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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccgacgaatagcacttgccgagagagtttgctgaatccacgacgaactgactggtatctcctgaggctttgaatgttgacacggtcttggtggttgaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGCCTGAAGGAATTCTACA

Basic information

species Zea mays
transcript GRMZM2G058450_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058450_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g67850.1 (Oryza sativa), 3'ss of exon 2
--gtaccgacgaatagcacttgccgaga---gagtttgctgaatccacgacgaactgactggtatctcctgaggctttg-aatgttga-cacggtcttg------gtggttgaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCA---TAGAAAGGAGGGCGAGCCTGAAGGAATTCTACA
   || |||    | |  | |  | ||    |   |   |||||    | | |  |    | | | |  | |  | | | |||| ||  |||  |||           |||  ||   ||||| ||||| ||||| |||||||| ||||||||||   | |||||||| || ||||| |||||||||||  
gtatatcgaattcttgatccttgcaagccttgcaatatatgaattaggggcaattttggggat-tttaataatccatggtaatggtgctcacaatctcacctgctactgttatacctccagGTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG
















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|211287515|gb|FL360425.1|FL360425
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGTGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211372879|gb|FL335377.1|FL335377
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|101401307|gb|EB822331.1|EB822331
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAGGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211535303|gb|FL356758.1|FL356758
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211049886|gb|FL343175.1|FL343175
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211165711|gb|FL359023.1|FL359023
EST:     CATACACGCTCCCTAGCTACCKTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211010674|gb|FL358964.1|FL358964
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|28931313|gb|CB334674.1|CB334674
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211425705|gb|FL364983.1|FL364983
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCTATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|33467297|gb|CF244346.1|CF244346
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GCTTATGTCCATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211523414|gb|FL361955.1|FL361955
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTCATGTCGATGAAGATGCCTCTATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211078311|gb|FL342740.1|FL342740
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCAT
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCAT
EST: gi|211213423|gb|FL335729.1|FL335729
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGARGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211282867|gb|FL309979.1|FL309979
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|50325950|gb|CO521076.1|CO521076
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211185710|gb|FL321585.1|FL321585
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCTATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211086863|gb|FL356810.1|FL356810
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211453267|gb|FL341700.1|FL341700
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCTATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|148930523|gb|EE285118.2|EE285118
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211021655|gb|FL358094.1|FL358094
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211488646|gb|FL313372.1|FL313372
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211083699|gb|FL340081.1|FL340081
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCTATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211180683|gb|FL313564.1|FL313564
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|108824167|gb|EC278175.1|EC278175
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211398188|gb|FL404159.1|FL404159
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211147996|gb|FL325032.1|FL325032
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GYTTATGTCGATGAAGAWGCCTCTATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211173505|gb|FL323750.1|FL323750
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGARGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|149109824|gb|EE293619.2|EE293619
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211335091|gb|FL315546.1|FL315546
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
EST: gi|211529046|gb|FL347500.1|FL347500
EST:     CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAG                         GTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC
genomic: CATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGC

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: 85

TCCAATCTTTCTCAACCTTATCCAATGGATGGACTGCAGCTGCTCCCTGTCATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGCCTGAAGGAATTCTACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 171

TCCAATCTTTCTCAACCTTATCCAATGGATGGACTGCAGCTGCTCCCTGTCATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGCCTGAAGGAATTCTACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 149

TCCAATCTTTCTCAACCTTATCCAATGGATGGACTGCAGCTGCTCCCTGTCATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGCCTGAAGGAATTCTACA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 229

TCCAATCTTTCTCAACCTTATCCAATGGATGGACTGCAGCTGCTCCCTGTCATACACGCTCCCTAGCTACCTTGGCCTGCTCGAGGTTCTCGTCTACAAGgtaccgacga ... gaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGCCTGAAGGAATTCTACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggtatctcctgaggctttgaatgttgacacggtcttggtggttgaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGCCTGAAGGAATTCTACA
                       tgttgac  putative branch site (score: 229)
                 tttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccgacgaatagcacttgccgagagagtttgctgaatccacgacgaactgactggtatctcctgaggctttgaatgttgacacggtcttggtggttgaacacgcagGTTTATGTCGATGAAGATGCCTCCATATCCACCATAGAAAGGAGGGCGAGCCTGAAGGAATTCTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA