Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcgctgtttcttgtgtcgctcgatgccttcttttctgtaggtttactttatcccaatcggcttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATGGAGCCACTACGGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCG

Basic information

species Zea mays
transcript GRMZM2G173321_T02
intron # 1
splice site 3'
intron type U2

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|211138903|gb|FL206376.1|FL206376
EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGT-ATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
EST: gi|26456740|gb|CA828323.1|CA828323
EST:     ACCTCTCCGCCGCCGTCAGAGAAGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
EST: gi|76936192|gb|DV174627.1|DV174627
EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
EST: gi|149051910|gb|EE156043.2|EE156043
EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
EST: gi|78093455|gb|DV521829.1|DV521829
EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
EST: gi|26457345|gb|CA828928.1|CA828928
EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
EST: gi|211138901|gb|FL206374.1|FL206374
EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
EST: gi|60397540|gb|DN230356.1|DN230356
EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
EST: gi|93281470|gb|EB673734.1|EB673734
EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
EST: gi|211138904|gb|FL206377.1|FL206377
EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
EST: gi|211138900|gb|FL206373.1|FL206373
EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
EST: gi|211139833|gb|FL206379.1|FL206379
EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
EST: gi|211139832|gb|FL206378.1|FL206378
EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
EST: gi|211138902|gb|FL206375.1|FL206375
EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCG-CGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
EST: gi|20507484|gb|BQ279652.1|BQ279652
EST:     ACCTCTCCGCCGCCG-CAGAGAAGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
EST: gi|71333335|gb|DR803729.1|DR803729
EST:     ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCG                         GTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG
genomic: ACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATG

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), 47 (downstream exon)
Score: 96

GAGGCAGGTGGAGGCGAACAAGCGGAAGCTGGAGGAGCTTCAGCTCCACTACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATGGAGCCACTACGGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCG


Block sizes: 28 (upstream exon), 43 (downstream exon)
Score: 23

GAGGCAGGTGGAGGCGAACAAGCGGAAGCTGGAGGAGCTTCAGCTCCACTACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATGGAGCCACTACGGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 27

GAGGCAGGTGGAGGCGAACAAGCGGAAGCTGGAGGAGCTTCAGCTCCACTACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATGGAGCCACTACGGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 10

GAGGCAGGTGGAGGCGAACAAGCGGAAGCTGGAGGAGCTTCAGCTCCACTACCTCTCCGCCGCCGTCAGAGAGGCCGCAGCCGCCGCCAAGCCCTCGCCGgtttgcgctg ... ttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATGGAGCCACTACGGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgctcgatgccttcttttctgtaggtttactttatcccaatcggcttttctgcagGTCAAGAAGCGGAAGGCGCGGGTGCCGCTTGACGCCGCCGACTCCGTGATGGAGCCACTACGGCGGTCCGGCCGGCTCGCCAACCTCCCCGATAAGTCCG
                                            cttttctgc  CT-rich tract
                         tttactttat  TA-rich tract