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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATCCCTCGATTGTTTTTGTTGGTGATACCTACACCTATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatccttaattatctcctacaagtttcactagtacttgatcatttataagtaaaaaatactcacccaacatgatgtatgttgtcaattgtttcct...

Basic information

species Zea mays
transcript GRMZM2G137707_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137707_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os07g46640.1 (Oryza sativa), 5'ss of exon 7
GTATCCCTCGATTGTTTTTGTTGGTGATACCTACACCTATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatccttaattatctcctacaagtttcactagtacttgatcatttataagtaaaaaatactcacccaacatgatgtatgttgtcaattgtttcct------
|||||| ||   |||||| |||||||||||||||||||||||| |||||||||| ||||||||| | ||||||||||| |||||||||||||| |||| | ||||| | |||| ||| |  || ||     |   || | | | ||          ||    | |||    || |   |||| | |       
GTATCCTTCATCTGTTTTCGTTGGTGATACCTACACCTATTTTTCTGGAATGGCATTGGCTGTGGTGGGAATTTTGGGTCATTTCAGgtaaacgtcctcagttatcccttacatgttccgttattatcct-ttggttgtgacttaa-----tctgtcctgtgtaatgatgcttttgctttgtctgcctgaatt

upper sequence: GRMZM2G137707_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA10G16320.1 (Glycine max), 5'ss of exon 7
GTATCCCTCGATTGTTTTTGTTGGTGATACCTACACCTATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatccttaattatctcctacaagtttcactagtacttgatcatttata-----agtaaaaaatactcacccaacatgatgtatgttgtcaattgtttcct
|||||||||    ||||||||||||||||| || || || |||||||| ||| || |||||||||| || ||||| || ||||| ||||| |         ||||||   |  | | | | |    ||     || | |       ||  ||| ||  ||   ||    |  |||  ||   | | |     
GTATCCCTCTTCAGTTTTTGTTGGTGATACATATACATACTTTGCTGGGATGACTATGGCTGTGATTGGTATTTTAGGCCATTTTAGgtacatccttacttttatctgtcaataatcttaatttggctatcctatctgtgtttttggtgcaaactaggcatagaatcatagatatactggggactct-----

upper sequence: GRMZM2G137707_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA02G34640.1 (Glycine max), 5'ss of exon 7
GTATCCCTCGATTGTTTTTGTTGGTGATACCTACACCTATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatccttaattatctcctacaagtttcactagtacttgatcatttataagtaaaaaatactcacccaacatga---tgtatgttgtcaattgtttcct
|||||||||    ||||||||||||||||| || || || |||||||| ||| || |||||||||| || ||||| || ||||| |||||  |||||||| || | ||   |||   ||   | |     ||| | | |  ||      | |  ||    |||       ||  |   ||   | |||  
GTATCCCTCTTCAGTTTTTGTTGGTGATACATATACATACTTTGCTGGGATGACTATGGCTGTGATTGGTATTTTAGGCCATTTTAGgta--catccttacttttatctgtcaatactcttcatttggctatcctatctgtgtttttggtgcaaactaggcatagaatcatagatatacaggggattct-

upper sequence: GRMZM2G137707_T01 (Zea mays), 5'ss of exon 7
lower sequence: PP1S281_35V6.1 (Physcomitrella patens), 5'ss of exon 6
GTATCCCTCGATTGTTTTTGTTGGTGATACCTACACCTATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatccttaattatctcctacaagtttcactagtacttgatcatttataagtaaa-aaatactca---cccaacatgatgt-atgttgtcaattgtttcct----------------------------------------------------------------
|||||| ||    || |||||||||||||| |||||||||||||| |||||||||||||| ||  |||| ||  | || || ||||||| |    | | | || | |  |  | ||||      |  |||| | | |     | |   ||| |  |   ||   | |  ||  ||| | |||| |  |   |                                                                
GTATCCTTCATCAGTGTTTGTTGGTGATACGTACACCTATTTTGCGGGAATGGCTTTGGCAGTAGTAGGCATCCTTGGTCACTTCAGgtga-tgccgtcatttttgtagtcaatgtttttgccttgattgaacttgttgggctgatcgaatgcggagttcctggctttctgagatggtatcaagttgtgattgcaacccaattaagtaccactctttttggtgaaagactgacatcatccttatatggttatgcag

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|67012698|gb|CO441447.1|CO441447
EST:     TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAG                         CGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
genomic: TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatcc ... gagtttgcagCGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
EST: gi|149107024|gb|EE188919.2|EE188919
EST:     TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAG                         CGAGACATTATTGTTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
genomic: TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatcc ... gagtttgcagCGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
EST: gi|71774748|gb|DR972626.1|DR972626
EST:     TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAG                         CGAGACATTATTGTTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
genomic: TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatcc ... gagtttgcagCGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
EST: gi|89106092|gb|DY576309.1|DY576309
EST:     CTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAG                         CGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
genomic: CTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatcc ... gagtttgcagCGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
EST: gi|88747666|gb|DY531807.1|DY531807
EST:     TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAG                         CGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
genomic: TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatcc ... gagtttgcagCGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
EST: gi|78108108|gb|DV526526.1|DV526526
EST:     TATTTTGCTGGAATGGTTTTGGCTGTGATAGGAATTTTGGGACATTTCAG                         CGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
genomic: TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatcc ... gagtttgcagCGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
EST: gi|32936074|gb|CF040886.1|CF040886
EST:     TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAG                         CGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
genomic: TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatcc ... gagtttgcagCGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
EST: gi|71442203|gb|DR823253.1|DR823253
EST:     TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAG                         CGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
genomic: TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatcc ... gagtttgcagCGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
EST: gi|33093800|gb|CF053794.1|CF053794
EST:     TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAG                         CGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
genomic: TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatcc ... gagtttgcagCGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
EST: gi|14204187|gb|BG837864.1|BG837864
EST:     TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAG                         CGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
genomic: TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatcc ... gagtttgcagCGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
EST: gi|32937138|gb|CF041957.1|CF041957
EST:     TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAG                         CGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
genomic: TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatcc ... gagtttgcagCGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
EST: gi|91874804|gb|EB404761.1|EB404761
EST:     TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAG                         CGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
genomic: TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatcc ... gagtttgcagCGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
EST: gi|78122709|gb|DV541093.1|DV541093
EST:     TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAG                         CGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
genomic: TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatcc ... gagtttgcagCGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
EST: gi|74232442|gb|DT640356.1|DT640356
EST:     TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAG                         CGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC
genomic: TATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatcc ... gagtttgcagCGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTC

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: 61

GTATCCCTCGATTGTTTTTGTTGGTGATACCTACACCTATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatcc ... gagtttgcagCGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 66

GTATCCCTCGATTGTTTTTGTTGGTGATACCTACACCTATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatcc ... gagtttgcagCGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 53

GTATCCCTCGATTGTTTTTGTTGGTGATACCTACACCTATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatcc ... gagtttgcagCGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 59

GTATCCCTCGATTGTTTTTGTTGGTGATACCTACACCTATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatcc ... gagtttgcagCGAGACATTATTGCTCTTCTTTTTACCTCAAGTTCTTAATTTCCTATGTTCAGTCCCACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATCCCTCGATTGTTTTTGTTGGTGATACCTACACCTATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatccttaattatctcctacaagtttcactagtacttgatcatttataagtaaaaaatactcacccaacatgatgtatgttgtcaattgtttcct

- - - - - - - - - - - - - - - - - - - - -  GCTGGA