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'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaccatccattgttttccaatttaagctatcaacataatataccttaacttttttttttatgcttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG

Basic information

species Zea mays
transcript AC196426.3_FGT007
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC196426.3_FGT007 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g39310.1 (Oryza sativa), 3'ss of exon 11
gtgagtaccatccattgttttccaatttaagctatcaacataatataccttaacttttttttttatgc-ttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG
|| || | | |       ||||       || |||||| || ||  |   | || | ||||     || || | ||||||||||||| ||||||||||| ||||||||||| |||||||||||| || |||| |||| ||||||||||
gtaagcatcctt-gcccctttcagtagcgagttatcaaaattatgcatgctgacatctttt---gcgcatttaattcagGTTATGGTCGCTACTGTACGCTGTGAGGAAATCGGTAATGAGAAAATTGCCAGTTTTACAGCTGATGAG
















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|211457038|gb|FK967316.1|FK967316
EST:     TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAA                         GTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
genomic: TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAAgtgagtacca ... ttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
EST: gi|211043098|gb|FK967329.1|FK967329
EST:     TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAA                         GTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
genomic: TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAAgtgagtacca ... ttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
EST: gi|211454906|gb|FK967300.1|FK967300
EST:     TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAA                         GTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
genomic: TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAAgtgagtacca ... ttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
EST: gi|211457037|gb|FK967315.1|FK967315
EST:     TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAA                         GTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
genomic: TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAAgtgagtacca ... ttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
EST: gi|211454909|gb|FK967303.1|FK967303
EST:     TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAA                         GTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
genomic: TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAAgtgagtacca ... ttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
EST: gi|211454913|gb|FK967307.1|FK967307
EST:     TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAA                         GTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
genomic: TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAAgtgagtacca ... ttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
EST: gi|211454904|gb|FK967298.1|FK967298
EST:     TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAA                         GTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
genomic: TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAAgtgagtacca ... ttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
EST: gi|211043097|gb|FK967328.1|FK967328
EST:     TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAA                         GTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
genomic: TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAAgtgagtacca ... ttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
EST: gi|211457040|gb|FK967318.1|FK967318
EST:     TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAA                         GTTATGGNGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
genomic: TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAAgtgagtacca ... ttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
EST: gi|211457033|gb|FK967311.1|FK967311
EST:     TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAA                         GTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
genomic: TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAAgtgagtacca ... ttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
EST: gi|211454911|gb|FK967305.1|FK967305
EST:     TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAA                         GTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
genomic: TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAAgtgagtacca ... ttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
EST: gi|211457035|gb|FK967313.1|FK967313
EST:     TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAA                         GTTATGGTGGCTACTGTACGTTG
genomic: TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAAgtgagtacca ... ttcacttcagGTTATGGTGGCTACTGTACGTTG
EST: gi|211457034|gb|FK967312.1|FK967312
EST:     TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAA                         GTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
genomic: TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAAgtgagtacca ... ttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
EST: gi|211457046|gb|FK967324.1|FK967324
EST:     TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAA                         GTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC
genomic: TTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAAgtgagtacca ... ttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACC

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: 315

TCGTCGTGGTGTTGTCCCAGCTTCAGGTTTCTCATTTAGTTCCCAGCAATTTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAAgtgagtacca ... ttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 404

TCGTCGTGGTGTTGTCCCAGCTTCAGGTTTCTCATTTAGTTCCCAGCAATTTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAAgtgagtacca ... ttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 340

TCGTCGTGGTGTTGTCCCAGCTTCAGGTTTCTCATTTAGTTCCCAGCAATTTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAAgtgagtacca ... ttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 377

TCGTCGTGGTGTTGTCCCAGCTTCAGGTTTCTCATTTAGTTCCCAGCAATTTTGGAAAGTCATCAAGGAGAACAAAGATCTTGATTTGCCTGCTCATAAAgtgagtacca ... ttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttaagctatcaacataatataccttaacttttttttttatgcttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG
                        ccttaac  putative branch site (score: 377)
                              cttttttttttatgct  CT-rich tract
         tatcaacataatatac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaccatccattgttttccaatttaagctatcaacataatataccttaacttttttttttatgcttcacttcagGTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT