Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaagaagaaaatatatgactttccaatccatttgcaccacagctacctttttctatttcttccaagaaagcttatgcctagctacctacacggctacaccaccatctaaaccatctccttcctcatatatttctgcagAGGCGTCAAGGTGAGGAGCCTATGGTACTTCTTCCACTGGCTCCTCGGGATCGCGATCTGCGCCACGGGGATCGTCAACGTCTACATCGGCCTCCGCACC

Basic information

species Zea mays
transcript GRMZM2G024448_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024448_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g47635.1 (Oryza sativa), 3'ss of exon 4
gtagaagaagaaaatatatgactttccaatccatttgcaccacagctacctttttctatttcttccaagaaagcttatgcctagc--tacctacacggctacaccaccatctaaaccatctccttcctcatatatttctgcagAGGCGTCAAGGTGAGGAGCCTATGGTACTTCTTCCACTGGCTCCTCGGGATCGCGATCTGCGCCACGGGGATCGTCAACGTCTACATCGGCCTCCGCACC
                                                               |  |||||| ||  |  ||     | | ||||  | |    |    ||||     | |||||  |    | |||||||||||| || ||||| |||||| | ||||||||| |||||||||| || || ||||| || ||||| || || ||    || |||||||| ||||| | ||| 
--------------------------------------------------------------gtagaagaaaactactttctcatgattcttacaaagttttgtc----tctaggatttatccttttt---gtgtttctgcagAGGTGTTAAGGTAAGGAGCTTGTGGTACTTCCTCCACTGGCTTCTTGGCATCGCAATTTGCGCAACTGGCATTACAAATGTCTACATTGGCCTTCACACA
















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|110223334|gb|EC905232.1|EC905232
EST:     TATGGAGTCATGTGGCTCCAGCCAATTCTCGGCTTCTTCAGACCAGAAAG                         AGGCGTCAAGGTGAGGAGCCTATGGTACTTCTTCCACTGGCTCCTCGGGAT
genomic: TATGGAGTCATGTGGCTCCAGCCAATTCTCGGCTTCTTCAGACCAGAAAGgtagaagaag ... atttctgcagAGGCGTCAAGGTGAGGAGCCTATGGTACTTCTTCCACTGGCTCCTCGGGAT
EST: gi|211324932|gb|FL352849.1|FL352849
EST:     ATNGGAGTCATGTGGCTCCAGCCAATTCTCGGCTTCTTCAGACCAGAAAG                         AGGCGTCAAGGTGAGGAGCCTATGGTACTTCTTCCACTG
genomic: AT-GGAGTCATGTGGCTCCAGCCAATTCTCGGCTTCTTCAGACCAGAAAGgtagaagaag ... atttctgcagAGGCGTCAAGGTGAGGAGCCTATGGTACTTCTTCCACTG
EST: gi|211421935|gb|FL433257.1|FL433257
EST:     TAT-GAGTCATGT-GCTCCAGCCAATTCTCGGCTTCTTCAGACCAGAAAG                         A-GCGTCAAGGTGAGGAGCCTATGGTACTTCTTCCACTGGCTCCTCGGGAT
genomic: TATGGAGTCATGTGGCTCCAGCCAATTCTCGGCTTCTTCAGACCAGAAAGgtagaagaag ... atttctgcagAGGCGTCAAGGTGAGGAGCCTATGGTACTTCTTCCACTGGCTCCTCGGGAT
EST: gi|211115536|gb|FL311598.1|FL311598
EST:     TATGGAGTCATGTGGCTCCAGCCAATTCTCGGCTTCTTCAGACCAGAAAG                         AGGCGTCAAGGTGAGGAGCCTATGGTACTTCTTCCACTGGCTCCTCGGGAT
genomic: TATGGAGTCATGTGGCTCCAGCCAATTCTCGGCTTCTTCAGACCAGAAAGgtagaagaag ... atttctgcagAGGCGTCAAGGTGAGGAGCCTATGGTACTTCTTCCACTGGCTCCTCGGGAT
EST: gi|101397326|gb|EB820586.1|EB820586
EST:     TATGGAGTCATGTGGCTCCAGCCAATTCTCGGCTTCTTCAGACCAGAAAG                         AGGCGTCAAGGTGAGGAGCCTATGGTACTTCTTCCACTGGCTCCTCGGGAT
genomic: TATGGAGTCATGTGGCTCCAGCCAATTCTCGGCTTCTTCAGACCAGAAAGgtagaagaag ... atttctgcagAGGCGTCAAGGTGAGGAGCCTATGGTACTTCTTCCACTGGCTCCTCGGGAT
EST: gi|148959084|gb|EE010572.2|EE010572
EST:     TATGGAGTCATGTGGCTCCAGCCAATTCTCGGCTTCTTCAGACCAGAAAG                         AGGCGTCAAGGTGAGGAGCCTATGGAACTTCTTCCACTGGCTC
genomic: TATGGAGTCATGTGGCTCCAGCCAATTCTCGGCTTCTTCAGACCAGAAAGgtagaagaag ... atttctgcagAGGCGTCAAGGTGAGGAGCCTATGGTACTTCTTCCACTGGCTC

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: 30 (upstream exon), 20 (downstream exon)
Score: 2

ACTTCGAGAACTCCTTCAGCAACAGCCACCAAAGAGTGGGGCTGGCGCTGTATGGAGTCATGTGGCTCCAGCCAATTCTCGGCTTCTTCAGACCAGAAAGgtagaagaag ... atttctgcagAGGCGTCAAGGTGAGGAGCCTATGGTACTTCTTCCACTGGCTCCTCGGGATCGCGATCTGCGCCACGGGGATCGTCAACGTCTACATCGGCCTCCGCACC


Block sizes: 30 (upstream exon), 49 (downstream exon)
Score: 5

ACTTCGAGAACTCCTTCAGCAACAGCCACCAAAGAGTGGGGCTGGCGCTGTATGGAGTCATGTGGCTCCAGCCAATTCTCGGCTTCTTCAGACCAGAAAGgtagaagaag ... atttctgcagAGGCGTCAAGGTGAGGAGCCTATGGTACTTCTTCCACTGGCTCCTCGGGATCGCGATCTGCGCCACGGGGATCGTCAACGTCTACATCGGCCTCCGCACC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 13

ACTTCGAGAACTCCTTCAGCAACAGCCACCAAAGAGTGGGGCTGGCGCTGTATGGAGTCATGTGGCTCCAGCCAATTCTCGGCTTCTTCAGACCAGAAAGgtagaagaag ... atttctgcagAGGCGTCAAGGTGAGGAGCCTATGGTACTTCTTCCACTGGCTCCTCGGGATCGCGATCTGCGCCACGGGGATCGTCAACGTCTACATCGGCCTCCGCACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctacacggctacaccaccatctaaaccatctccttcctcatatatttctgcagAGGCGTCAAGGTGAGGAGCCTATGGTACTTCTTCCACTGGCTCCTCGGGATCGCGATCTGCGCCACGGGGATCGTCAACGTCTACATCGGCCTCCGCACC
                    atctaaa  putative branch site (score: 13)
                              tctccttcctcatata  putative PPT
                                       tcatatattt  TA-rich tract