Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtatgcgttcatgcgtttccttatttcttcccggggatggactgggttcgattcgatctggtttggatttcctctgcggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATCAACGCCGGCGACCGCGTTGACAGCGCGCTCAAGGACATGGCCATCGTGA

Basic information

species Zea mays
transcript GRMZM2G050268_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050268_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g36740.1 (Oryza sativa), 3'ss of exon 1
gtaagtgtatgcgttcatgcgtttccttatttcttcccggggatggactgggttcgattcgatctggtttggatttcctctgcggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATCAACGCCGGCGACCGCGTTGACAGCGCGCTCAAGGACATGGCCATCGTGA
||| |||  ||||  |  |||||            |  |  | |||  ||| || |    |||  ||||  |||       | |     ||||||||||||||||||||| |||||||||||||| |||||||||   |||||||||||||||||||| || |||||||||||||||||||||||||||||||
gtacgtgattgcgagcgagcgtt------------cttgatggtggtttggattgg----gattgggttgtgatggtggtggtgattcggcagCTGGTGGACAAGGATCCGGAGAAGGCGATCGCGCTGTTCTGGGCGGCGATCAACGCCGGCGACCGGGTGGACAGCGCGCTCAAGGACATGGCCATCGTGA

upper sequence: GRMZM2G050268_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ08332 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtgtatgcgttca--tgcgtttccttatttcttc--ccggggatggactgggttcgattcgatctggtttggatttcctctgcggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATCAACGCCGGCGACCGCGTTGACAGCGCGCTCAAGGACATGGCCATCGTGA
||||  | | | |  ||  | | |    |   |   ||   |||    | ||||  |   ||   ||||      ||   ||  |  ||     ||||||||||||||||| || || ||||| ||||| || ||||||   |||||||| || ||||||||||| ||||||||||||||||||||||| |||||||
gtaaaagaaagggaccaattccatccgatcgatcgatcgatcggtcgcgcactgtctcgcatcgcatctctgagagaacccccttttgg-----cagCTGGTGGACAAGGAGCCGGACAAGGCCATCGCGCTCTTCTGGGCGGCGATCAATGCGGGCGACCGCGTGGACAGCGCGCTCAAGGACATGGCGATCGTGA

upper sequence: GRMZM2G050268_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ30150 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtgtatgcgttca--tgcgtttccttatttcttc--ccggggatggactgggttcgattcgatctggtttggatttcctctgcggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATCAACGCCGGCGACCGCGTTGACAGCGCGCTCAAGGACATGGCCATCGTGA
||||  | | | |  ||  | | |    |   |   ||   |||    | ||||  |   ||   ||||      ||   ||  |  ||     ||||||||||||||||| || || ||||| ||||| || ||||||   |||||||| || |||||||| || ||||||||||||||||||||||| |||||||
gtaaaagaaagggaccaattccatccgatcgatcgatcgatcggtcgcgcactgtctcgcatcgcatctctgagagaacccccttttgg-----cagCTGGTGGACAAGGAGCCCGACAAGGCCATCGCGCTCTTCTGGGCGGCGATCAATGCGGGCGACCGTGTGGACAGCGCGCTCAAGGACATGGCGATCGTGA

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|78113367|gb|DV531759.1|DV531759
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|94479425|gb|EB708383.1|EB708383
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|76294345|gb|DV033913.1|DV033913
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|76922892|gb|DV169228.1|DV169228
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|89758318|gb|DY687540.1|DY687540
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|37423828|gb|CF649643.1|CF649643
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|74234535|gb|DT642449.1|DT642449
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|71775124|gb|DR973002.1|DR973002
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|211332358|gb|FL287652.1|FL287652
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|89759856|gb|DY688538.1|DY688538
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|148955352|gb|EC900908.2|EC900908
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|50322683|gb|CO517809.1|CO517809
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|71306833|gb|DR789574.1|DR789574
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|149023761|gb|EE045952.2|EE045952
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|148965097|gb|EE015913.2|EE015913
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|76010983|gb|DT938153.1|DT938153
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|94480565|gb|EB709523.1|EB709523
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCGGACAAGGCCATCGCCCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|93283827|gb|EB676091.1|EB676091
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|149095665|gb|EE181288.2|EE181288
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|149084073|gb|EE173471.2|EE173471
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|76292412|gb|DV031980.1|DV031980
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|149015540|gb|EE045418.2|EE045418
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATT
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|211332357|gb|FL287651.1|FL287651
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|211332356|gb|FL287650.1|FL287650
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|78104441|gb|DV522859.1|DV522859
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
EST: gi|50333368|gb|CO528494.1|CO528494
EST:     ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAG                         CTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC
genomic: ACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATC

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: 47 (upstream exon), 48 (downstream exon)
Score: 72

GGCGGCGGCGGCCATGCTGCGGACCCACTCCGACTCCTTCCACGTCGCGCACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATCAACGCCGGCGACCGCGTTGACAGCGCGCTCAAGGACATGGCCATCGTGA


Block sizes: 44 (upstream exon), 28 (downstream exon)
Score: 14

GGCGGCGGCGGCCATGCTGCGGACCCACTCCGACTCCTTCCACGTCGCGCACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATCAACGCCGGCGACCGCGTTGACAGCGCGCTCAAGGACATGGCCATCGTGA


Block sizes: 44 (upstream exon), 27 (downstream exon)
Score: 9

GGCGGCGGCGGCCATGCTGCGGACCCACTCCGACTCCTTCCACGTCGCGCACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATCAACGCCGGCGACCGCGTTGACAGCGCGCTCAAGGACATGGCCATCGTGA


Block sizes: 21 (upstream exon), 29 (downstream exon)
Score: 1

GGCGGCGGCGGCCATGCTGCGGACCCACTCCGACTCCTTCCACGTCGCGCACAAGGTGCCCGTCGGCGACACGCCCTACGTGAGAGCCAAGCGCGTCCAGgtaagtgtat ... ggcggtgcagCTGGTGGACAAGGATCCAGAGAAGGCGATCGCTCTGTTCTGGAGTGCGATCAACGCCGGCGACCGCGTTGACAGCGCGCTCAAGGACATGGCCATCGTGA