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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgttccgtattccacatccttactattttggtcagcatcgtggttatctgaaagcatgtatatttggtgtttttag

Basic information

species Zea mays
transcript GRMZM2G069916_T02
intron # 11
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|13178061|gb|BG349319.1|BG349319
EST:     GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGC-CAGCAAGGATCGCAACGG
genomic: GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGG
EST: gi|60349607|gb|DN216580.1|DN216580
EST:     GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|32847638|gb|CD987319.1|CD987319
EST:     GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|88757903|gb|DY542044.1|DY542044
EST:     CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|83278840|gb|DV942848.1|DV942848
EST:     CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|94476347|gb|EB705305.1|EB705305
EST:     GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|32833686|gb|CD973364.1|CD973364
EST:     AAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCATCGGCCGGTCGTCCAGGGATAGAGA
genomic: AAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|149000972|gb|EE038212.2|EE038212
EST:     GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|32847430|gb|CD987111.1|CD987111
EST:     GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|32835473|gb|CD975151.1|CD975151
EST:     GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|88756296|gb|DY540437.1|DY540437
EST:     GAGCAGGGAAATAAAAGGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: GAGCAGAGAAATAAAA-GGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|60340812|gb|DN207785.1|DN207785
EST:     GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|32834150|gb|CD973828.1|CD973828
EST:     GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|13178510|gb|BG349768.1|BG349768
EST:     GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|60400106|gb|DN232913.1|DN232913
EST:     GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|13178184|gb|BG349442.1|BG349442
EST:     GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCGCGGTCGTCCAGGGATAGAG
genomic: GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGC-CGGTCGTCCAGGGATAGAG
EST: gi|16377976|gb|BI992214.1|BI992214
EST:     GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCA
genomic: GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCA
EST: gi|71330189|gb|DR801853.1|DR801853
EST:     CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA

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: 358

GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGAACCAGAAAGGAGAGACAGGGTTGAGTCTCGAGATGGTAGAAGAGATTAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 253

GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGAACCAGAAAGGAGAGACAGGGTTGAGTCTCGAGATGGTAGAAGAGATTAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 259

GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGAACCAGAAAGGAGAGACAGGGTTGAGTCTCGAGATGGTAGAAGAGATTAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 168

GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGAACCAGAAAGGAGAGACAGGGTTGAGTCTCGAGATGGTAGAAGAGATTAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgttccgtattccacatccttactattttggtcagcatcgtggttatctgaaagcatgtatatttggtgtttttag

- - - - - - - AAGGAG
- - - - - - -  AGGAGA
- - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - AAGATG