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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcatttgtctctatttagatatgcctctctacactgtccatttcttttcccattatctggctaccagctttgcactgatcagtaaaacataaga...

Basic information

species Zea mays
transcript GRMZM2G116427_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116427_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os06g49890.1 (Oryza sativa), 5'ss of exon 5
GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcatttgtctctatttagatatgcctctctacactgtccatttc-ttttcccattatctggctaccagctttgcactgatcagtaaaacataaga
||||||||| ||||||||||| ||||| |||||  ||||||| || ||||||||||||||||||  | |||  || ||||  | | |  |   |   ||    | || ||       |   ||    |   |     |||    |||  |    ||  
GTATGAGATTGACAAGGTCACTGCAGGTCAGCGGCTGGATCTAAACCTTGAAAGAGGgtaagatt-tatgttgctgtttatgtgtactacctgatcatgaatgtatcattcaattgctgcttgatagctgaccagaaacttcagagtgcattccaacc

upper sequence: GRMZM2G116427_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT2G16460.1 (Arabidopsis thaliana), 5'ss of exon 5
GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcatttgtctctatttagatatgcctctctacactgtccatttcttttccca-ttatctg-------------gctaccagctttgcactgatcagtaaaacataaga
||| || || || |||||||| || ||||| || |||||| ||||||||||||||||||||||  ||||     | |  | |  | |    || |  |  ||||||     |  | | |||||             | ||   | ||     |  |  || |  ||||   
GTACGAAATTGATAAGGTCACAGCGGGACAACGCTTGGATTTGAATCTTGAAAGAGGgtaagaaaattttgaattttgcaca-gtactctcctcctataaccatttaccaacgtagtcatctgcaagtgaaggcgtgatatatgattctggttattttgttactcatag--

upper sequence: GRMZM2G116427_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT2G16460.2 (Arabidopsis thaliana), 5'ss of exon 5
GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcatttgtctctatttagatatgcctctctacactgtccatttcttttcccattatctggctaccagctttgcactgatcagtaaaacataaga----
||| || || || |||||||| || ||||| || |||||| ||||||||||||||||||||||  ||||     | |  | |  | |    || |  |  ||||||     |  | |      || | ||    |   ||||   | |  |     |    
GTACGAAATTGATAAGGTCACAGCGGGACAACGCTTGGATTTGAATCTTGAAAGAGGgtaagaaaattttgaattttgcaca-gtactctcctcctataaccatttaccaacgtagt---catctgcaagtgaaggcgtgatatatgattctggttatttt

upper sequence: GRMZM2G116427_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT3G51090.1 (Arabidopsis thaliana), 5'ss of exon 5
GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcatttgtctctatttagatatgcctctctacactgtccatttcttttcccattatctggctaccagctttgcactgat-cagtaaaacataaga
  | |||||||| || ||||| |||||||| || ||||| ||||||||||||| ||||| |||  |   |   |||  |   |||  |||| | |   |   || |||||    ||| ||||  |   |  ||| || ||||   | |          
ACACGAGATCGATAAAGTCACAGCAGGACAACGGTTGGACCTGAATCTTGAAAAAGGgtcagagaaacag---ctacct---tatttctctgttcttaggttatgtctttcgaaattgtctg--tgatatgttt-caatgatgtcgcag---------

upper sequence: GRMZM2G116427_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S84_251V6.1 (Physcomitrella patens), 5'ss of exon 5
GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcatttgtctctatttagatatgcctctctacactgtccatttcttttcccattatctggctaccagctttgcactgatca-gtaaaacataaga---
||||||||| ||||| || || ||||| |||||  ||||| ||||||| ||||||||||||     | |    || ||  | | |   | | |    |  ||  ||  | |    | | || ||| | ||  ||||| ||| |  ||     ||   |   
GTATGAGATTGACAAAGTGACAGCAGGTCAGCGTCTGGATTTGAATCTAGAAAGAGGgtaattctttcttaaactgtt-ggttttctatttgtgatttaaccgctttctctttt-taaccttgctccaag--ttgcattgagcgcgtgccgaatgctatgt

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|21330027|gb|BQ485408.1|BQ485408
EST:     ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG                         GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
genomic: ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
EST: gi|32869175|gb|CF008857.1|CF008857
EST:     ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG                         GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
genomic: ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
EST: gi|21390796|gb|BQ528845.1|BQ528845
EST:     ATCGACAAGGTCTCCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG                         GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
genomic: ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
EST: gi|21480752|gb|BQ577435.1|BQ577435
EST:     ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG                         GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
genomic: ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
EST: gi|7227834|gb|AW566475.1|AW566475
EST:     AAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG                         GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
genomic: AAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
EST: gi|14324103|gb|BG929580.1|BG929580
EST:     ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG                         GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
genomic: ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
EST: gi|6851592|gb|AW352602.1|AW352602
EST:     ATCGNCAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG                         GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
genomic: ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
EST: gi|21390595|gb|BQ528644.1|BQ528644
EST:     ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG                         GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
genomic: ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
EST: gi|21480787|gb|BQ577470.1|BQ577470
EST:     ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG                         GCGCATACGTGATGAGC
genomic: ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGC
EST: gi|5922394|gb|AW055683.1|AW055683
EST:     ATCGNCAAGGTCNCCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG                         GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
genomic: ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
EST: gi|22546799|gb|BU099110.1|BU099110
EST:     ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG                         GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
genomic: ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
EST: gi|4730313|gb|AI649479.1|AI649479
EST:     AGCGATTGGATCTGAATCTTGAAAGAGG                         GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCCCTGAGCTTAC
genomic: AGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
EST: gi|211128611|gb|FL432588.1|FL432588
EST:     ATCGACAAGGTCACCGCAGAACAGCGATTGGATYTGAATCTTGAAAGAGG                         GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
genomic: ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
EST: gi|21481481|gb|BQ578164.1|BQ578164
EST:     ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG                         GCGCATACGTGATGAGCTNGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
genomic: ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
EST: gi|87154790|gb|DY399579.1|DY399579
EST:     ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG                         GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
genomic: ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
EST: gi|22546847|gb|BU099158.1|BU099158
EST:     ATCGACANGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG                         GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
genomic: ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
EST: gi|32906186|gb|CF010999.1|CF010999
EST:     ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG                         GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
genomic: ATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
EST: gi|7238187|gb|AW573409.1|AW573409
EST:     TCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG                         GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC
genomic: TCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTAC

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), 48 (downstream exon)
Score: 47

GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 74

GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 57

GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 86

GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcat ... catgctccagGCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGGgtaagatcatttgtctctatttagatatgcctctctacactgtccatttcttttcccattatctggctaccagctttgcactgatcagtaaaacataaga

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaacata