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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCGCCCGCCTCGGCCTCATCTACGAGGATGTCTGGCTCCGTGCCGCGGACGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgccagcaccctcaccgtcgtcttctgtattcaatcctcccatgcgctctttgcttgcgtcttcgtctccttccctgtgaaccatggctgctgct...

Basic information

species Zea mays
transcript GRMZM2G412888_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G412888_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g41730.2 (Oryza sativa), 5'ss of exon 1
CCCGCCCGCCTCGGCCTCATCTACGAGGATGTCTGGCTCCGTGCCGCGGACGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgccagcaccctcaccgtcgtcttctgtattcaatcctc--ccatgcgctctttgcttgcgtcttcgtctccttccctgtgaaccatggctgctgct
|||| ||||||| |||||||||||||||| ||||||||||| ||||| |||||||| || |||||||||||||||||||| |||||||||| || ||||||  ||| ||  |||   |  | ||     || |  |  ||  |   |  | ||   ||||||  |   |  ||          || | || | | |  ||  
CCCGACCGCCTCCGCCTCATCTACGAGGACGTCTGGCTCCGCGCCGCCGACGGCGTCCGCCTCCACTCCTGGTTCATCCGCCACTCCCCCACCTGCCGAGgcaagcacctccacatacctcctctcgacctctcctagattttgtgcagttcgtggtttgctccctggtgtgttagtacttaggttagcctttgtttttg--
















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|26557244|gb|CA829479.1|CA829479
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|30087677|gb|CB885883.1|CB885883
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCT
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCT
EST: gi|71425140|gb|DR806559.1|DR806559
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|76018058|gb|DT945228.1|DT945228
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|71430933|gb|DR811983.1|DR811983
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|211463531|gb|FL255623.1|FL255623
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|71427907|gb|DR808957.1|DR808957
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|89250823|gb|DY622609.1|DY622609
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|29129758|gb|CB380462.1|CB380462
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|149008856|gb|EE041069.2|EE041069
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|71448310|gb|DR829360.1|DR829360
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|71316274|gb|DR794814.1|DR794814
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|89253014|gb|DY624800.1|DY624800
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|148933213|gb|EC876864.2|EC876864
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|148939301|gb|EC883808.2|EC883808
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|31664225|gb|CD572950.1|CD572950
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|30705302|gb|CD058738.1|CD058738
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|76293689|gb|DV033257.1|DV033257
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|89252853|gb|DY624639.1|DY624639
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|67011215|gb|CO439964.1|CO439964
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|8103365|gb|AW928006.1|AW928006
EST:     CCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|88750379|gb|DY534520.1|DY534520
EST:     CGGCGTGCGGCTCCACTCGTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|91055111|gb|EB165529.1|EB165529
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|88752413|gb|DY536554.1|DY536554
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCA-GAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|67041292|gb|CO467547.1|CO467547
EST:     CGGCGTGCGGCTCCTCTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|29576736|gb|CB616848.1|CB616848
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|148947394|gb|EC892802.2|EC892802
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|149014757|gb|EE044444.2|EE044444
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|71437275|gb|DR818325.1|DR818325
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
EST: gi|148933571|gb|EC877438.2|EC877438
EST:     CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAG                         GTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA
genomic: CGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA

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), 45 (downstream exon)
Score: 195

CCCGCCCGCCTCGGCCTCATCTACGAGGATGTCTGGCTCCGTGCCGCGGACGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 222

CCCGCCCGCCTCGGCCTCATCTACGAGGATGTCTGGCTCCGTGCCGCGGACGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 222

CCCGCCCGCCTCGGCCTCATCTACGAGGATGTCTGGCTCCGTGCCGCGGACGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 221

CCCGCCCGCCTCGGCCTCATCTACGAGGATGTCTGGCTCCGTGCCGCGGACGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgcca ... tctgatgcagGTCCAACCATTCTGTTCTTCCAAGAAAATGCTGGCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCGCCCGCCTCGGCCTCATCTACGAGGATGTCTGGCTCCGTGCCGCGGACGGCGTGCGGCTCCACTCCTGGTTCATCCGTCACTCCCCCAGCTACCGAGgttagcgccagcaccctcaccgtcgtcttctgtattcaatcctcccatgcgctctttgcttgcgtcttcgtctccttccctgtgaaccatggctgctgct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccttcc