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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgctcgacttgtgaaatagatgtgctattctgttcatcttatgatgagttgtatcatcaacgtcatcatctaaaactaactgccatggtcttcactacagCTTCAAAAGCTAAAAATTGAGCCAGTACTACTACACTACCTCTCCCGCATGAGCATACTTCAAG

Basic information

species Zea mays
transcript GRMZM5G871336_T01
intron # 8
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|71430125|gb|DR811175.1|DR811175
EST:     TCTTGGTTGGTGGACCAGCAGATTACTTTGTAATTGAACTCGCTGATCAG                         CTTCAAAAGCTAAAAATTGAGCCAGTACTACT
genomic: TCTTGGTTGGTGGACCAGCAGATTACTTTGTAATTGAACTCGCTGATCAGgttgctcgac ... ttcactacagCTTCAAAAGCTAAAAATTGAGCCAGTACTACT
EST: gi|71432140|gb|DR813190.1|DR813190
EST:     TCTTGGTTGGTGGACCAGCAGATTACTTTGTTATTGAACTCGCTGATCAG                         CTTCAAAAGCTAAAAATTGAGCCAGTACTACTA
genomic: TCTTGGTTGGTGGACCAGCAGATTACTTTGTAATTGAACTCGCTGATCAGgttgctcgac ... ttcactacagCTTCAAAAGCTAAAAATTGAGCCAGTACTACTA
EST: gi|71311972|gb|DR792494.1|DR792494
EST:     TCTTGGTTGGTGGACCAGCAGATTACTTTGTAATTGAACTCGCTGATCAG                         CTTCAAA-GCTAAAAATTGAGCCAGTACTACTACACTA
genomic: TCTTGGTTGGTGGACCAGCAGATTACTTTGTAATTGAACTCGCTGATCAGgttgctcgac ... ttcactacagCTTCAAAAGCTAAAAATTGAGCCAGTACTACTACACTA
EST: gi|148950551|gb|EC896128.2|EC896128
EST:     CTTTGGT-GGTGGACCAGCAGAATACTTTGTAATTGAACTCGCTGATCAG                         CTTCAAAAGCTAAAAATTGAGCCAGTACTACTACACTACCTCTCCCGCATG
genomic: CTT-GGTTGGTGGACCAGCAGATTACTTTGTAATTGAACTCGCTGATCAGgttgctcgac ... ttcactacagCTTCAAAAGCTAAAAATTGAGCCAGTACTACTACACTACCTCTCCCGCATG

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: 47 (upstream exon), 49 (downstream exon)
Score: 73

TCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCAATTTCCCAAATTCCTTCTTGGTTGGTGGACCAGCAGATTACTTTGTAATTGAACTCGCTGATCAGgttgctcgac ... ttcactacagCTTCAAAAGCTAAAAATTGAGCCAGTACTACTACACTACCTCTCCCGCATGAGCATACTTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 57

TCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCAATTTCCCAAATTCCTTCTTGGTTGGTGGACCAGCAGATTACTTTGTAATTGAACTCGCTGATCAGgttgctcgac ... ttcactacagCTTCAAAAGCTAAAAATTGAGCCAGTACTACTACACTACCTCTCCCGCATGAGCATACTTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 39

TCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCAATTTCCCAAATTCCTTCTTGGTTGGTGGACCAGCAGATTACTTTGTAATTGAACTCGCTGATCAGgttgctcgac ... ttcactacagCTTCAAAAGCTAAAAATTGAGCCAGTACTACTACACTACCTCTCCCGCATGAGCATACTTCAAG


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 55

TCACATGCTTTCTAGTTTCCTAGAGCATTTTCCCAATTTCCCAAATTCCTTCTTGGTTGGTGGACCAGCAGATTACTTTGTAATTGAACTCGCTGATCAGgttgctcgac ... ttcactacagCTTCAAAAGCTAAAAATTGAGCCAGTACTACTACACTACCTCTCCCGCATGAGCATACTTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagttgtatcatcaacgtcatcatctaaaactaactgccatggtcttcactacagCTTCAAAAGCTAAAAATTGAGCCAGTACTACTACACTACCTCTCCCGCATGAGCATACTTCAAG
                            aactaac  putative branch site (score: 55)
                                           tcttcact  putative PPT
                         taaaactaa  TA-rich tract