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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcccatccccatgcatcgtttatctaatctaatgaaggacggactagctagtatttccggcctcatctagcagtatttctttgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCATGGTATTGGTCACATCACTAGCAATGTGTCCTTCGCTGCTGTTGCAGTCT

Basic information

species Zea mays
transcript GRMZM2G070605_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g13770.3 (Oryza sativa), 3'ss of exon 3
gtagcccatccccatgcatcgtttatctaatctaatgaaggacggactagctagt------atttccggc---ctcatctagcagtatttctttgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCATGGTATTGGTCACATCACTAGCAATGTGTCCTTCGCTGCTGTTGCAGTCT
    |   |   | || ||  |   | |   || ||  | |||     | ||| |      ||| ||  |    | |   |  || |  |  |  |||||||||||||||||   || ||| ||||||| ||||||||||| ||  ||||||||| | |||||||  ||||||||||||| || || ||| |||||||||| |
---acattttttcttgaattatcagtttctactcatccaagacaatgcatctaatgtggaaattaccaacaaattgacaaaaaagaaccttgtctttttgtagCCTATCAATTCGACACTCTTGAAGCTGCTCTTTCCAGTTGCGTTGTGCCATGCTCTTGGTCATGTCACTAGCAATGTATCGTTTGCTACTGTTGCAGTTT
















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|149095141|gb|EE180755.2|EE180755
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
EST: gi|76914837|gb|DV165713.1|DV165713
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
EST: gi|149013546|gb|EE043037.2|EE043037
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
EST: gi|101394747|gb|EB819306.1|EB819306
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
EST: gi|32925288|gb|CF030100.1|CF030100
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
EST: gi|148966890|gb|EE018012.2|EE018012
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
EST: gi|149075192|gb|EE163691.2|EE163691
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
EST: gi|148986357|gb|EE030094.2|EE030094
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
EST: gi|211519067|gb|FL311546.1|FL311546
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTCAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
EST: gi|116820056|gb|EC863241.1|EC863241
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGCGCCAT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
EST: gi|149075125|gb|EE163618.2|EE163618
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
EST: gi|211407726|gb|FL367074.1|FL367074
EST:     GGGTCGTATACTGCCTCATCAGCTGGAATGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACCCTTCCTGAAGCTT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCT-CCTGAAGCTT
EST: gi|149112153|gb|EE191267.2|EE191267
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
EST: gi|32925201|gb|CF030013.1|CF030013
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
EST: gi|91050012|gb|EB160430.1|EB160430
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
EST: gi|149026859|gb|EE046212.2|EE046212
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
EST: gi|149097452|gb|EE183315.2|EE183315
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
EST: gi|149015293|gb|EE045098.2|EE045098
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
EST: gi|71766326|gb|DR964263.1|DR964263
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
EST: gi|211475706|gb|FL352571.1|FL352571
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTGAAGCTTCTCTTTTCCA-TCGCCCTGTGGCA
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTT-CCAGTCGCCCTGTGCCA
EST: gi|78077772|gb|DV506204.1|DV506204
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
EST: gi|32925598|gb|CF030410.1|CF030410
EST:     GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG                         CCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT
genomic: GTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCAT

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), 46 (downstream exon)
Score: 23

CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCATGGTATTGGTCACATCACTAGCAATGTGTCCTTCGCTGCTGTTGCAGTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 487

CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCATGGTATTGGTCACATCACTAGCAATGTGTCCTTCGCTGCTGTTGCAGTCT


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 18

CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCATGGTATTGGTCACATCACTAGCAATGTGTCCTTCGCTGCTGTTGCAGTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCGgtagcccatc ... tgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCATGGTATTGGTCACATCACTAGCAATGTGTCCTTCGCTGCTGTTGCAGTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggacggactagctagtatttccggcctcatctagcagtatttctttgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCATGGTATTGGTCACATCACTAGCAATGTGTCCTTCGCTGCTGTTGCAGTCT
                                     tatttctttgtttt  CT-rich tract
                                     tatttctttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcccatccccatgcatcgtttatctaatctaatgaaggacggactagctagtatttccggcctcatctagcagtatttctttgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCATGGTATTGGTCACATCACTAGCAATGTGTCCTTCGCTGCTGTTGCAGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT