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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtgacttcttagattagtaagtgtattttcatattaccacttttcatgtgcatttccagttcatttaggattctgcatttgtgtttcagCCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG

Basic information

species Zea mays
transcript GRMZM2G012501_T02
intron # 9
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|32838433|gb|CD978111.1|CD978111
EST:     GTGCTGTCAGCACGCTGGCAAAGTTTGGTGCCCTGGTTGATACGCTCAAG                         CCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG
genomic: GTGCTGTCAGCACGCTGGCAAAGTTTGGTGCCCTGGTTGATACGCTCAAGgtatggtgac ... tgtgtttcagCCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG
EST: gi|32839407|gb|CD979088.1|CD979088
EST:     GTGCTGTCAGCACGCTGGCAAAGTTTGGTGCCCTGGTTGATACGCTCAAG                         CCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG
genomic: GTGCTGTCAGCACGCTGGCAAAGTTTGGTGCCCTGGTTGATACGCTCAAGgtatggtgac ... tgtgtttcagCCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG
EST: gi|67012331|gb|CO441080.1|CO441080
EST:     GTGCTGTCAGCACGCTGGCAAAGTTTTTTGCCCTGGTTGATACGCTCAAG                         CCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG
genomic: GTGCTGTCAGCACGCTGGCAAAGTTTGGTGCCCTGGTTGATACGCTCAAGgtatggtgac ... tgtgtttcagCCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG
EST: gi|74243906|gb|DT651820.1|DT651820
EST:     GTGCTGTCAGCACGCTGGCAAAGTTTGGTGCCCTGGATGATACGCTCAAG                         CCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG
genomic: GTGCTGTCAGCACGCTGGCAAAGTTTGGTGCCCTGGTTGATACGCTCAAGgtatggtgac ... tgtgtttcagCCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG
EST: gi|67030306|gb|CO459055.1|CO459055
EST:     GTGCTGTCAGCACGCTGGCAAAGTTTGGTGCCCTGGTTGATACGCTCAAG                         CCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG
genomic: GTGCTGTCAGCACGCTGGCAAAGTTTGGTGCCCTGGTTGATACGCTCAAGgtatggtgac ... tgtgtttcagCCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG
EST: gi|67021265|gb|CO450014.1|CO450014
EST:     GTGCTGTCAGCACGCTGGCAAAGTTTGGTGCCCTGGTTGATACGCTCAAG                         CCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG
genomic: GTGCTGTCAGCACGCTGGCAAAGTTTGGTGCCCTGGTTGATACGCTCAAGgtatggtgac ... tgtgtttcagCCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG
EST: gi|211185421|gb|FL310763.1|FL310763
EST:     TGCTGTCAGC-MGCNTGGCAAAGTTTGGTGCCCTGGTTGATACGCTCAAG                         CCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG
genomic: TGCTGTCAGCACGC-TGGCAAAGTTTGGTGCCCTGGTTGATACGCTCAAGgtatggtgac ... tgtgtttcagCCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG

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: 46 (upstream exon), 49 (downstream exon)
Score: 241

TCGCTACATATACAACCGTGTGATATTGGAAAATGCCACTGTTCGTGCTAGTGCTGTCAGCACGCTGGCAAAGTTTGGTGCCCTGGTTGATACGCTCAAGgtatggtgac ... tgtgtttcagCCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 180

TCGCTACATATACAACCGTGTGATATTGGAAAATGCCACTGTTCGTGCTAGTGCTGTCAGCACGCTGGCAAAGTTTGGTGCCCTGGTTGATACGCTCAAGgtatggtgac ... tgtgtttcagCCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 173

TCGCTACATATACAACCGTGTGATATTGGAAAATGCCACTGTTCGTGCTAGTGCTGTCAGCACGCTGGCAAAGTTTGGTGCCCTGGTTGATACGCTCAAGgtatggtgac ... tgtgtttcagCCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 295

TCGCTACATATACAACCGTGTGATATTGGAAAATGCCACTGTTCGTGCTAGTGCTGTCAGCACGCTGGCAAAGTTTGGTGCCCTGGTTGATACGCTCAAGgtatggtgac ... tgtgtttcagCCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccacttttcatgtgcatttccagttcatttaggattctgcatttgtgtttcagCCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG
                         ttcattta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtgacttcttagattagtaagtgtattttcatattaccacttttcatgtgcatttccagttcatttaggattctgcatttgtgtttcagCCTCAGATCTTTGTTCTCTTGCAACGATGCCTGTTTGATACTGAAGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG