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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtagctagtccctccttgtattttgcttatatttcttgaacttttaatgattctttggttaattttagctcatcactcaaattgatttttctcttcactgtatgcgtcttcccagcatgatatttcattcaccattctattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGGTTGAACAGGAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCC

Basic information

species Zea mays
transcript GRMZM2G170595_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170595_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g47940.1 (Oryza sativa), 3'ss of exon 4
gtgtgtagctagtccctccttgtattttgcttatatttcttgaacttttaatgattctttggttaattttagctcatcactcaaattgatttttctcttcactgtatgcgtcttcccagcatgatatttcattcaccattctattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGGTTGAACAGGAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCC
    |||| |||| | | ||||   | | ||| |||||  ||| | ||   | ||   ||  ||   |   | |||   || | | || |||  |    || |   | |  |   | |   | ||  |   || | |    | ||||||||| || ||||| || |||||||| ||||| ||||  |  |||||| |||||||||||||||||| |||||||| ||||||||||||||| || || || ||
----gtaggtagttctttcttgagctgtacttctatttactgagccttctgtaatgtcttaattcggt---gttcacttcttatactg-tttgacatgccagt---taccaccctctaatgtaatcctgatttgaac----tcttatgtagTACCGAGACTTCCTGATTTTTCTCTAGACGTTGCACAGATTGTCAAAGTGGTTGAACAGGAAAAGCCAAAATCCATATTTCTGACATCTCCGAACAACCC
















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:     CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGG                         TTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
genomic: CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGGgtgtgtagct ... tattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
EST: gi|78078617|gb|DV507029.1|DV507029
EST:     CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGG                         TTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
genomic: CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGGgtgtgtagct ... tattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
EST: gi|148974572|gb|EE025361.2|EE025361
EST:     CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGG                         TTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
genomic: CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGGgtgtgtagct ... tattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
EST: gi|32930096|gb|CF034908.1|CF034908
EST:     CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGG                         TTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
genomic: CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGGgtgtgtagct ... tattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
EST: gi|91048897|gb|EB159315.1|EB159315
EST:     CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGG                         TTCCAAGACTGCCCGATTTTTCTCTAGATGTTGATCTCATTGTCGAAGTGG
genomic: CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGGgtgtgtagct ... tattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
EST: gi|148963664|gb|EE014723.2|EE014723
EST:     CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGG                         TTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
genomic: CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGGgtgtgtagct ... tattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
EST: gi|148932895|gb|EE285676.2|EE285676
EST:     CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGG                         TTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
genomic: CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGGgtgtgtagct ... tattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
EST: gi|78079657|gb|DV508069.1|DV508069
EST:     CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGG                         TTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
genomic: CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGGgtgtgtagct ... tattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
EST: gi|148932277|gb|EC875831.2|EC875831
EST:     CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGG                         TTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
genomic: CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGGgtgtgtagct ... tattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
EST: gi|76289509|gb|DV029077.1|DV029077
EST:     CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGG                         TTCCAAGACC-CCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
genomic: CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGGgtgtgtagct ... tattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
EST: gi|71332195|gb|DR803018.1|DR803018
EST:     CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGG                         TTCCAAGACTGCTCGATTTTTTCCCTAGATGTTGATCTCATTGTCGAAGTG
genomic: CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGGgtgtgtagct ... tattatgtagTTCCAAGACTGCCCGATTTTT-CCCTAGATGTTGATCTCATTGTCGAAGTG
EST: gi|149109171|gb|EE190055.2|EE190055
EST:     CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGG                         TTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
genomic: CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGGgtgtgtagct ... tattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
EST: gi|71328633|gb|DR800987.1|DR800987
EST:     CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGG                         TTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
genomic: CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGGgtgtgtagct ... tattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
EST: gi|149111871|gb|EE191026.2|EE191026
EST:     CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGG                         TTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
genomic: CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGGgtgtgtagct ... tattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
EST: gi|6020568|gb|AW065601.1|AW065601
EST:     CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGG                         TTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG
genomic: CACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGGgtgtgtagct ... tattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGG

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: 130

ATGTGTGCTTGAACCAGGCGACAAAATTGTTGATTGCCCTCCAACATTCACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGGgtgtgtagct ... tattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGGTTGAACAGGAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCC


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 107

ATGTGTGCTTGAACCAGGCGACAAAATTGTTGATTGCCCTCCAACATTCACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGGgtgtgtagct ... tattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGGTTGAACAGGAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

ATGTGTGCTTGAACCAGGCGACAAAATTGTTGATTGCCCTCCAACATTCACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGGgtgtgtagct ... tattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGGTTGAACAGGAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 112

ATGTGTGCTTGAACCAGGCGACAAAATTGTTGATTGCCCTCCAACATTCACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGGgtgtgtagct ... tattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGGTTGAACAGGAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcactgtatgcgtcttcccagcatgatatttcattcaccattctattatgtagTTCCAAGACTGCCCGATTTTTCCCTAGATGTTGATCTCATTGTCGAAGTGGTTGAACAGGAAATGCCAAAATGCATATTTCTGACATCCCCAAATAATCC
                                       ccattct  CT-rich tract
                           atatttcatt  TA-rich tract