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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatacatcacatactagtactgatgaaatacctattttcactggcttggatatttgttcattgtggataagcttattcttttgcattaaatttctactattgatttgattgctgaggataataactacttatccagGGACAACCTTCCTCAAGATTGAGGATCTGGCAGGTACCAGCTGGCGTTATTGTATATCTCTCTATTCCCGCTAACTGTACAAAACTTTGTATTTGCACAC

Basic information

species Zea mays
transcript GRMZM2G052434_T01
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|71314803|gb|DR794022.1|DR794022
EST:     AAAGTGCAAATCGGGAAATACAGG                         GGACAACCTTCCTCAAGATTGAGGATCTGGCAGGTACCAGCTGGCGTTAT
genomic: AAAGTGCAAATCGGGAAATACA-Ggtgatacatc ... acttatccagGGACAACCTTCCTCAAGATTGAGGATCTGGCAGGTACCAGCTGGCGTTAT
EST: gi|116818784|gb|EC861832.1|EC861832
EST:     AT-CAGAGGTTGGAGAGCAGCATGAGT-AAGTGCAAATCGGGAAATACAG                         GGACAACCTTCCTCAAGATTGAGGATCTGGCAGGTACCAGCTGGCGTTATT
genomic: ATACAGAGGTTGGAGAGCAGCATGAGTAAAGTGCAAATCGGGAAATACAGgtgatacatc ... acttatccagGGACAACCTTCCTCAAGATTGAGGATCTGGCAGGTACCAGCTGGCGTTATT

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: 45 (upstream exon), 43 (downstream exon)
Score: 7

GTGATTACAGCGCTGACTCAAAACAAAACATTGGCCGGGTTGCTGCAAGCATACAGAGGTTGGAGAGCAGCATGAGTAAAGTGCAAATCGGGAAATACAGgtgatacatc ... acttatccagGGACAACCTTCCTCAAGATTGAGGATCTGGCAGGTACCAGCTGGCGTTATTGTATATCTCTCTATTCCCGCTAACTGTACAAAACTTTGTATTTGCACAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 16

GTGATTACAGCGCTGACTCAAAACAAAACATTGGCCGGGTTGCTGCAAGCATACAGAGGTTGGAGAGCAGCATGAGTAAAGTGCAAATCGGGAAATACAGgtgatacatc ... acttatccagGGACAACCTTCCTCAAGATTGAGGATCTGGCAGGTACCAGCTGGCGTTATTGTATATCTCTCTATTCCCGCTAACTGTACAAAACTTTGTATTTGCACAC


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 16

GTGATTACAGCGCTGACTCAAAACAAAACATTGGCCGGGTTGCTGCAAGCATACAGAGGTTGGAGAGCAGCATGAGTAAAGTGCAAATCGGGAAATACAGgtgatacatc ... acttatccagGGACAACCTTCCTCAAGATTGAGGATCTGGCAGGTACCAGCTGGCGTTATTGTATATCTCTCTATTCCCGCTAACTGTACAAAACTTTGTATTTGCACAC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 45

GTGATTACAGCGCTGACTCAAAACAAAACATTGGCCGGGTTGCTGCAAGCATACAGAGGTTGGAGAGCAGCATGAGTAAAGTGCAAATCGGGAAATACAGgtgatacatc ... acttatccagGGACAACCTTCCTCAAGATTGAGGATCTGGCAGGTACCAGCTGGCGTTATTGTATATCTCTCTATTCCCGCTAACTGTACAAAACTTTGTATTTGCACAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcattaaatttctactattgatttgattgctgaggataataactacttatccagGGACAACCTTCCTCAAGATTGAGGATCTGGCAGGTACCAGCTGGCGTTATTGTATATCTCTCTATTCCCGCTAACTGTACAAAACTTTGTATTTGCACAC
                                     taataac  putative branch site (score: 45)
                                              cttatcc  putative PPT
     taaatttctactatt  TA-rich tract