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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGGCGGCGGCCGAGGCGAAGGGGCGGCTGACCGGTGACTCCTTCATCCGGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaatacgagccccgccgctaagattctcttgtatggggaaaaggcacaccgacttttgctatgcacgcgaggtgctcgccgaaatgccccagtggtaacattcgctgtctcgctgaaaacggtaccccttaacag

Basic information

species Zea mays
transcript GRMZM2G170595_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170595_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g47940.1 (Oryza sativa), 5'ss of exon 1
GACGGCGGCGGCCGAGGCGAAGGGGCGGCTGACCGGTGACTCCTTCATCCGGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaatacgagccccgccgctaagattctcttgtatggggaaaaggcacaccgacttttgctatgc-acgcgaggtgctcgccgaaatgccccagtggtaacattcgctgtctcgctgaaaacggtaccccttaacag
| |||||||||| ||| ||||| || | | || ||| | |||||||||||||   ||||||||||  ||||||||||| ||||||||||||||||| ||||||       |   |    || ||     |    | | ||| |||  |   |||||   ||| |  |||  ||||||||| | |  ||||| |||| | ||                                        
GGCGGCGGCGGCTGAGACGAAGAGGGGACCGAGCGGCGCCTCCTTCATCCGGGAACACCTCAGGAGTCTCGCCCCGTACCAGCCCATCCTGCCCTTCGAGgtaggagcagcactctttcccactggtggttgagtttgtggagaac-gctgcaccg---tttcccgtgccgcgcgaggtgtttgtggaaattcccccgaggccc-------------------------------------
















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|71437833|gb|DR818883.1|DR818883
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|22489861|gb|BU049784.1|BU049784
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTCGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|78078617|gb|DV507029.1|DV507029
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|148974572|gb|EE025361.2|EE025361
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|87153226|gb|DY398015.1|DY398015
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTCGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|91048897|gb|EB159315.1|EB159315
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|148963664|gb|EE014723.2|EE014723
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|148932895|gb|EE285676.2|EE285676
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|78079657|gb|DV508069.1|DV508069
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|19822775|gb|BQ048799.1|BQ048799
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTCGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|211221376|gb|FL266596.1|FL266596
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTCGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|18650024|gb|BM498843.1|BM498843
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTCGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|89756009|gb|DY686211.1|DY686211
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|148932277|gb|EC875831.2|EC875831
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|211221377|gb|FL266597.1|FL266597
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTCGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|76289509|gb|DV029077.1|DV029077
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|71332195|gb|DR803018.1|DR803018
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|149109171|gb|EE190055.2|EE190055
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|211221375|gb|FL266595.1|FL266595
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTCGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|71328633|gb|DR800987.1|DR800987
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|211221367|gb|FL266587.1|FL266587
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTCGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
EST: gi|149111871|gb|EE191026.2|EE191026
EST:     GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAG                         GTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT
genomic: GGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGAT

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: 110

GACGGCGGCGGCCGAGGCGAAGGGGCGGCTGACCGGTGACTCCTTCATCCGGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

GACGGCGGCGGCCGAGGCGAAGGGGCGGCTGACCGGTGACTCCTTCATCCGGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

GACGGCGGCGGCCGAGGCGAAGGGGCGGCTGACCGGTGACTCCTTCATCCGGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 107

GACGGCGGCGGCCGAGGCGAAGGGGCGGCTGACCGGTGACTCCTTCATCCGGCGCCACCTCAGGACCCTCGCCCCGTATCAGCCCATCCTGCCCTTTGAGgtacacaata ... cccttaacagGTGTTATCTGCTCGCCTTGGGCGTAGACCAGAGGACATAATCAAGTTGGATGCAAATGAGAATCCATATGGTCCACCCCCGGAG