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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGATAATCTCATTGTCTGGCGTGCTCCACTTTTCCACTgtatgatcccaactcccctttctttggtgcttagtcttgttgattcagttatgcagatcttgaaatattactacacatgtttttaagtactgttgtacat...

Basic information

species Zea mays
transcript GRMZM2G150251_T02
intron # 5
splice site 5'
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|60353103|gb|DN220076.1|DN220076
EST:     AAAAGAGTGGAATGATAATCTCATTGTCTGGCGTGCTCCACTTTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCTTCAATACCTGGAT
genomic: AAAAGAGTGGAATGATAATCTCATTGTCTGGCGTGCTCCACTTTTCCACTgtatgatccc ... tttatttcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCTTCAATACCTGGAT
EST: gi|60349110|gb|DN216083.1|DN216083
EST:     AAAAGAGTGGAATGATAATCTCATTGTCTGGCGTGCTCCACTTTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCTTCAATACCTGGAT
genomic: AAAAGAGTGGAATGATAATCTCATTGTCTGGCGTGCTCCACTTTTCCACTgtatgatccc ... tttatttcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCTTCAATACCTGGAT
EST: gi|76020573|gb|DT947743.1|DT947743
EST:     AAAAGAGTGGAATGATAATCTCATTGTCTGGCGTGCTCCACTTTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCTTCAATACCTGGAT
genomic: AAAAGAGTGGAATGATAATCTCATTGTCTGGCGTGCTCCACTTTTCCACTgtatgatccc ... tttatttcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCTTCAATACCTGGAT
EST: gi|33092200|gb|CF052194.1|CF052194
EST:     TCTGGCGTGCTCCACTTTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCTTCAATACCTGGAT
genomic: TCTGGCGTGCTCCACTTTTCCACTgtatgatccc ... tttatttcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCTTCAATACCTGGAT
EST: gi|33093608|gb|CF053602.1|CF053602
EST:     TCTGGCGTGCTCCACTTTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCTTCAATACCTGGAT
genomic: TCTGGCGTGCTCCACTTTTCCACTgtatgatccc ... tttatttcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCTTCAATACCTGGAT
EST: gi|32837706|gb|CD977384.1|CD977384
EST:     AAAAGAGTGGAATGATAATCTCATTGTCTGGCGTGCTCCACTTTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCTTCAATACCTGGAT
genomic: AAAAGAGTGGAATGATAATCTCATTGTCTGGCGTGCTCCACTTTTCCACTgtatgatccc ... tttatttcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCTTCAATACCTGGAT
EST: gi|76282341|gb|DV021909.1|DV021909
EST:     AAAAGAGTGGAATGATAATCTCATTGTCTGGTGTGCTCCACTTTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCTTCAATACCTGGAT
genomic: AAAAGAGTGGAATGATAATCTCATTGTCTGGCGTGCTCCACTTTTCCACTgtatgatccc ... tttatttcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCTTCAATACCTGGAT
EST: gi|93282675|gb|EB674939.1|EB674939
EST:     AAAAGAGTGGAATGATAATCTCATTGTCTGGCGTGCTCCACTTTTCCACT                         CACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCTTCAATACCTGGAT
genomic: AAAAGAGTGGAATGATAATCTCATTGTCTGGCGTGCTCCACTTTTCCACTgtatgatccc ... tttatttcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCTTCAATACCTGGAT

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), 47 (downstream exon)
Score: 146

TGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGATAATCTCATTGTCTGGCGTGCTCCACTTTTCCACTgtatgatccc ... tttatttcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCTTCAATACCTGGATTTTTCTTCTGCTTGTGGTATGCGTCAAAGAAGCATTGGCTTGCAAATAA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 122

TGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGATAATCTCATTGTCTGGCGTGCTCCACTTTTCCACTgtatgatccc ... tttatttcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCTTCAATACCTGGATTTTTCTTCTGCTTGTGGTATGCGTCAAAGAAGCATTGGCTTGCAAATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

TGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGATAATCTCATTGTCTGGCGTGCTCCACTTTTCCACTgtatgatccc ... tttatttcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCTTCAATACCTGGATTTTTCTTCTGCTTGTGGTATGCGTCAAAGAAGCATTGGCTTGCAAATAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 210

TGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGATAATCTCATTGTCTGGCGTGCTCCACTTTTCCACTgtatgatccc ... tttatttcagCACTCTCGGTGGAGTTCACAAAGTCCCAGATTGTTGCTTCAATACCTGGATTTTTCTTCTGCTTGTGGTATGCGTCAAAGAAGCATTGGCTTGCAAATAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGATAATCTCATTGTCTGGCGTGCTCCACTTTTCCACTgtatgatcccaactcccctttctttggtgcttagtcttgttgattcagttatgcagatcttgaaatattactacacatgtttttaagtactgttgtacat

- - - - - - - - - - - - - - - - - - - -  AGTGGA