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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttgggatatctcggtagttgaattttatctttgttgcataaatacagttgcttagacgtccagttttggactgtagtcttccttggcaatttggta...

Basic information

species Zea mays
transcript GRMZM5G806449_T03
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G806449_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g56850.1 (Oryza sativa), 5'ss of exon 10
TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttgggatatctcggtagttgaattttat---ctttgttgcataaatacagttgcttagacgtccagttttggactgtagtcttccttggcaatttggta-
||||||||||| || || || ||||||||||| ||||| |||||||| ||| |||||||||||||||| || ||||| |||||||||| |||||  ||  | | ||||  ||||   || |||  | | |||| | ||  ||  |        | | ||     ||  ||  ||     |    | 
TTGAGTAAAACAGCCGATGGCATAAAAGTTGTCACTGACAAAGGAGAGGAGATCATTGCAGATGTTGTTCTGTTTGCTACAGgtatttaggatagttcaat-gctgaaagttatgttctctgtcactttaata-atttctttgaatacatctctcttgatgactgt--tctgtgctggatgaaaaa
















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|161407234|gb|DW042290.1|DW042290
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|211287654|gb|FL367858.1|FL367858
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|62550294|gb|DN830714.1|DN830714
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|67018787|gb|CO447536.1|CO447536
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|8368856|gb|BE051801.1|BE051801
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|211462691|gb|FL336836.1|FL336836
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|211123447|gb|FL321141.1|FL321141
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|67026810|gb|CO455559.1|CO455559
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|211135367|gb|FL349825.1|FL349825
EST:     AACTGATAAAGGAGAAGANCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|32919439|gb|CF024251.1|CF024251
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|32794339|gb|CD946575.1|CD946575
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|24934507|gb|CA452725.1|CA452725
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|211396212|gb|FL320934.1|FL320934
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|47961736|gb|CN844445.1|CN844445
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|211460047|gb|FL333663.1|FL333663
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|51593048|gb|CV072194.1|CV072194
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|47962782|gb|CN845491.1|CN845491
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|33942527|gb|CF349127.1|CF349127
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|211540781|gb|FL336428.1|FL336428
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|108823920|gb|EC277928.1|EC277928
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|148937230|gb|EC881412.2|EC881412
EST:     TGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: TGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|211318389|gb|FL341246.1|FL341246
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
EST: gi|24934516|gb|CA452734.1|CA452734
EST:     AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAG                         GGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA
genomic: AACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGA

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: 516

TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 3929

TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 3059

TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 730

TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttggga ... ttggttgcagGGCGCACACCAAACTCCCAGAGACTGAACTTGCAAGCTGCAGGCGTTGAGATTGACCGGGTTGGAGCCATCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGAGTAAAACGGCTGACGGAATAAAAGTTGTAACTGATAAAGGAGAAGAGCTCATTGCAGATGTTGTCCTATTTGCGACAGgtatttgggatatctcggtagttgaattttatctttgttgcataaatacagttgcttagacgtccagttttggactgtagtcttccttggcaatttggta

- - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG