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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAGCAACTTTTCTTGCATTTCATCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatggtggctttgtttttctttcattgcacagatagaagttaagtatgacttatttgctctttgtacag

Basic information

species Zea mays
transcript GRMZM2G030422_T02
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030422_T03 (Zea mays), 5'ss of exon 23
lower sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 22
GGCAGCAACTTTTCTTGCATTTCATCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattca------tggtggctttgtttttcttt--cattgcacagatagaagttaagtatgacttattt--------gctctttgtacag
||| ||||| |||||||| || ||||| |||||||||||||| || ||||||||||||||||||||||||||||||||||| ||||| |||||||||||||||||        |  |||| ||| | | | ||    ||  | | |  | |   |  |   |   ||||          |||||| ||||
GGCGGCAACGTTTCTTGCTTTCCATCCTCAAGATAACAACATTATAGCAATTGGAATGGATGACTCAACCATCCAAATCTACAATGTTCGAATTGATGAGgtattagcacatctaatggcattgctctgcgttattcttataaaaaatggaacaagattcaatcaattttttttttgattctttgcacag

upper sequence: GRMZM2G030422_T03 (Zea mays), 5'ss of exon 23
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 21
GGCAGCAACTTTTCTTGCATTTCATCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtat-tcatggtggctttgtt------------tttctttcattgcacagatagaagttaagtatgacttatttgctctttgtacag--------------------------------------------
 ||||| |||||||||||||||||||| ||||| ||||| || ||||| || |||||||| || || || || || || |||||||| ||  | |||||||||| | ||   | | |||               || | | |||   || |     ||| | |     |   | | | ||  || |                                             
AGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtatgttatcaagtccttgccagataagttgcgcttttgtgatttgtcacacttgtgttga-tgcatatgtctcggttttaatataagactgtcgttgatacgcttaataagatttctctgctgttcacag

upper sequence: GRMZM2G030422_T03 (Zea mays), 5'ss of exon 23
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 21
GGCAGCAACTTTTCTTGCATTTCATCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattc-atggtggctttgtttttctttcattgcacagatagaagttaagtatgacttatttgctctttgtacag-------------------------------------------
 ||||| ||||||||||| || ||||||||||| |||||||| ||||| || |||||||| || ||||| || || || |||||||| ||  | |||||||||||  |    | | || ||| | | | ||  | |  |   | ||| | |   | |  |  | |  |  |  ||                                           
AGCAGCTACTTTTCTTGCGTTCCATCCCCAAGACAACAACATCATTGCCATAGGAATGGAGGATTCAACAATACAGATTTATAATGTTCGTGTAGATGAGgtattttaccaggccgttctttctttgtgatctcccgtacctatgttgatttgtattcgtcagtttgtattctagatcccgaataatgtgcctaattagagctttctgctgttggcag

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|211016182|gb|FL013386.1|FL013386
EST:     TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAG                         GTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGNCTTGCCTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatgg ... ctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
EST: gi|211016174|gb|FL013378.1|FL013378
EST:     TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAG                         GTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatgg ... ctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
EST: gi|211016178|gb|FL013382.1|FL013382
EST:     TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAG                         GTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatgg ... ctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
EST: gi|211018955|gb|FL013387.1|FL013387
EST:     TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAG                         GTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatgg ... ctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
EST: gi|211016172|gb|FL013376.1|FL013376
EST:     TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAG                         GTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatgg ... ctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
EST: gi|37422204|gb|CF648808.1|CF648808
EST:     TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAG                         GTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatgg ... ctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
EST: gi|211016173|gb|FL013377.1|FL013377
EST:     TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAG                         GTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGNCTTGCCTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatgg ... ctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
EST: gi|211016170|gb|FL013374.1|FL013374
EST:     TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAG                         GTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatgg ... ctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
EST: gi|211018956|gb|FL013388.1|FL013388
EST:     TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAG                         GTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatgg ... ctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
EST: gi|211016176|gb|FL013380.1|FL013380
EST:     TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAG                         GTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatgg ... ctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
EST: gi|31360482|gb|CD444839.1|CD444839
EST:     TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAG                         GTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatgg ... ctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
EST: gi|211016181|gb|FL013385.1|FL013385
EST:     TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAG                         GTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatgg ... ctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
EST: gi|211016177|gb|FL013381.1|FL013381
EST:     TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAG                         GTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatgg ... ctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
EST: gi|211016179|gb|FL013383.1|FL013383
EST:     TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAG                         GTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatgg ... ctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
EST: gi|22473365|gb|BU037845.1|BU037845
EST:     TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAG                         GTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatgg ... ctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
EST: gi|76010934|gb|DT938104.1|DT938104
EST:     TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAG                         GTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT
genomic: TTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatgg ... ctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTT

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), 48 (downstream exon)
Score: 384

GGCAGCAACTTTTCTTGCATTTCATCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatgg ... ctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTTTCAAATGTGCTAAATGTTTTAGTCTCGTCAGGAGCTGATGCCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 234

GGCAGCAACTTTTCTTGCATTTCATCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatgg ... ctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTTTCAAATGTGCTAAATGTTTTAGTCTCGTCAGGAGCTGATGCCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 186

GGCAGCAACTTTTCTTGCATTTCATCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatgg ... ctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTTTCAAATGTGCTAAATGTTTTAGTCTCGTCAGGAGCTGATGCCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 257

GGCAGCAACTTTTCTTGCATTTCATCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCATCCAAATCTATAATGTCCGAATTGATGAGgtattcatgg ... ctttgtacagGTCAAAAGCAAGCTCAGAGGTCACTCTAAGAGAATCACAGGTCTTGCCTTTTCAAATGTGCTAAATGTTTTAGTCTCGTCAGGAGCTGATGCCCAG