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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCGTAGTCCCCCAATCGAAGAGGTGATCAGCACAGGAGTGGTGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaacagtagcactgatcaattatatggttttactttattttctctcttattaatcggtggcaatttgcgatatataacttatgctgcag

Basic information

species Zea mays
transcript GRMZM2G088088_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088088_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g06350.1 (Oryza sativa), 5'ss of exon 3
AGCGTAGTCCCCCAATCGAAGAGGTGATCAGCACAGGAGTGGTGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaacagtagcactgatcaattatatggttttactttatttt--ctctcttattaatcggtggcaatttgcgatatataacttatgctgcag
|||| ||||| ||||| || |||||||||| |||||| |||||||| || || ||||  || ||   |||||||||  |||||||||||||||| ||  ||||||  || ||||  | | ||    |    || | |      |  ||  |||  | |  | ||   | ||   |   || |   ||||
AGCGGAGTCCTCCAATTGAGGAGGTGATCAACACAGGGGTGGTGCCTCGCTTTATTGCCTTCCTCCAACGTGAGGATTATCCCCAACTCCAGgtgtgtcaacagtcacagtgatttaatttactaatagtgttaactaggaaccatttgctaaa-gctaaccatcccccatgggt--tttcttgcgcag
















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|211466271|gb|FL273962.1|FL273962
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGG
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGG
EST: gi|88758378|gb|DY542747.1|DY542747
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|13558022|gb|BG549378.1|BG549378
EST:     CACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: CACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|211413307|gb|FL164847.1|FL164847
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|211376201|gb|FL253486.1|FL253486
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|211410763|gb|FL164838.1|FL164838
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|211410759|gb|FL164834.1|FL164834
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCA-CATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|211410766|gb|FL164841.1|FL164841
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|211008179|gb|FL253536.1|FL253536
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|211466268|gb|FL273959.1|FL273959
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGC
EST: gi|211468801|gb|FL273976.1|FL273976
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCAC
EST: gi|211466274|gb|FL273965.1|FL273965
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|148943100|gb|EC888155.2|EC888155
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGGCACTCACCAACATTGCATCAGGCACATCAGAGAA
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGG-CACTCACCAACATTGCATCAGGCACATCAGAGAA
EST: gi|211466276|gb|FL273967.1|FL273967
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGA-C
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|211466277|gb|FL273968.1|FL273968
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|211468797|gb|FL273972.1|FL273972
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|29167750|gb|CB411010.1|CB411010
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|211466272|gb|FL273963.1|FL273963
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCC-AACTCCAG                         TTTGAAGCTGCATGGGCACTCACCAACATTGCATCAAGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|18053175|gb|BM318833.1|BM318833
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|91052953|gb|EB163371.1|EB163371
EST:     TGCCGCGATTCCTTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACTTTGCATC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATC
EST: gi|211466270|gb|FL273961.1|FL273961
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|67023557|gb|CO452306.1|CO452306
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|211466273|gb|FL273964.1|FL273964
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGGGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATC
EST: gi|211468798|gb|FL273973.1|FL273973
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|211008180|gb|FL253537.1|FL253537
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|78078677|gb|DV507089.1|DV507089
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|211413309|gb|FL164849.1|FL164849
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCA
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCA
EST: gi|211468795|gb|FL273970.1|FL273970
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATC
EST: gi|18385029|gb|BM418228.1|BM418228
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|22489097|gb|BU049020.1|BU049020
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
EST: gi|5555266|gb|AI881217.1|AI881217
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAA
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAA
EST: gi|211331752|gb|FL022649.1|FL022649
EST:     TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAG                         TTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC
genomic: TGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAAC

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), 49 (downstream exon)
Score: 365

AGCGTAGTCCCCCAATCGAAGAGGTGATCAGCACAGGAGTGGTGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAACACTAAGGTGGTGGTTGAGAGTGGTGCTGTGCCCATCTTTGTCAAGCTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 506

AGCGTAGTCCCCCAATCGAAGAGGTGATCAGCACAGGAGTGGTGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAACACTAAGGTGGTGGTTGAGAGTGGTGCTGTGCCCATCTTTGTCAAGCTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 499

AGCGTAGTCCCCCAATCGAAGAGGTGATCAGCACAGGAGTGGTGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAACACTAAGGTGGTGGTTGAGAGTGGTGCTGTGCCCATCTTTGTCAAGCTAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 311

AGCGTAGTCCCCCAATCGAAGAGGTGATCAGCACAGGAGTGGTGCCGCGATTCATTGAGTTTCTTACACGTGAGGACCATCCCCAACTCCAGgtctgggaac ... tatgctgcagTTTGAGGCTGCATGGGCACTCACCAACATTGCATCAGGCACATCAGAGAACACTAAGGTGGTGGTTGAGAGTGGTGCTGTGCCCATCTTTGTCAAGCTAC