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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacaaactgtagggttttggttatcctattccgatgcattccatgtttacaagctgtagcaagcatcaattgctaattatgcatttccatatatatatattaaaaaaacaaaattacttgccgtctagctagattaatttgaaagcaagctaaatccattccccttcatgcatgtcatgtcatgtcatgtagGAGGACGTGAATATCATGAAGAATATGGGGTTCGACGCTTACCGGTTTTCGATCTCTTGGTCAAGAATATTCCCAA

Basic information

species Zea mays
transcript AC234160.1_FGT003
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC234160.1_FGT003 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g32364.1 (Oryza sativa), 3'ss of exon 2
gtgacaaactgtagggttttggttatcctattccgatgcattccatgtttacaagctgtagcaagcatcaattgctaattatgcatttccatatatatat-attaaaaaaacaaaattacttgccgtctagctagattaatttgaaagcaagctaaatccattccccttcatgcatgtcatgtcatgtcatgtagGAGGACGTGAATATCATGAAGAATATGGGGTTCGACGCTTACCGGTTTTCGATCTCTTGGTCAAGAATATTCCCAA
                                                                        ||  | |||| ||||  | | ||    | |||     ||| | |  |          |   ||||  |  ||| ||||    || |  | |   |||                  || || |||||||||| || |||||||| | |||||| ||||| || ||||| || || ||||| |||||||||||||||||||
----------------------------------------------------------------------catggaatttattcattcgcttgtactcctgattccgggaactatagaata--------aaacagat-gacctgagagcagag-aattaaacttggctttgc---------------tcttgcagGAGGACGTAAACATCATGAAAAGTATGGGTTTCGATGCGTACCGCTTCTCAATCTCATGGTCAAGAATATTCCCAA
















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|78081257|gb|DV509669.1|DV509669
EST:     CAAACAACGCCACCGCGGACGTGACTGTTGACGAGTACCATCGCTACAAG                         GAGGACGTGAATATCATGAAGAATATGGGGTTCGACGCTTACCGGTTTTCG
genomic: CAAACAACGCCACCGCGGACGTGACTGTTGACGAGTACCATCGCTACAAGgtgacaaact ... tgtcatgtagGAGGACGTGAATATCATGAAGAATATGGGGTTCGACGCTTACCGGTTTTCG
EST: gi|78104077|gb|DV522495.1|DV522495
EST:     CAAACAACGCCACCGCGGACGTGACTGTTGACGAGTACCATCGCTACAAG                         GAGGACGTGAATATCATGAAGAATATGGGGTTCGACGCTTACCGGTTTTCG
genomic: CAAACAACGCCACCGCGGACGTGACTGTTGACGAGTACCATCGCTACAAGgtgacaaact ... tgtcatgtagGAGGACGTGAATATCATGAAGAATATGGGGTTCGACGCTTACCGGTTTTCG
EST: gi|148941093|gb|EC885955.2|EC885955
EST:     CAAACAACGCCACCGCGGACGTGACTGTTGACGAGTACCATCGCTACAAG                         GAGGACGTGAATATCATGAAGAATATGGGGTTCGACGCTTACCGGTTTTCG
genomic: CAAACAACGCCACCGCGGACGTGACTGTTGACGAGTACCATCGCTACAAGgtgacaaact ... tgtcatgtagGAGGACGTGAATATCATGAAGAATATGGGGTTCGACGCTTACCGGTTTTCG
EST: gi|93016856|gb|EB642376.1|EB642376
EST:     CAAACAACGCCACCGCGGACGTGACTGTTGACGAGTACCATCGCTACAAG                         GAGGACGTGAATATCATGAAGAATATGGGGTTCGACGCTTACCGGTTTTCG
genomic: CAAACAACGCCACCGCGGACGTGACTGTTGACGAGTACCATCGCTACAAGgtgacaaact ... tgtcatgtagGAGGACGTGAATATCATGAAGAATATGGGGTTCGACGCTTACCGGTTTTCG
EST: gi|101386378|gb|EB815208.1|EB815208
EST:     CAAACAACGCCACCGCGGACGTGACTGTTGACGAGTACCATCGCTACAAG                         GAGGACGTGAATATCATGAAGAATATGGGGTTCGACGCTTACCGGTTTTCG
genomic: CAAACAACGCCACCGCGGACGTGACTGTTGACGAGTACCATCGCTACAAGgtgacaaact ... tgtcatgtagGAGGACGTGAATATCATGAAGAATATGGGGTTCGACGCTTACCGGTTTTCG
EST: gi|71437588|gb|DR818638.1|DR818638
EST:     CAAACAACGCCACCGCGGACGTGACTGTTGACGAGTACCATCGCTACAAG                         GAGGACGTGAATATCATGAAGAATATGGGGTTCGACGCTTACCGGTTTTCG
genomic: CAAACAACGCCACCGCGGACGTGACTGTTGACGAGTACCATCGCTACAAGgtgacaaact ... tgtcatgtagGAGGACGTGAATATCATGAAGAATATGGGGTTCGACGCTTACCGGTTTTCG
EST: gi|148979769|gb|EE026820.2|EE026820
EST:     CAAACAACGCCACCGCGGACGTGACTGTTGACGAGTACCATCGCTACAAG                         GAGGACGTGAATATCATGAAGAATATGGGGTTCGACGCTTACCGGTTTTCG
genomic: CAAACAACGCCACCGCGGACGTGACTGTTGACGAGTACCATCGCTACAAGgtgacaaact ... tgtcatgtagGAGGACGTGAATATCATGAAGAATATGGGGTTCGACGCTTACCGGTTTTCG

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: 44 (upstream exon), 25 (downstream exon)
Score: 7

GCGAGATCGCAAACAACGCCACCGCGGACGTGACTGTTGACGAGTACCATCGCTACAAGgtgacaaact ... tgtcatgtagGAGGACGTGAATATCATGAAGAATATGGGGTTCGACGCTTACCGGTTTTCGATCTCTTGGTCAAGAATATTCCCAA


Block sizes: 41 (upstream exon), 33 (downstream exon)
Score: 5

GCGAGATCGCAAACAACGCCACCGCGGACGTGACTGTTGACGAGTACCATCGCTACAAGgtgacaaact ... tgtcatgtagGAGGACGTGAATATCATGAAGAATATGGGGTTCGACGCTTACCGGTTTTCGATCTCTTGGTCAAGAATATTCCCAA


Block sizes: 47 (upstream exon), 33 (downstream exon)
Score: 17

GCGAGATCGCAAACAACGCCACCGCGGACGTGACTGTTGACGAGTACCATCGCTACAAGgtgacaaact ... tgtcatgtagGAGGACGTGAATATCATGAAGAATATGGGGTTCGACGCTTACCGGTTTTCGATCTCTTGGTCAAGAATATTCCCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgaaagcaagctaaatccattccccttcatgcatgtcatgtcatgtcatgtagGAGGACGTGAATATCATGAAGAATATGGGGTTCGACGCTTACCGGTTTTCGATCTCTTGGTCAAGAATATTCCCAA
          agctaaa  putative branch site (score: 17)
             taaat  TA-rich tract