Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcactgcagaaatgttactatgactctctgtttcaatacagaaaatcagaaatccaataatatatgcctgagcatccggcctcatctcttgcag

Basic information

species Zea mays
transcript GRMZM2G087095_T01
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|211463197|gb|FL126646.1|FL126646
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|50331176|gb|CO526302.1|CO526302
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGC
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGC
EST: gi|32808460|gb|CD960694.1|CD960694
EST:     TAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: TAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|74236437|gb|DT644351.1|DT644351
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|78122333|gb|DV540717.1|DV540717
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|50331175|gb|CO526301.1|CO526301
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|32838769|gb|CD978450.1|CD978450
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|18383542|gb|BM416742.1|BM416742
EST:     TTAAAGAGAAAG                         GACCAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: TTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|78112770|gb|DV531164.1|DV531164
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|76285512|gb|DV025080.1|DV025080
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|71425166|gb|DR806565.1|DR806565
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|148951816|gb|EC897579.2|EC897579
EST:     AAGAAAGACTCAAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: AAGAAAGACTC-AAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|26557907|gb|CA830142.1|CA830142
EST:     CTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: CTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|71421466|gb|DR805441.1|DR805441
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|5055580|gb|AI734467.1|AI734467
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|71330056|gb|DR801767.1|DR801767
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|32847296|gb|CD986977.1|CD986977
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|71421467|gb|DR805442.1|DR805442
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|76285511|gb|DV025079.1|DV025079
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|5030602|gb|AI714796.1|AI714796
EST:     GAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: GAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|21809509|gb|BQ667827.1|BQ667827
EST:     AGACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAGCAGGGTTCTGAAAAGGAAG
genomic: AGACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|32835484|gb|CD975162.1|CD975162
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|71330054|gb|DR801766.1|DR801766
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|87157198|gb|DY401987.1|DY401987
EST:     AGACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: AGACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
EST: gi|71425163|gb|DR806564.1|DR806564
EST:     ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 311

ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG


Block sizes: 22 (upstream exon), 31 (downstream exon)
Score: 2

ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 126

ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcac ... tctcttgcagGAACAAATGCTGCAAGATGCAAACAGGGTTCTGAAAAGGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTCAAGTGTTACTTGATGAACTTTGTGACTTAAAGAGAAAGgtaatatcactgcagaaatgttactatgactctctgtttcaatacagaaaatcagaaatccaataatatatgcctgagcatccggcctcatctcttgcag

- - - - - - - - - - - - - - - -  AAGAGA