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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggatttattctagcatcttttgttgtcttatttattaactacgcagttaagattaacaggtagacttattaactatttaagattctatgcagGTCAAATATGGAATTGACCGCATTAATTGTACATTACCTCGGATGTACCAG

Basic information

species Zea mays
transcript GRMZM2G010823_T01
intron # 6
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|148999094|gb|EE030327.2|EE030327
EST:     ATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAG                         GTCAAATATGGAATTGACCGCATTAATTGTACATTACCTCGGATGTACCAG
genomic: ATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAGgtaggattta ... ttctatgcagGTCAAATATGGAATTGACCGCATTAATTGTACATTACCTCGGATGTACCAG
EST: gi|78111379|gb|DV529776.1|DV529776
EST:     ATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAG                         GTCAAATATGGAATTGACCGCATTAATTGTACATTACCTCGGATGTACCAG
genomic: ATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAGgtaggattta ... ttctatgcagGTCAAATATGGAATTGACCGCATTAATTGTACATTACCTCGGATGTACCAG
EST: gi|149089384|gb|EE178623.2|EE178623
EST:     TGCCACCCCATTGACTCTTGGCTCA-GAATTCAGTGGCTACACTACACAG                         GTCAAATATGGAATTGACCGCA
genomic: TGCCACCCCATTGACTCTTGGC-CAAGAATTCAGTGGCTACACTACACAGgtaggattta ... ttctatgcagGTCAAATATGGAATTGACCGCA
EST: gi|148951891|gb|EC897665.2|EC897665
EST:     TGCCACCCCATTGACTCTTGGCCAAAGA-TTCAGTGGCTACACTACACAG                         GTCAAATATGGAATTGACCGCATTAATTGTACATTACCTCGG
genomic: TGCCACCCCATTGACTCTTGGCCAA-GAATTCAGTGGCTACACTACACAGgtaggattta ... ttctatgcagGTCAAATATGGAATTGACCGCATTAATTGTACATTACCTCGG

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), 49 (downstream exon)
Score: 130

ACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAGgtaggattta ... ttctatgcagGTCAAATATGGAATTGACCGCATTAATTGTACATTACCTCGGATGTACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

ACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAGgtaggattta ... ttctatgcagGTCAAATATGGAATTGACCGCATTAATTGTACATTACCTCGGATGTACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

ACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAGgtaggattta ... ttctatgcagGTCAAATATGGAATTGACCGCATTAATTGTACATTACCTCGGATGTACCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 142

ACTATTGAGTTTAAAGACATAATTAAAATTGGACGTACACATACCCAAGATGCCACCCCATTGACTCTTGGCCAAGAATTCAGTGGCTACACTACACAGgtaggattta ... ttctatgcagGTCAAATATGGAATTGACCGCATTAATTGTACATTACCTCGGATGTACCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actacgcagttaagattaacaggtagacttattaactatttaagattctatgcagGTCAAATATGGAATTGACCGCATTAATTGTACATTACCTCGGATGTACCAG
                             tattaac  putative branch site (score: 142)
                            ttattaactatttaag  TA-rich tract