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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcagcgatgggctttccccccgtcctccgcccctcctgtattcagtggaatcaatcgaattctgaagcagcatctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCGCAGTATAAGCACACGCTCGCGGGCCCCTCACTCAAGGTGGATCCCCACA

Basic information

species Zea mays
transcript GRMZM2G113470_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113470_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g08660.1 (Oryza sativa), 3'ss of exon 1
gtacgcagcgatgggctttccccccgtcctccgcccctcctgtattcagtggaatcaatcgaattctgaagcagcatctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCGCAGTATAAGCACACGCTCGCGGGCCCCTCACTCAAGGTGGATCCCCACA
|||   |    |  |  | | |||  ||| || | | | ||                ||   | | ||     ||    |||  ||||||| || || ||||| || ||  |||| ||||||||||||||||||| |||||| ||||||| ||||| ||| || || ||||||||||||| |||||
gtataaactactcagtctcctcccaatccccctcgctttcttctccttcgattgctgatgagaatttggtttggc----ttggcagGCCGCGGGTGCGGTGGGTGGGGCGATGGCGATCTCGGAGCTGATGCCGGAGCAGTACAAGCACATGCTCGGGGGGCCATCGCTCAAGGTGGATCTCCACA
















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|211158470|gb|FL301945.1|FL301945
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGGC
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGG-C
EST: gi|211158472|gb|FL301947.1|FL301947
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGANCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|211158465|gb|FL301940.1|FL301940
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|211350454|gb|FL030225.1|FL030225
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGT-GGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|211158471|gb|FL301946.1|FL301946
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTKGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGC
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGC
EST: gi|15208907|gb|BI430791.1|BI430791
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|211153670|gb|FL301902.1|FL301902
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAACTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|211155275|gb|FL301916.1|FL301916
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGARCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|211153668|gb|FL301900.1|FL301900
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|211350458|gb|FL030229.1|FL030229
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGT-GGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|211153667|gb|FL301899.1|FL301899
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|211156876|gb|FL301932.1|FL301932
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGTGGGCGGCGCC-TGGCCATCTCGGAGCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|211156873|gb|FL301929.1|FL301929
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGARCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|4827620|gb|AI668312.1|AI668312
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|211156881|gb|FL301937.1|FL301937
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|211156869|gb|FL301925.1|FL301925
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|9825030|gb|BE575232.1|BE575232
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|149100062|gb|EE186113.2|EE186113
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|211156880|gb|FL301936.1|FL301936
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|149100063|gb|EE186114.2|EE186114
EST:     GACTCGACAGCCCCTCCCTCTTTTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|211155268|gb|FL301909.1|FL301909
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGTGGGCGGCGCC-TGGCCATCTCGGAGCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|211155272|gb|FL301913.1|FL301913
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|211155279|gb|FL301920.1|FL301920
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
EST: gi|211350455|gb|FL030226.1|FL030226
EST:     GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAG                         GCCGCCGGCGCTGT-GGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG
genomic: GACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCG

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: 107

CGGCGGCGCCAGCTTCAACCCCACCGACTTCGCCGCCTCCTATGCCGCCGGACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCGCAGTATAAGCACACGCTCGCGGGCCCCTCACTCAAGGTGGATCCCCACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 367

CGGCGGCGCCAGCTTCAACCCCACCGACTTCGCCGCCTCCTATGCCGCCGGACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCGCAGTATAAGCACACGCTCGCGGGCCCCTCACTCAAGGTGGATCCCCACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 336

CGGCGGCGCCAGCTTCAACCCCACCGACTTCGCCGCCTCCTATGCCGCCGGACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCGCAGTATAAGCACACGCTCGCGGGCCCCTCACTCAAGGTGGATCCCCACA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 157

CGGCGGCGCCAGCTTCAACCCCACCGACTTCGCCGCCTCCTATGCCGCCGGACTCGACAGCCCCTCCCTCTTCTCGGTTGCGCTCCGCTTCCCGGCGCAGgtacgcagcg ... tctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCGCAGTATAAGCACACGCTCGCGGGCCCCTCACTCAAGGTGGATCCCCACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcccctcctgtattcagtggaatcaatcgaattctgaagcagcatctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCGCAGTATAAGCACACGCTCGCGGGCCCCTCACTCAAGGTGGATCCCCACA
                                             tctttgtt  CT-rich tract
                     aatcaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcagcgatgggctttccccccgtcctccgcccctcctgtattcagtggaatcaatcgaattctgaagcagcatctttgttagGCCGCCGGCGCTGTGGGCGGCGCCCTGGCCATCTCGGAGCTGATGCCGGCGCAGTATAAGCACACGCTCGCGGGCCCCTCACTCAAGGTGGATCCCCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA