: 1

CACAAGGGCAGAAGGACTCTGCCCAGGAAGGCTTCAATGCTGGGTTCAGGCAATCTGTAAACGCTGGCTACAAGTGGGGCCTTGTTCGCGGGGTTGCCAGgtgtatatcc ... cattccaaagTAGTGCGCTAGCCAATCTTCCAGACAGCTTGAAAGAGAAACTGGTGCCGGACGTCCAGTGCAGAGGGAAACTACAGGATCTGCACAGCTCCGTGCGAGAA


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 3

CACAAGGGCAGAAGGACTCTGCCCAGGAAGGCTTCAATGCTGGGTTCAGGCAATCTGTAAACGCTGGCTACAAGTGGGGCCTTGTTCGCGGGGTTGCCAGgtgtatatcc ... cattccaaagTAGTGCGCTAGCCAATCTTCCAGACAGCTTGAAAGAGAAACTGGTGCCGGACGTCCAGTGCAGAGGGAAACTACAGGATCTGCACAGCTCCGTGCGAGAA