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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgtaatttatttttatgtttcaacgtgcagagtcttctctcaagttgcaattattttaatcaattggttaacattaaaaagtgtgatttttagaataacgg...

Basic information

species Zea mays
transcript GRMZM2G113202_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113202_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 5'ss of exon 14
AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgtaatttatttttatgtttcaacgtgcagagtct-tctctcaag-ttgcaattat-----tttaatcaattggttaacattaaaaagtgtgatttttagaataacgg
| ||||||||||||||||||||| ||||| ||||||||||||||| | || |||||||||||||| ||||||||||||||||| |||||||| |  ||||  |||| || ||  | |||| | | | | ||| | ||||||   |     | | ||   ||    | |||    |   |   |||||   |      
AGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCCAACAACATTTCAATCGCCATTTGTTTAAGCTTGAACAAGAGgtgagctattgctatggttaaa-atccagaatatatgtttcaggattgcaaccttcaacctcttatttttttcccatcatcggcagtggcacttttttaga------

upper sequence: GRMZM2G113202_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA10G43230.1 (Glycine max), 5'ss of exon 13
AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgtaatttatttttatgtttcaacgtgcagagtcttctctcaagttgcaat-tattttaatcaattggttaacattaaaaagtgtgatttttagaataacgg---
| |||||||||||| |||||||| || |||||||| ||||| || || || ||||| |||||||||||||| || ||| | || || ||||||  |      |||      |  |||  |    |   | |||      |  ||   | |  ||  |  || | | || | | | |||   | | |  |     
AGGAACAGTTTTGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTACAACAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAGgtatgtgccacatattaactgat-tgcttaacagtggatgaagaataggtgcatagcattttatcagccaa-actgaataatttcattc--aaatttgcaagtt

upper sequence: GRMZM2G113202_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA20G23660.1 (Glycine max), 5'ss of exon 15
AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgtaatttatttttatgtttcaacgtgcagagtcttctctcaagttgcaat-tattttaatcaattggttaacattaaaaagtgtgatttttagaataacgg--
| |||||||||||| ||||||||||| |||||||| ||||| || || || ||||| |||||||||||||| || ||| | || || ||||||  |      |||      || |||  | |  |   | |||      |  |||  | |  ||  |  ||  | ||||| |   |  || | | |  |    
AGGAACAGTTTTGAGCAGTTCTGCATAAATTATGCAAATGAGAGATTACAACAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAGgtatgtgccacatataaactgac-tgcttaataatggatgaagaataggtgcattgcattttatcagccaaactgaaaaaatc--acattcaaatttgcaagt

upper sequence: GRMZM2G113202_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA09G42180.1 (Glycine max), 5'ss of exon 13
AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgta---attt------atttttatgtttcaacgtgcagagtcttctctcaagttgca--attattttaatcaattggttaacattaaaaagtgtgatttttagaataacgg-------
| |||||||||||| ||||||||||| |||||||| ||||| || || |||||||| || ||||||||||| || ||| | || || ||||||   ||         | |  ||| ||||||  | |  |   ||  |  |  || |  |  || || |  |  |   | | |   |||  | ||  | |          |       
AGGAACAGTTTTGAGCAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTTAATCGTCATTTATTCAAGTTAGAACAGGAGgtatggatcctgcagagtctgaatgcttcaacaagtattgatgtccttttaaatgaaggaaaatattgaatacct--ctgaaagctaaatatctgcctatgcacgcggttgatttcag

upper sequence: GRMZM2G113202_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA20G00320.1 (Glycine max), 5'ss of exon 15
AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgta---attt------atttttatgtttcaacgtgcagagtcttctctcaagttgcaattattttaatcaattggttaacattaaa----aagtgtgatttttagaataacgg----------
| |||||||||||||||||||||||| |||||||| ||||| || || |||||||| |||||||||||||| || ||| | || || ||||||   ||         | |  ||| || |||  | |  |  |   ||    |   || |     || | ||||  || |  | ||    ||   |    ||  | |    |           
AGGAACAGTTTTGAACAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAGgtatggatcctgcggagtctgaatgcttaaacaagtattgaatgtccttgtatcttaaatgaaagaaactattgaatacctctgaatgccaaacatctgcttatgcacgtggattgatttcag

upper sequence: GRMZM2G113202_T01 (Zea mays), 5'ss of exon 14
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 5'ss of exon 15
AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgtaattta----tttttatgtttcaa---cgtgcagagtcttctctcaagttgcaattattttaat--caattggttaacattaaaaagtgtg-atttttagaataacgg----
|| || |||||||| |||||||| || |||||||| ||||| || ||||||||||| ||||| |||||| | || ||||||||||| |||||||  ||      ||| || |       | || ||  | |     ||          || |  |   ||  |    |    | |    | |  |||| |    |  |      
AAAAATAGTTTTGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTCAACCGTCATCTCTTCAAGCTTGAGCAGGAGgtaacgtaaacccctttctgctatgggtccttgtagtatatctaggcagagcatggacatgtacacaccagctaccgagttctgagggatttatatttctgtcttctcttccag

upper sequence: GRMZM2G113202_T01 (Zea mays), 5'ss of exon 14
lower sequence: AT3G19960.1 (Arabidopsis thaliana), 5'ss of exon 15
AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgtaa---tttatttttatgtttcaac-gtgcagagtcttctctcaagt-tgc-aattattttaatcaattgg--ttaacattaaaaagtgtgatttttagaataacgg----------------------------
|| || || || || |||||||| || |||||||| ||||| || ||||||||||| || || |||||| | || ||||| |||||||||||||   |     |||||   | |||  | | |   | | | | || | | | |  |  |  | |||  | |   ||  |   |||||    | |||  |     |                              
AAAAATAGCTTCGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTTAACCGTCATCTATTCAAGCTGGAGCAAGAGgtaaagttgctcctttataaatgaactatacgggcacatgtattaaatatactaggtcgtgcattcacatagaactacaacctaaaagctcaactttctgtcatccaagttattaatgttctttctactgtttcag

upper sequence: GRMZM2G113202_T01 (Zea mays), 5'ss of exon 14
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 5'ss of exon 14
AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgtaatttatttttatgtttcaacgtg-cagagtcttctctcaagttgcaattattttaatcaattggttaacattaaaaagtgtgatttttagaataacgg-
|  || || ||||| ||||||||||| |||||||| ||||| ||||||||||| || || || |||||||| || ||| | ||||||||||||| |      |||   |   | |  ||   |   |    |   ||  || |  | |  ||  |     |   || |   |  ||||  |  | |   |  
AGAAATAGCTTTGAGCAGTTCTGCATAAATTATGCAAATGAGAGGTTGCAGCAGCACTTTAACCGTCATTTATTCAAGTTAGAGCAAGAGgtaactgtccaatattccttctcttatcaatataaacaaatatagtgatataaactca--catataacagattctagatgatccgattacttcagttctgaa

upper sequence: GRMZM2G113202_T01 (Zea mays), 5'ss of exon 14
lower sequence: PP1S228_18V6.1 (Physcomitrella patens), 5'ss of exon 14
AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgtaat-------ttatttttatgtttcaacgtgcagagtcttctctcaagttgcaattattttaatcaattggtt----aacattaaaaagtgtg---atttttagaataacgg----------------------------------------------------------------
|| ||||||||||| || || || || |||||||| |||||||||||||| |||||||||||||||||| |||| ||||||||||||||||||||       | ||| ||| |          |     ||  || || ||    ||| | | | ||  ||   |    |   | | |   | ||   | || |   ||  |||                                                                
AAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAGgtaatacgaggatgattgttacggccatgttatctttccctgttcgcacgtactgattttgtaattctcttatcttcccactgtcacagcatctgtgtacttctcccattccggactcagtcacgaaatgctacgccgaacgattaacagaggtcggctttttgcgtgaatttttcag

upper sequence: GRMZM2G113202_T01 (Zea mays), 5'ss of exon 14
lower sequence: PP1S199_21V6.1 (Physcomitrella patens), 5'ss of exon 14
AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgtaatttatttttatgtttcaacgtgcaga-----------gtcttctc-tcaagttgcaattatttt--aatcaatt---ggttaacattaaaaagtgtgattt--ttagaataacgg------------------------------------------------------------
|  || ||||| || ||  | || || || ||||| ||||| ||| |||||||||||||||| |||||  | ||||||||||||||||| |||  |  | |  | | ||  |      ||            |||| || | || ||    ||||  |  |||  |     | ||| |        || |  ||   ||    |  |                                                              
AGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAAgtatgtgttatgaaagcttagatacagtgatagatatagctatcttttccttaaattaatgttatactggaattgaacccagattagctccttgctgtttccttccgtttttgtggcattcattctacaccagcttgcaaaatacttattctgttcgggttgctttgatgatcatgcag

upper sequence: GRMZM2G113202_T01 (Zea mays), 5'ss of exon 14
lower sequence: PP1S17_368V6.1 (Physcomitrella patens), 5'ss of exon 13
AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgtaatttat---ttttatgtttcaacgtgcagagtc--ttctctcaagttgcaattattttaatcaattggttaacattaaaaagtgtgatttttagaataacgg-----------------------------------------------------------------------------------------
|| ||||||||||| ||||| || ||||| || || || ||||| ||||| ||||||||||||||||| ||||| ||||||||||||||||||   |      |  || |||   |        ||  ||   |   |   || ||| ||||    ||   | | | |       | ||  | |||    ||| |                                                                                         
AAAAACAGTTTTGAGCAGTTGTGTATTAACTACGCAAACGAAAGATTGCAACAACATTTCAATCGTCACTTGTTCAAGCTTGAGCAAGAGgtaccatgaaggctgaatatttttgctattgatttcgattgatttctgcctcagttactttacatgatctataatcctacctttttttggctattactgcaacagtttctatactgttttccactggggactagatcgtgaagtgccgcatcaaacatctaacagagtccgactttgttgtgttaacttatcag

upper sequence: GRMZM2G113202_T01 (Zea mays), 5'ss of exon 14
lower sequence: PP1S174_120V6.1 (Physcomitrella patens), 5'ss of exon 14
AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgta-atttatttttatgtttcaacgtgcagagtcttctctcaag---ttgcaattattttaatcaattggttaacattaaaaagtgtgatttttagaataacgg-----------------------------------------------------------------------
|||||||||||||| ||||| ||||| || ||||| || ||||||||||| |||||||||||||| ||| ||||||||||||||||||||||| |   |    ||  | |   |   |      |||| ||  |   ||  |  |  ||  |  | |    |         || |  |||||||   ||  |                                                                         
AAGAACAGTTTTGAGCAGTTATGCATAAACTATGCAAACGAAAGGTTGCAACAACATTTCAATCGCCATCTGTTTAAGCTTGAGCAAGAGgtacacaaaaagctaattatttgcaaactagtctttctttctgggtcttttaggttgttgtacgattccaatgtttccctgaaattcgatttttttcatctcttgcgtctgaatggatcttggagtagaattatgcaactgatagagtacgactttggctgtgacaaatttacag

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|32934816|gb|CF039628.1|CF039628
EST:     AAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG                         GAATATGTGGAGGATGGCATCGACTGGGCAAAGGTTGACTTCGAGGATAAT
genomic: AAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgtaatttatt ... ctttgaacagGAATATGTGGAGGATGGCATCGACTGGGCAAAGGTTGACTTCGAGGATAAT
EST: gi|32932787|gb|CF037599.1|CF037599
EST:     AGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG                         GAATATGTGGAGGATGGCATCGACTGGGCAAAGGTTGACTTCGAGGATAAT
genomic: AGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgtaatttatt ... ctttgaacagGAATATGTGGAGGATGGCATCGACTGGGCAAAGGTTGACTTCGAGGATAAT
EST: gi|32930639|gb|CF035451.1|CF035451
EST:     AAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAACAAGAG                         GAATATGTGGAGGATGGCATCGACTGGGCAAAGGTTGACTTCGAGGATAAT
genomic: AAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgtaatttatt ... ctttgaacagGAATATGTGGAGGATGGCATCGACTGGGCAAAGGTTGACTTCGAGGATAAT
EST: gi|211452365|gb|FL406340.1|FL406340
EST:     AAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG                         GAATATGTGGANGATGGCATCGACTGGGCAAAGGTTGACTTCGAGGATAAT
genomic: AAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgtaatttatt ... ctttgaacagGAATATGTGGAGGATGGCATCGACTGGGCAAAGGTTGACTTCGAGGATAAT

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: 176

AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgtaatttatt ... ctttgaacagGAATATGTGGAGGATGGCATCGACTGGGCAAAGGTTGACTTCGAGGATAATCAGGACTGTTTGAGCCTCTTTGAGAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 107

AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgtaatttatt ... ctttgaacagGAATATGTGGAGGATGGCATCGACTGGGCAAAGGTTGACTTCGAGGATAATCAGGACTGTTTGAGCCTCTTTGAGAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 79

AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgtaatttatt ... ctttgaacagGAATATGTGGAGGATGGCATCGACTGGGCAAAGGTTGACTTCGAGGATAATCAGGACTGTTTGAGCCTCTTTGAGAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 158

AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgtaatttatt ... ctttgaacagGAATATGTGGAGGATGGCATCGACTGGGCAAAGGTTGACTTCGAGGATAATCAGGACTGTTTGAGCCTCTTTGAGAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAGgtaatttatttttatgtttcaacgtgcagagtcttctctcaagttgcaattattttaatcaattggttaacattaaaaagtgtgatttttagaataacgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaagtg