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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACAATGGGGATGCTTAGCACTGCAGGGTATGTTCTCACCATGGACATGTTTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcacatgtttcttttatagctcaaacctccgctgtagcctataggttgtagcaaacaacctgtattatttaatactctttccattacaagatctc...

Basic information

species Zea mays
transcript GRMZM2G069410_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069410_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 5'ss of exon 10
AACAATGGGGATGCTTAGCACTGCAGGGTATGTTCTCACCATGGACATGTTTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcacatgtttcttttatagctcaaacctccgctgtagcctataggttgtagcaaacaacctgtattatttaatactctttccattacaagatctc
 |||||||||||||||||||| ||||  ||||||||||||||||||||||||||||| ||||||||||| |||||||||||||| |||||||| |||||||||   |||  || | ||||       | |   | | |  | || |||  ||||             | |||||||    |  |   | ||     |   
TACAATGGGGATGCTTAGCACAGCAGCATATGTTCTCACCATGGACATGTTTGGTCCAATAGCTGACAATGCTGGTGGTATTGTGGAGATGAGTCAGCAGgtaatacactcgtattttttcccatgtatatagcagttcaaaccaatattttgtctttgctgtaggtttttatttaccgtttctgttaatatgctttact

upper sequence: GRMZM2G069410_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA07G00350.1 (Glycine max), 5'ss of exon 10
AACAATGGGGATGCTTAGCACTGCAGGGTATGTTCTCACCATGGACATGTTTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcacatgtttcttttatagctcaaacctccgctgtagcctataggttgtagcaaacaacctgtattatttaatactctttccattacaagatctc
||||||||| |||||||||||||| |  ||| |||| |||||||| |||||||| || |||||||| || ||||| || ||||| |||||||| |||||||||   |     || ||   |||  |    ||   | |||    | |  | |    |   | |  | || |   || ||  || |               
AACAATGGGAATGCTTAGCACTGCTGCCTATATTCTTACCATGGATATGTTTGGCCCAATAGCTGATAATGCTGGAGGAATTGTAGAGATGAGTCAGCAGgtagttc-----ttgctagaataatttggtccatag-tgttatttctgagattcctcttgctatgtatactgactattaacctgttttcag---------

upper sequence: GRMZM2G069410_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G78920.2 (Arabidopsis thaliana), 5'ss of exon 10
AACAATGGGGATGCTTAGCACTGCAGGGTATGTTCTCACCATGGACATGTTTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgta---tggcacatgttt--cttttatagctcaaacctccgctgtagcctataggttgtagcaaacaacctgtattatttaatactctttccattacaagatctc
 |||||||| ||||| ||||||||||  ||||| || || |||||||||||||| || |||||||||||||||||||| ||||| ||||||||||||||||||   || |||||| ||  |||  |  ||||  |  | |  | |    | || || | |  ||  ||  ||| |  |  |                        
TACAATGGGAATGCTAAGCACTGCAGCTTATGTCCTTACTATGGACATGTTTGGCCCCATAGCTGACAACGCTGGTGGGATTGTCGAGATGAGCCAGCAGgtaagatgtcacatgattggcttgaaaggctcttatgttccatctttattctatgtagaaataataaa--tgtttcgtgcag-----------------------

upper sequence: GRMZM2G069410_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G16780.1 (Arabidopsis thaliana), 5'ss of exon 11
AACAATGGGGATGCTTAGCACTGCAGGGTATGTTCTCACCATGGACATGTTTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcacatgtttcttttatagctcaaacctccgctgtagcctataggttgtagcaaacaacctgtattatttaatactctttccattacaagatctc
 |||||||| ||| | ||||||||||  |||||||| || ||||||||||||||||| |||||||| || || ||||| ||||||||||||||||||||||||||   ||||  |  ||   |  | |  |||  | ||||  || |   || |  ||| |   || ||  | |||       || ||            
TACAATGGGAATGTTGAGCACTGCAGCTTATGTTCTTACAATGGACATGTTTGGTCCCATAGCTGATAATGCAGGTGGGATTGTTGAGATGAGCCAGCAGgtatgagtcatgagtggttcgaa--ttatgcctatgttgta-tctttgaatttt--caagct-tctataaaacttatcgtgtcttgcag-----------

upper sequence: GRMZM2G069410_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 5'ss of exon 10
AACAATGGGGATGCTTAGCACTGCAGGGTATGTTCTCACCATGGACATGTTTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcacatgtttcttttatagctcaaacctccgctgtagcctataggttgtagcaaaca-acctgtattatttaatactctttccattacaagat-ctc------
||||||||| ||||| |||||||| |  |||||||| || ||||| ||||||||||| |||||||| || |||||||| || || |||||||| ||||||||| | ||        || || | || ||   | |  |      | | || || | ||||   | || || |  ||  |  |        ||||| || |||      
AACAATGGGAATGCTGAGCACTGCTGCCTATGTTCTAACTATGGATATGTTTGGTCCAATAGCTGATAATGCTGGTGGAATAGTAGAGATGAGTCAGCAGgta-gcca--------ttctacaactgaatttttcaata----atgttggctgaatcaaaaggaactttagtgctttgtttttaacttgatacaaaatgctcttacag

upper sequence: GRMZM2G069410_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S28_200V6.1 (Physcomitrella patens), 5'ss of exon 11
AACAATGGGGATGCTTAGCACTGCAGGGTATGTTCTCACCATGGACATGTTTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatgg---cacatgtttcttttatagctcaaac-ctccgctgtagcctataggttgtagcaaacaacctgtatt---atttaat--actctttccattacaa-gatctc--
||| ||||| ||||| || || || || || ||  | || |||||||||||||| || || || ||||| ||||| ||||||||||| ||||| || |||||  ||     |||| || |||| ||  |||    ||  | ||||    |   |||| |       |  ||  |      ||  |  | || |   |    || | |  |  
AACTATGGGCATGCTCAGTACCGCTGGTTACGTGTTGACAATGGACATGTTTGGACCCATTGCAGACAATGCTGGAGGTATTGTTGAAATGAGTCAACAGgtgagggcgttcatgatttttttctatatcatgttctttggtgtaatgaactcgttgaacttttgtatttgggtgtcggcttcgttgattcctgttaacgtaatggttgcag

upper sequence: GRMZM2G069410_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S105_42V6.1 (Physcomitrella patens), 5'ss of exon 11
AACAATGGGGATGCTTAGCACTGCAGGGTATGTTCTCACCATGGACATGTTTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcacatgtttcttttatagctcaaacctccgctgta--gcctataggttgtagcaaa-caacctgtattatt-taatactctttccattacaagatctc-----
 || ||||| ||||| || ||||| || |||||  | || |||||||||||||| || || || ||||||||||| || |||||||| ||||| || ||||||||      || | |   |  | |   || |  | | ||  |    ||     ||  |   | |  || | | ||  | | ||  ||   | |   | | ||     
GACTATGGGCATGCTCAGTACTGCGGGCTATGTGTTGACGATGGACATGTTTGGACCCATTGCAGACAACGCTGGAGGCATTGTTGAAATGAGTCAACAGgtatga-----gtgtataggagcgattgcacttttggtataagggtagtaatgcttaatatttctatttggagttttgcattgctgatttgctgatttgctgtctgcag

upper sequence: GRMZM2G069410_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ13082 (Selaginella moellendorffii), 5'ss of exon 9
AACAATGGGGATGCTTAGCACTGCAGGGTATGTTCTCACCATGGACATGTTTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatg-gcacatgtttcttttatagctcaaacctccgctgtagcctataggttgtagcaaacaacctgtattatttaatactctttccattacaagatctc
 |||||||||||||| || || || | ||| ||  | |||||||||||||||||||| || ||||| || ||||| || ||||||||||||||||| || ||| | |||  |   | || |||   |  |||      |      |  ||                                                   
TACAATGGGGATGCTGAGTACAGCTGCGTACGTGTTGACCATGGACATGTTTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAAgtaagtgcaatttcgtgttctatgttttgaactggaatttggttttgcag---------------------------------------------------

upper sequence: GRMZM2G069410_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ14101 (Selaginella moellendorffii), 5'ss of exon 9
AACAATGGGGATGCTTAGCACTGCAGGGTATGTTCTCACCATGGACATGTTTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatg-gcacatgtttcttttatagctcaaacctccgctgtagcctataggttgtagcaaacaacctgtattatttaatactctttccattacaagatctc
 |||||||||||||| || || || | ||| || || |||||||||||||||||||| || ||||| || ||||| || ||||||||||||||||| || ||| | |||  |   | || |||   |  ||| |    | | |  |  ||                                                   
TACAATGGGGATGCTGAGTACAGCTGCGTACGTGCTGACCATGGACATGTTTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAAgtaagtgcaatttcgtgttctatgtttttaac-tggaatttggtttgcag---------------------------------------------------

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|211330978|gb|FL100740.1|FL100740
EST:     TTGGTCCTATAGCTGACAACGCTGGTGGTATTGYTGARATGAGCCAGCAG                         CCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGCAACACA
genomic: TTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcaca ... accggtgcagCCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGCAACACA
EST: gi|211333136|gb|FL100748.1|FL100748
EST:     TTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAG                         CCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGCAACACA
genomic: TTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcaca ... accggtgcagCCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGCAACACA
EST: gi|32832570|gb|CD972248.1|CD972248
EST:     TTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAG                         CCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGNTGG-CANCAC
genomic: TTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcaca ... accggtgcagCCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTG-TGGGCAACAC
EST: gi|194717044|gb|FK934197.1|FK934197
EST:     TTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAG                         CCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGCAACACA
genomic: TTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcaca ... accggtgcagCCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGCAACACA
EST: gi|211330981|gb|FL100743.1|FL100743
EST:     TTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAG                         CCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGCAACACA
genomic: TTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcaca ... accggtgcagCCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGCAACACA
EST: gi|211461669|gb|FL297430.1|FL297430
EST:     TTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAG                         CCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGCAACACA
genomic: TTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcaca ... accggtgcagCCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGCAACACA
EST: gi|32832566|gb|CD972244.1|CD972244
EST:     TTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAG                         CCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGCAACACA
genomic: TTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcaca ... accggtgcagCCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGCAACACA
EST: gi|211333135|gb|FL100747.1|FL100747
EST:     TTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAG                         CCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGCAACACA
genomic: TTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcaca ... accggtgcagCCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGCAACACA
EST: gi|32838135|gb|CD977813.1|CD977813
EST:     TTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAG                         CCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGCAACACA
genomic: TTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcaca ... accggtgcagCCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGCAACACA
EST: gi|211333137|gb|FL100749.1|FL100749
EST:     TTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAG                         CCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGC
genomic: TTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcaca ... accggtgcagCCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGC

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: 331

AACAATGGGGATGCTTAGCACTGCAGGGTATGTTCTCACCATGGACATGTTTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcaca ... accggtgcagCCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGCAACACAACTAAAGCTACTACGAAAGGATTTGCCATAGGGTCAGCAGCTCTGGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 218

AACAATGGGGATGCTTAGCACTGCAGGGTATGTTCTCACCATGGACATGTTTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcaca ... accggtgcagCCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGCAACACAACTAAAGCTACTACGAAAGGATTTGCCATAGGGTCAGCAGCTCTGGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 271

AACAATGGGGATGCTTAGCACTGCAGGGTATGTTCTCACCATGGACATGTTTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcaca ... accggtgcagCCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGCAACACAACTAAAGCTACTACGAAAGGATTTGCCATAGGGTCAGCAGCTCTGGCTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 398

AACAATGGGGATGCTTAGCACTGCAGGGTATGTTCTCACCATGGACATGTTTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcaca ... accggtgcagCCTGAAAGTGTGAGGGAAATCACAGATGTTCTAGATGCTGTGGGCAACACAACTAAAGCTACTACGAAAGGATTTGCCATAGGGTCAGCAGCTCTGGCTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACAATGGGGATGCTTAGCACTGCAGGGTATGTTCTCACCATGGACATGTTTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcacatgtttcttttatagctcaaacctccgctgtagcctataggttgtagcaaacaacctgtattatttaatactctttccattacaagatctc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctccgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaaacaa