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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCTCCTAGACCGCCTCGAGGACTGCAGGAAAGCCTTCCCCTCCGCACTCTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCGgtgagccaccttgcatcctgctcctctagtcttctttctttagtcggtactgtactccagatagagccttgccgccatcaagtttccaccaattttgcacagaaatgcactgaatgcctccgtcgcag

Basic information

species Zea mays
transcript GRMZM2G087692_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087692_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os12g10200.1 (Oryza sativa), 5'ss of exon 1
AATCTCCTAGACCGCCTCGAGGACTGCAGGAAAGCCTTCCCCTCCGCACTCTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCGgtgagcca---ccttgcatcctgctcctctagtcttctttctttagtcggtactgtactccagatagagccttgccgccatcaagtttccaccaattttgcacagaaatgcactgaatgcctccgtcgcag-------------------------------
|| ||||| ||||||||||||||||||||||| || ||||||||||| |||||||| || ||||||||||||||||||||||||| |||||| ||||||||||||  |   |||   |||   ||||||| ||  |   ||||  ||    ||    || || ||  | |  |     |    | |||   |   ||||     || | | | |   |      || |                                  
AACCTCCTCGACCGCCTCGAGGACTGCAGGAAGGCGTTCCCCTCCGCGCTCTGCCTCGGCGGCTCCGCCGGCGCCGTCCGCCGCTCGCTCCGCGGCCGCGgtgagtgagctcctcaaatctatctcctcttgttgt---tcttgcgtgacaacccctctacatatgcaccagtagaatcgctgaatttttccagcttttaacttgatagggagtatgttgtaatgtggtgatgggaggaattggggttttcttgtgtaacag
















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|50328095|gb|CO523221.1|CO523221
EST:     CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCG                         GTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
genomic: CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCGgtgagccacc ... tccgtcgcagGTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
EST: gi|87157627|gb|DY402416.1|DY402416
EST:     CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCG                         GTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
genomic: CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCGgtgagccacc ... tccgtcgcagGTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
EST: gi|101393422|gb|EB818643.1|EB818643
EST:     CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCG                         GTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
genomic: CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCGgtgagccacc ... tccgtcgcagGTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
EST: gi|89762249|gb|DY689931.1|DY689931
EST:     CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCG                         GTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
genomic: CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCGgtgagccacc ... tccgtcgcagGTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
EST: gi|71440891|gb|DR821941.1|DR821941
EST:     CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCG                         GTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
genomic: CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCGgtgagccacc ... tccgtcgcagGTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
EST: gi|22819976|gb|BU500066.1|BU500066
EST:     CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCG                         GTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
genomic: CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCGgtgagccacc ... tccgtcgcagGTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
EST: gi|13316098|gb|BG410545.1|BG410545
EST:     CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCG                         GTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
genomic: CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCGgtgagccacc ... tccgtcgcagGTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
EST: gi|78078319|gb|DV506734.1|DV506734
EST:     CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCG                         GTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
genomic: CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCGgtgagccacc ... tccgtcgcagGTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
EST: gi|211216128|gb|FL114057.1|FL114057
EST:     CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCG                         GTGGGATTGAGAGGCTGATCATGATGGMACATGTCAGCCGATATGGTGAAG
genomic: CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCGgtgagccacc ... tccgtcgcagGTGGGATTGAGAGGCTGATCATGATGG-ACATGTCAGCCGATATGGTGAAG
EST: gi|74241982|gb|DT649896.1|DT649896
EST:     CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCG                         GTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
genomic: CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCGgtgagccacc ... tccgtcgcagGTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
EST: gi|26560078|gb|CA832313.1|CA832313
EST:     CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCG                         GTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
genomic: CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCGgtgagccacc ... tccgtcgcagGTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
EST: gi|211216133|gb|FL114062.1|FL114062
EST:     CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCG                         GTGGGATTGAGAGGCTGATCATGATGGAC
genomic: CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCGgtgagccacc ... tccgtcgcagGTGGGATTGAGAGGCTGATCATGATGGAC
EST: gi|26456098|gb|CA827681.1|CA827681
EST:     CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCG                         GTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
genomic: CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCGgtgagccacc ... tccgtcgcagGTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
EST: gi|93282992|gb|EB675256.1|EB675256
EST:     CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCG                         GTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA
genomic: CTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCGgtgagccacc ... tccgtcgcagGTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGA

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: 48 (upstream exon), 48 (downstream exon)
Score: 41

AATCTCCTAGACCGCCTCGAGGACTGCAGGAAAGCCTTCCCCTCCGCACTCTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCGgtgagccacc ... tccgtcgcagGTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGAAGTGGCGAGAGTCAGAGAATGCCACTGGTGATGGGCCTGAGACCCACTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 29

AATCTCCTAGACCGCCTCGAGGACTGCAGGAAAGCCTTCCCCTCCGCACTCTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCGgtgagccacc ... tccgtcgcagGTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGAAGTGGCGAGAGTCAGAGAATGCCACTGGTGATGGGCCTGAGACCCACTT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 39

AATCTCCTAGACCGCCTCGAGGACTGCAGGAAAGCCTTCCCCTCCGCACTCTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCGgtgagccacc ... tccgtcgcagGTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGAAGTGGCGAGAGTCAGAGAATGCCACTGGTGATGGGCCTGAGACCCACTT


Block sizes: 40 (upstream exon), 46 (downstream exon)
Score: 29

AATCTCCTAGACCGCCTCGAGGACTGCAGGAAAGCCTTCCCCTCCGCACTCTGCCTTGGGGGCTCCGCCGGCGCCGTCCGCCGCTTGCTCCGTGGCCGCGgtgagccacc ... tccgtcgcagGTGGGATTGAGAGGCTGATCATGATGGACATGTCAGCCGATATGGTGAAGAAGTGGCGAGAGTCAGAGAATGCCACTGGTGATGGGCCTGAGACCCACTT