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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCGGAACCTCTTCTGCAAGTGGTGGAGTGTCGCATTTGTCAGGAGGAAGATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgttactccattcttcttattcatttattatggatatataattatactccatatctaattattatctgaagtgtcaagagttttgcctgtagcga...

Basic information

species Zea mays
transcript GRMZM2G113619_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113619_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os09g24650.3 (Oryza sativa), 5'ss of exon 3
AGCGGAACCTCTTCTGCAAGTGGTGGAGTGTCGCATTTGTCAGGAGGAAGATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttc--gtgttactccattcttcttattcatttattatggatatataattatac-tccatatctaa---ttattatctgaagtgtcaagagttttgcctgtagcga
||  ||||||||||||||  ||||||| ||||||||||||||||||||||| ||||| |||||| | ||||| |||||||| || |||||||||||||||||||     |||  ||||       | |  ||  ||     | | || | |    ||  | | |||     |  || |||| |      || ||  |  ||     
AGAAGAACCTCTTCTGCAGTTGGTGGAATGTCGCATTTGTCAGGAGGAAGACAGTATAAAAAATCTGGAGAGCCCATGTGCCTGTACTGGCAGTCTAAAGgttcaaacattatcccatgaactccagtt-ttagttgcaagtgtttattcaagtatctctgtttaaagggcaacatatgaaattaggcaagattaactcgt-----
















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|78086642|gb|DV515035.1|DV515035
EST:     ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAG                         TATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgtta ... ttctatgcagTATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|78089708|gb|DV518082.1|DV518082
EST:     ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAG                         TATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgtta ... ttctatgcagTATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|76280760|gb|DV020328.1|DV020328
EST:     ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAG                         TATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgtta ... ttctatgcagTATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|91053257|gb|EB163675.1|EB163675
EST:     ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAG                         TATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgtta ... ttctatgcagTATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|71424785|gb|DR806435.1|DR806435
EST:     ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAG                         TATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgtta ... ttctatgcagTATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|50325343|gb|CO520469.1|CO520469
EST:     ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAG                         TATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgtta ... ttctatgcagTATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|91877839|gb|EB407796.1|EB407796
EST:     ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAG                         TATGCTCATAGGACTTGTGTACAACGA
genomic: ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgtta ... ttctatgcagTATGCTCATAGGACTTGTGTACAACGA
EST: gi|93283253|gb|EB675517.1|EB675517
EST:     ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAG                         TATGCTCATAGGACTTGTGTACAACGATGGTGCCATGAGAAAGGAGATGTA
genomic: -TAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgtta ... ttctatgcagTATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|211143062|gb|FL281157.1|FL281157
EST:     ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAG                         TATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgtta ... ttctatgcagTATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|91057080|gb|EB167498.1|EB167498
EST:     ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAG                         TATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgtta ... ttctatgcagTATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|8551597|gb|BE128942.1|BE128942
EST:     ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAG                         TATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgtta ... ttctatgcagTATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|71766653|gb|DR964590.1|DR964590
EST:     ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAG                         TATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgtta ... ttctatgcagTATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|71311806|gb|DR792364.1|DR792364
EST:     ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAG                         TATGCTCATAGGACTTGTGTACAACGATGGTGCAAT
genomic: ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgtta ... ttctatgcagTATGCTCATAGGACTTGTGTACAACGATGGTGCAAT
EST: gi|440689|gb|T14710.1|T14710
EST:     ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAG                         TATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgtta ... ttctatgcagTATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|91049342|gb|EB159760.1|EB159760
EST:     ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAG                         TATGCTCATAGGACTT
genomic: ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgtta ... ttctatgcagTATGCTCATAGGACTT
EST: gi|76291932|gb|DV031500.1|DV031500
EST:     ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAG                         TATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgtta ... ttctatgcagTATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTA

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: 145

AGCGGAACCTCTTCTGCAAGTGGTGGAGTGTCGCATTTGTCAGGAGGAAGATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgtta ... ttctatgcagTATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTAACATGTGAAATATGTCATGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 62

AGCGGAACCTCTTCTGCAAGTGGTGGAGTGTCGCATTTGTCAGGAGGAAGATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgtta ... ttctatgcagTATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTAACATGTGAAATATGTCATGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 112

AGCGGAACCTCTTCTGCAAGTGGTGGAGTGTCGCATTTGTCAGGAGGAAGATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgtta ... ttctatgcagTATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTAACATGTGAAATATGTCATGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 133

AGCGGAACCTCTTCTGCAAGTGGTGGAGTGTCGCATTTGTCAGGAGGAAGATAGTATCAAAAATTTAGAGAGTCCATGTGCTTGCACTGGCAGTCTAAAGgttcgtgtta ... ttctatgcagTATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTAACATGTGAAATATGTCATGAG