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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttcacgtcacctttagtattttatcattgtggctttgaaaaaacaagtatcgtttgaacataacataattatgttttcatattgcagGCTTCACAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG

Basic information

species Zea mays
transcript GRMZM2G170699_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170699_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g31900.1 (Oryza sativa), 3'ss of exon 4
----gtatt-ttcacgtcacctttagtattttatcattgtggctttgaaaaaacaagtatcgtttgaacat---aacataattatgttttcatattgcagGCTTCACAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG
     || |  |      || ||   |||| ||||        || |||| |     | |   |   ||||   ||||| ||||| ||||| |||| ||||||||||| || ||||||||| | || || || |||||||| |||||||||||||| ||||||
cagtatactgcttctaaaactttctttattatatctaaacattttcgaaatataggatttaaatatcacatggtaacatgattatcttttcttattccagGCTTCACAAGACAAGAAGAGCCTTGATGTAGGGGCAAATCTTTTTATTGGCAATCTCGATCCG

upper sequence: GRMZM2G170699_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G36950.1 (Glycine max), 3'ss of exon 4
-------------gtattttca-cgtcacctttagtattttatcattgtggctttgaaaaaacaagtatcgtttgaacataacataattatgttttcatattgcagGCTTCACAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG
             ||| ||  | |  |||| ||   | || || |      | || |     ||  |   ||||||     |  | || || ||||    ||  |||| || || ||||| |||||| |||| ||||| |||||||| || ||||||||||||||||| 
tccttgtagtaatgtagttgtatcaacacccttgtcacttgattaacaaaacatttagttttca--tgctgtttgatgg--attttatgattttttgg--ttctagGCATCCCAAGATAAAAAGAGCCTGGATGTTGGTGCAAATCTTTTCATTGGCAATCTTGATCCT

upper sequence: GRMZM2G170699_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G00310.1 (Glycine max), 3'ss of exon 4
------gtattttcacgtcacctttagtattttatcattgtggctttgaaaaaacaagtatcgtttgaacataacataattatg---ttttcatattgcagGCTTCACAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG
       |||||   | |    || |      |  || |         ||| |   ||| ||  |    | | |  | ||| |    ||||    || ||||| || || ||||| ||||||||||| ||||| |||||||| || ||||||||||| ||||| 
cctgctatatttcttccttgtattaacacccatgccacttgattaacaaaatatttagtttctatgctgcttgat-tgattttacaattttttggttccagGCATCCCAAGATAAAAAGAGCTTGGATGTTGGGGCAAATCTTTTCATTGGCAATCTAGATCCT

upper sequence: GRMZM2G170699_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0023g01470.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------------------------------gtattttca--cgtcacctttagtattttatcattgtggctttgaaaaa-----acaagtatcgtttgaacataacataattatgttttcatattg----cagGCTTCACAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG
                                                           | | | |    | |  | ||||  | | |  |||  || |  | |||     | ||     || |    || |  |  ||    |||  |||||    ||||| || || ||||| ||||||||||| ||||||||||| || ||| |||| || |||||||| 
gtgtgacatttattttcactagctatctcatttgccttatttcttatgttctttttcagactatgagttatgaagtgtagttatatttgtttggagcgtccataaattcttataaaatatgtgtttgtatgatctttttccccttttttattggttccagGCATCTCAAGATAAAAAGAGCTTGGATGTTGGAGCAAACCTTTTTGTTGGAAACCTTGATCCT

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|74240862|gb|DT648776.1|DT648776
EST:     AGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCACAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttcac ... catattgcagGCTTCACAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|89248214|gb|DY620000.1|DY620000
EST:     AGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCACAGGATAAGAAGAGCTTGGACGTTTGGAGCAAATCTGTTTATTGG
genomic: AGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttcac ... catattgcagGCTTCACAGGATAAGAAGAGCTTGGACGTT-GGAGCAAATCTGTTTATTGG
EST: gi|88746230|gb|DY530371.1|DY530371
EST:     AGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCACAGGATAAAAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttcac ... catattgcagGCTTCACAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|78124096|gb|DV542480.1|DV542480
EST:     AGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCACAGGATAAAAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttcac ... catattgcagGCTTCACAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|21843149|gb|BQ703730.1|BQ703730
EST:     AGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCACAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttcac ... catattgcagGCTTCACAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
EST: gi|101395862|gb|EB819858.1|EB819858
EST:     AGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG                         GCTTCACAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC
genomic: AGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttcac ... catattgcagGCTTCACAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGC

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: 48 (upstream exon), 49 (downstream exon)
Score: 117

GCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttcac ... catattgcagGCTTCACAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 75

GCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttcac ... catattgcagGCTTCACAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 113

GCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttcac ... catattgcagGCTTCACAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 97

GCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAGgtattttcac ... catattgcagGCTTCACAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgaaaaaacaagtatcgtttgaacataacataattatgttttcatattgcagGCTTCACAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG
                         acataac  putative branch site (score: 97)
                                       tgttttc  putative PPT
                        aacataacataattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttcacgtcacctttagtattttatcattgtggctttgaaaaaacaagtatcgtttgaacataacataattatgttttcatattgcagGCTTCACAGGATAAGAAGAGCTTGGACGTTGGAGCAAATCTGTTTATTGGCAATCTTGATCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA