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

...taatttaatcacaatgaagttaaaataagtttcttaatgtgaatgtgtaatgcttagctaagatgcatgtaattgattttggctttattggctattacagGAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCAGCTTGAGAAGCAAATTGATTCATCCTTAAGTCACATAAGATCCACAAGG

Basic information

species Zea mays
transcript GRMZM2G097059_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097059_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g32948.1 (Oryza sativa), 3'ss of exon 3
---taatttaatcacaatga---agttaaaataagtttcttaatgtgaatgtgtaatgcttagctaagatgcatgtaattgattttggctttattggctattacagGAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCAGCTTGAGAAGCAAATTGATTCATCCTTAAGTCACATAAGATCCACAAGG
   |  |||  |||||  |    | ||     ||  || | ||| | | |||| ||  || |    ||    |  || | ||| ||   | | ||| | ||||||||||| | |||||||||||||| ||  |||||||  | |||||||| || ||||||||||| ||| ||||||||||||| || ||||| ||||||||||||
aacttttttgttcacatcgttccaatttcttcaaactt-tcaattttagtgtggaa--ctaaatacagcctaacttagtagatctt---tctgttgacaattacagGAATCTTCTTGGTGAAGATCTTGGGACACTTGGCATAAAAGAGCTAGAGCAGCTTGAGAAACAACTTGATTCATCCTTGAGGCACATTAGATCCACAAGG
















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|32833483|gb|CD973161.1|CD973161
EST:     ACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
genomic: ACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAGgcaagttgag ... gctattacagGAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
EST: gi|67039080|gb|CO465335.1|CO465335
EST:     GAGTACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
genomic: GAGTACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAGgcaagttgag ... gctattacagGAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
EST: gi|24961636|gb|CA483635.1|CA483635
EST:     GAGTACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
genomic: GAGTACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAGgcaagttgag ... gctattacagGAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
EST: gi|78115260|gb|DV533648.1|DV533648
EST:     GAGTACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
genomic: GAGTACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAGgcaagttgag ... gctattacagGAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
EST: gi|32839046|gb|CD978727.1|CD978727
EST:     CTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
genomic: CTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAGgcaagttgag ... gctattacagGAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
EST: gi|78074567|gb|DV503001.1|DV503001
EST:     GAGTACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
genomic: GAGTACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAGgcaagttgag ... gctattacagGAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
EST: gi|8665529|gb|BE186345.1|BE186345
EST:     GAGTACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
genomic: GAGTACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAGgcaagttgag ... gctattacagGAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
EST: gi|67016010|gb|CO444759.1|CO444759
EST:     GAGTACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
genomic: GAGTACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAGgcaagttgag ... gctattacagGAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
EST: gi|87153067|gb|DY397856.1|DY397856
EST:     GAGTACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
genomic: GAGTACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAGgcaagttgag ... gctattacagGAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
EST: gi|8383276|gb|BE056219.1|BE056219
EST:     GAGTACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
genomic: GAGTACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAGgcaagttgag ... gctattacagGAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
EST: gi|18648993|gb|BM497812.1|BM497812
EST:     GAGTACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAG                         GAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA
genomic: GAGTACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAGgcaagttgag ... gctattacagGAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCA

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 2 RNA-Seq libraries.


Block sizes: 42 (upstream exon), 42 (downstream exon)
Score: 173

TTAGTCCAGAACAGCCGCAATGAGTACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAGgcaagttgag ... gctattacagGAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCAGCTTGAGAAGCAAATTGATTCATCCTTAAGTCACATAAGATCCACAAGG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 318

TTAGTCCAGAACAGCCGCAATGAGTACCTTAAACTGAAAGCAAAGGTGGATAATTTACAGAGGACTCAGAGgcaagttgag ... gctattacagGAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCAGCTTGAGAAGCAAATTGATTCATCCTTAAGTCACATAAGATCCACAAGG




<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaatgcttagctaagatgcatgtaattgattttggctttattggctattacagGAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCAGCTTGAGAAGCAAATTGATTCATCCTTAAGTCACATAAGATCCACAAGG
                         aattgat  putative branch site (score: 318)
                     atgtaattgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatttaatcacaatgaagttaaaataagtttcttaatgtgaatgtgtaatgcttagctaagatgcatgtaattgattttggctttattggctattacagGAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCAGCTTGAGAAGCAAATTGATTCATCCTTAAGTCACATAAGATCCACAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - -atcacaa
- - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - gtgaatg
- - - - - - - - - - - - - - - - - - - - - - - - -atgctta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgt