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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcaattgcattatccttatctaatgctatttagtgaggtagtgttaatgcctctgtactgtccgaaggacacaatgctaatacaaaatatgttgcttttatagGTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAG

Basic information

species Zea mays
transcript GRMZM5G841619_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|211089057|gb|FL454767.1|FL454767
EST:     GTGCAAATGTAAGCGGCAAGGTGCAATCTCTTCTTCAGGATATCAAGAAG                         GTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCAT
genomic: GTGCAAATGTAAGCGGCAAGGTGCAATCTCTTCTTCAGGATATCAAGAAGgtttgcaatt ... gcttttatagGTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCAT
EST: gi|7118996|gb|AW497556.1|AW497556
EST:     TGCAAATGTAAGCGGCAAGGTGCAATCTCTTCTTCAGGAATATCAAGAAG                         GTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCAT
genomic: TGCAAATGTAAGCGGCAAGGTGCAATCTCTTCTTCAGG-ATATCAAGAAGgtttgcaatt ... gcttttatagGTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCAT
EST: gi|78025299|gb|DV493686.1|DV493686
EST:     GTGCAAATGTAAGCGGCAAGGTGCAATCTCTTCTTCAGGATATCAAGAAG                         GTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCAT
genomic: GTGCAAATGTAAGCGGCAAGGTGCAATCTCTTCTTCAGGATATCAAGAAGgtttgcaatt ... gcttttatagGTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCAT
EST: gi|211342884|gb|FL240574.1|FL240574
EST:     GTGCAAATGTAAGCGGCAAGGTGCAATCTCTTCTTCAGGATATCAAGAAG                         GTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGA
genomic: GTGCAAATGTAAGCGGCAAGGTGCAATCTCTTCTTCAGGATATCAAGAAGgtttgcaatt ... gcttttatagGTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGA
EST: gi|6827013|gb|AW330656.1|AW330656
EST:     GTGCAAATGTAAGCGGCAAGGTGCAATCTCTTCTTCAGGATATCAAGAAG                         GTGACAGAAAAACCCGNGGCTGNTGGCTTTGGTGTGTCGACTCCAGAGCAT
genomic: GTGCAAATGTAAGCGGCAAGGTGCAATCTCTTCTTCAGGATATCAAGAAGgtttgcaatt ... gcttttatagGTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCAT
EST: gi|211342885|gb|FL240575.1|FL240575
EST:     GTGCAAATGTAAGCGGCAAGGTGCAATCTCTTCTTCAGGATATCAAGAAG                         GTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCAT
genomic: GTGCAAATGTAAGCGGCAAGGTGCAATCTCTTCTTCAGGATATCAAGAAGgtttgcaatt ... gcttttatagGTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCAT
EST: gi|4874356|gb|AI673876.1|AI673876
EST:     GTGCAAATGTAAGCGGCAAGGTGCAATCTCTTCTTCAGGATATCAAGAAG                         GTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCAT
genomic: GTGCAAATGTAAGCGGCAAGGTGCAATCTCTTCTTCAGGATATCAAGAAGgtttgcaatt ... gcttttatagGTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCAT
EST: gi|32863333|gb|CF003015.1|CF003015
EST:     GTGCAAATGTAAGCGGCAAGGTGCAATCTCTTCTTCAGGATATCAAGAAG                         GTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCAT
genomic: GTGCAAATGTAAGCGGCAAGGTGCAATCTCTTCTTCAGGATATCAAGAAGgtttgcaatt ... gcttttatagGTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCAT

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), 48 (downstream exon)
Score: 73

GTAAGCACTGTTGGAGTTACTGGTACACGTGCAAATGTAAGCGGCAAGGTGCAATCTCTTCTTCAGGATATCAAGAAGgtttgcaatt ... gcttttatagGTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 343

GTAAGCACTGTTGGAGTTACTGGTACACGTGCAAATGTAAGCGGCAAGGTGCAATCTCTTCTTCAGGATATCAAGAAGgtttgcaatt ... gcttttatagGTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 773

GTAAGCACTGTTGGAGTTACTGGTACACGTGCAAATGTAAGCGGCAAGGTGCAATCTCTTCTTCAGGATATCAAGAAGgtttgcaatt ... gcttttatagGTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 177

GTAAGCACTGTTGGAGTTACTGGTACACGTGCAAATGTAAGCGGCAAGGTGCAATCTCTTCTTCAGGATATCAAGAAGgtttgcaatt ... gcttttatagGTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctctgtactgtccgaaggacacaatgctaatacaaaatatgttgcttttatagGTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAG
                          tgctaat  putative branch site (score: 177)
                                           ttgctttt  putative PPT
                             taatacaaaatatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcaattgcattatccttatctaatgctatttagtgaggtagtgttaatgcctctgtactgtccgaaggacacaatgctaatacaaaatatgttgcttttatagGTGACAGAAAAACCCGTGGCTGTTGGCTTTGGTGTGTCGACTCCAGAGCATGTCCGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA