Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caattacattatttatttatttatttattttgtcactttatctttaatcatcatctccattcagttttctcatgtcaaatgaaaactgcaatccttatagGTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAG

Basic information

species Zea mays
transcript GRMZM2G104133_T01
intron # 2
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|60352799|gb|DN219772.1|DN219772
EST:     GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAG                         GTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
genomic: GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAGgtgcgtgtga ... atccttatagGTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
EST: gi|211416489|gb|FL082392.1|FL082392
EST:     GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAG                         GTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
genomic: GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAGgtgcgtgtga ... atccttatagGTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
EST: gi|211170332|gb|FK988414.1|FK988414
EST:     GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAG                         GTGCGTCGCCTTGCYATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
genomic: GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAGgtgcgtgtga ... atccttatagGTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
EST: gi|211170335|gb|FK988417.1|FK988417
EST:     GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAG                         GTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
genomic: GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAGgtgcgtgtga ... atccttatagGTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
EST: gi|211170328|gb|FK988410.1|FK988410
EST:     GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAG                         GTGCGTCGCCTTGCCATGGAGGTCCCGGCAACTTGGTAATTCACGTTCAAT
genomic: GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAGgtgcgtgtga ... atccttatagGTGCGTCGCCTTGCCATGGAGGTCC-GGCAACTTGGTAATTCACGTTCAAT
EST: gi|211170338|gb|FK988420.1|FK988420
EST:     GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAG                         GTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
genomic: GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAGgtgcgtgtga ... atccttatagGTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
EST: gi|211170331|gb|FK988413.1|FK988413
EST:     GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAG                         GTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
genomic: GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAGgtgcgtgtga ... atccttatagGTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
EST: gi|211170336|gb|FK988418.1|FK988418
EST:     GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAG                         GTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
genomic: GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAGgtgcgtgtga ... atccttatagGTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
EST: gi|211170337|gb|FK988419.1|FK988419
EST:     GAGGAGGGGGAGACGGGGAAACCAATCTCAACGAGGCTCTTACCTCGCAG                         GTGCGTCGCCTTGCCATGGAAGGTCCGGCAACTTGGTAATTCACGTTCAAT
genomic: GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAGgtgcgtgtga ... atccttatagGTGCGTCGCCTTGCCATGGA-GGTCCGGCAACTTGGTAATTCACGTTCAAT
EST: gi|211170340|gb|FK988422.1|FK988422
EST:     GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAG                         GTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
genomic: GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAGgtgcgtgtga ... atccttatagGTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
EST: gi|60338640|gb|DN205613.1|DN205613
EST:     GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAG                         GTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
genomic: GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAGgtgcgtgtga ... atccttatagGTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
EST: gi|211170339|gb|FK988421.1|FK988421
EST:     GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAG                         GTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
genomic: GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAGgtgcgtgtga ... atccttatagGTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
EST: gi|211170333|gb|FK988415.1|FK988415
EST:     GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAG                         GTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA
genomic: GAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAGgtgcgtgtga ... atccttatagGTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATA

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: 122

GAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAGgtgcgtgtga ... atccttatagGTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 239

GAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAGgtgcgtgtga ... atccttatagGTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 221

GAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAGgtgcgtgtga ... atccttatagGTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

GAGATACTCGACAAGGGGAAGAAGGTGAAGGATGGAGGAGGGGGAGACGGGGAAACCGATCTCAACGAGGCTCTTACCTCGCAGgtgcgtgtga ... atccttatagGTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcatcatctccattcagttttctcatgtcaaatgaaaactgcaatccttatagGTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAG
 ctttaat  putative branch site (score: 190)
                                              tccttat  putative PPT
                               aaatgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caattacattatttatttatttatttattttgtcactttatctttaatcatcatctccattcagttttctcatgtcaaatgaaaactgcaatccttatagGTGCGTCGCCTTGCCATGGAGGTCCGGCAACTTGGTAATTCACGTTCAATAACTGTTCTCAATGGAGGTTCTGCACAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactgca