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

CATGGCATGCCCTGCCTTGCCACTGTGCCCTTTGGCACAAACAGAAGCTGAACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtctgacatattgtgagaaatttgttttgtagatgcagatgcatatatttggagccctgtcatttcatgttactgtatctgcttaatag

Basic information

species Zea mays
transcript GRMZM2G090338_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090338_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g42350.1 (Oryza sativa), 5'ss of exon 5
CATGGCATGCCCTGCCTTGCCACTGTGCCCTTTGGCACAAACAGAAGCTGAACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtctgacatattgtgagaaatttgttttgtagatgcagatgcatatatttggagccctgtcatttcatgttactgtatctgcttaatag
||||||||| |||||||| |||||||||||| | |||||||||||||||||||| |||||  | || ||||||||||||||||||||||| ||  |||||||||  ||||| | | |||| | ||| ||    || | ||     ||  |  ||  ||| || ||||| || |  | |   | |||  |||||||
CATGGCATGTCCTGCCTTACCACTGTGCCCTCTAGCACAAACAGAAGCTGAACGAGGGATTCTGCCGATTCTTAAACGAATTAGAGCAGTTTTTGATAAGgtata-gtctgtcgtcttgtcacaaaatt----tgaacat-----tgtgtgcatc-ggatccatgtcagttgacataatgttctctcattaatag
















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|78114428|gb|DV532817.1|DV532817
EST:     AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAG                         GTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
genomic: AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
EST: gi|32840970|gb|CD980651.1|CD980651
EST:     AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAG                         GTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
genomic: AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
EST: gi|32841089|gb|CD980770.1|CD980770
EST:     AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAG                         GTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
genomic: AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
EST: gi|60339740|gb|DN206713.1|DN206713
EST:     AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAG                         GTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
genomic: AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
EST: gi|76015451|gb|DT942621.1|DT942621
EST:     AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAG                         GTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
genomic: AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
EST: gi|60349845|gb|DN216818.1|DN216818
EST:     CTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAG                         GTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
genomic: CTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
EST: gi|13562272|gb|BG550492.1|BG550492
EST:     AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAG                         GTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
genomic: AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
EST: gi|67030464|gb|CO459213.1|CO459213
EST:     AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAG                         GTTGGTATAAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
genomic: AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
EST: gi|71330578|gb|DR802057.1|DR802057
EST:     AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAG                         GTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
genomic: AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
EST: gi|60355018|gb|DN221991.1|DN221991
EST:     AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAG                         GTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
genomic: AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
EST: gi|47961924|gb|CN844633.1|CN844633
EST:     AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAG                         GTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGCTGCCCT
genomic: AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
EST: gi|60400045|gb|DN232852.1|DN232852
EST:     CGAATTAGAGCAGTCTTCAATAAG                         GTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
genomic: CGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
EST: gi|110540151|gb|EE044071.1|EE044071
EST:     AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAG                         GTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
genomic: AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
EST: gi|60343246|gb|DN210219.1|DN210219
EST:     AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAG                         GTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
genomic: AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
EST: gi|211330976|gb|FL100738.1|FL100738
EST:     AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAG                         GTTGGTATAAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
genomic: AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
EST: gi|148947629|gb|EC893109.2|EC893109
EST:     AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAG                         GTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
genomic: AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
EST: gi|33091872|gb|CF051866.1|CF051866
EST:     AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAG                         GTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
genomic: AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
EST: gi|32840868|gb|CD980549.1|CD980549
EST:     AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAG                         GTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
genomic: AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
EST: gi|149085314|gb|EE174820.2|EE174820
EST:     AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAG                         GTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
genomic: AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
EST: gi|32834834|gb|CD974512.1|CD974512
EST:     AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAG                         GTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT
genomic: AACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCT

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), 49 (downstream exon)
Score: 299

CATGGCATGCCCTGCCTTGCCACTGTGCCCTTTGGCACAAACAGAAGCTGAACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCTAATGGATGCGCTAGACCATATATGGCAGAGCTTGGTTTTGTTGGTGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1172

CATGGCATGCCCTGCCTTGCCACTGTGCCCTTTGGCACAAACAGAAGCTGAACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCTAATGGATGCGCTAGACCATATATGGCAGAGCTTGGTTTTGTTGGTGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1399

CATGGCATGCCCTGCCTTGCCACTGTGCCCTTTGGCACAAACAGAAGCTGAACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCTAATGGATGCGCTAGACCATATATGGCAGAGCTTGGTTTTGTTGGTGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 388

CATGGCATGCCCTGCCTTGCCACTGTGCCCTTTGGCACAAACAGAAGCTGAACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtct ... tgcttaatagGTTGGTATCAAGGATTCGGAGTCTGTGGTTGTGAGGATAACTGGATGCCCTAATGGATGCGCTAGACCATATATGGCAGAGCTTGGTTTTGTTGGTGATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGGCATGCCCTGCCTTGCCACTGTGCCCTTTGGCACAAACAGAAGCTGAACGGGGGATCTTACCCATTCTTAAACGAATTAGAGCAGTCTTCAATAAGgtatttgtctgacatattgtgagaaatttgttttgtagatgcagatgcatatatttggagccctgtcatttcatgttactgtatctgcttaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG