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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatacagcaaaaagcttatgcttgcattctgattagtaaacacatccaatcatatgtaatgtag

Basic information

species Zea mays
transcript GRMZM2G057576_T02
intron # 25
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 25
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 27
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatacagcaaaaagcttatgcttgcattctgattagtaaacacatccaatcatatgtaatgtag
 |||||||||||||||||||||||||| |||||||||||||||||||| ||||| ||||| || |||||||| || ||||| || ||||||||||| |||||||| ||  | |||||   |||      | || |  | || |   ||| |  |     |  || |    || |   |||| |     ||| |  | | | || | | ||           
GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgtttgatttaagcccataa-atttctatcttatttttgtgttgaatatttagca-----tgtagtatgctgcattaacttgtaac---att-gccatctcttctagttat-----------

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 25
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 27
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcgaacccattgtattggctgatgatatgggagtagctaattca-atactatatacagcaaaaagcttatgcttgcattctgattagtaaacacatccaatcatatgtaatgtag
 |||||||||||||||||||||||||| |||||||||||||||||||| ||||| ||||| || |||||||| || ||||| || ||||||||||| ||||||   ||  | |||||    ||   |  || | | |   |   || ||   ||    ||| | |||  || ||| |     ||||   ||       | | || | | ||           
GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaatttaagcccataaatttctattttgtttttgtgttgaatatttagcatgtagtatgctgcattaa-cttgta---acattgccat-------ctcttctagttat-----------

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 25
lower sequence: GLYMA14G37510.1 (Glycine max), 5'ss of exon 25
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatacagcaaaaagcttatgcttgcattctgattagtaaacacatccaatcatatgtaatgtag
 || || ||||||||  | ||||||||||| ||||| || ||||| |||||||| ||||||||||| || ||||| ||||| || || || ||||||||||| |  ||    |  |||   ||   |||  |||    | |     |||||   ||  | ||      | |       |||   | |||    |    | |                    
GTCAAAAAAAGACAATCTTTACAAGGACTGTATGGAAACTTGCTCTCAATCTGGTGACCGTGAACTCTCGGAGGATTTGCTTGTTTACTTTATTGAGCAGgtctatttt---cttattcccttccttga-aataccaaactcttctattcatatctcaaaaccttgccaggtcccactttgtggtttgacctctgctaaaaatt-----------------

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 25
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 27
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatacagcaaaaagcttatgcttgcattctgattagtaa-acacatccaatcatatgtaatgtag
 || || ||||||||  | ||||||||||| ||||| || ||||| |||||||| ||||||||||| |||||||| ||||| || || || ||||||||||| |  ||    |  |||   ||   |||  ||||   | |     |||||   ||  | ||      | |        |||| | |||    |   ||| ||                   
GTCAAAAAAAGACAATCTTTACAAGGACTGTATGGAAACTTGCTCTCAATCTGGTGACCGTGAACTCTCAGAGGATTTGCTTGTTTACTTTATTGAGCAGgtctatttt---cttattcccttccttga-aatatcaaactcttctattcatatctcaaaaccttgccaggtcccactgtgcaatttgacctctgctacaaatt------------------

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 25
lower sequence: GLYMA11G06720.1 (Glycine max), 5'ss of exon 27
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttgg---ttcgaacccattgtattgg---ctgatgatatgggagtagctaattcaatactatatacagcaaaaagcttatgctt---gcattctgattagtaaacacatccaatcatatgtaatgtag-----------------------------------------------------------------
 || |||||||||||  | ||||||||||| ||||| |||||||| |||||||| ||||||||||| || || || ||||| || || || ||||||||||| |     |||    || ||   ||     || |   | ||| | | |  ||||  ||||||  ||    | |    ||  || |   ||| | |||        ||| |  ||     | |  ||                                                                    
GTCAAAGAAAGACAATCTTTACAAGGACTGTATGGAAACATGCTCTCAATCTGGTGACCGTGAACTCTCGGAAGATTTGCTTGTCTACTTTATTGAGCAGgtgtttattttcttgtccttttccttaagatctcaaactctggtattcgtaaattagatactaactaggttagacccttttggcatagtgcactttgaccctgcttcacttagaaatgattttgctgctttctttcctcacctcccgcaccagtttttctctcttaattaacaaagggattatattgatttgcag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 25
lower sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 27
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatacagcaaaaagcttatgc-ttgcattctgat-tagtaaacaca-tccaatcatatgtaatgtag-----------------------------------------------------------------------
 || |||||||||||  | ||||||||||| ||||| |||||||| |||||||| ||||||||||| ||||| || |||||  | || || ||||||||||  || ||     |   |   ||  || | |||||   | |     ||||  ||   || | |  ||  || |||  | ||      |  |  ||| | |    | || | | |  | || | |                                                                       
GTCAAAGAAAGACAATCTTTACAAGGACTGTATGGAAACATGCTCTCAATCTGGTGACCGTGAACTTTCAGAAGATTTGCTTATCTACTTTATTGAGCAGg--tgtttattttcttgtccttttccttaagatatcaaactccagtattcg-taaattagatactaactaggttagaccttttggcatagtgcagtgaccctgcttcacttagaaattattttgctgctttctttcttcacctccagtgctggttcttttcttttaattaacaaagggattatattgatttgcag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 25
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 26
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcgaacccattgtattggctgatgatatgggagt-agcta-attcaatactatatacagcaaaaagcttatgcttgcattctgattagtaaacacatccaatcatatgtaatgtag
 || |||||||| ||| | ||||| ||   ||||||||||  |||||||||||| |||||||||||  | ||||| ||||| || ||||||||||| |||||        |  | |||  |  |||  || ||       | ||| | |||    |  ||   ||   || |  || |  ||| |  || |   |  ||   |                    
GTCAAAGAAAGATAACCTTTACAAAGATGCCATGGAGACAGCCTCACAATCTGGTGACCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgt---accaaattcaatttcaacggcatataattcattttttagcaacattgcccagcattctcatttaacatgttttatttgaagactaagatgctaagcta--------------------

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 25
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 26
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatac-agcaaaaagcttatgcttgcattctgattagtaaacacatccaatcatatgtaatgtag
 || ||||| || ||| | ||||| ||   ||||||||||  ||| |||||||| |||||||||||  | ||||| ||||| || ||||||||||| |||||   |    |  | |||  | ||||  || ||       |    ||       |   | || ||||  | | ||  | |||  |  |  | | | ||||  |                   
-TCAAAGAAGGATAACCTTTACAAAGATGCCATGGAGACAGCCTCGCAATCTGGTGACCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGGt---gccaaattcaatttcaatggcatataattcattttttagcaacattgcccagcagaccagcattatgatttgggttgactcattctcatttaacatttt------------------

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 25
lower sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 27
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgt--ttggttcgaaccca----ttgtat-tggctgatgatatgggagtagctaattcaatactatatacagcaaaaagcttatgct-tgcattctgattagtaaacacatccaatcatatgtaatgtag
 || ||||| || ||| | ||||| ||   ||||||||||  ||||||||||||||| ||||||||  | ||||| ||||| || ||||||||||| |||||  |   |||     ||    |  ||| |   | ||  | | | | || ||  ||  ||  ||  |  | ||  |  |||      ||  || || ||| |                           
GTCAAAGAAGGATAACCTTTACAAAGATGCCATGGAGACAGCCTCACAATCTGGCGAGCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgtgctaaattcagtttcaaacttcatatataattcattttcttgcaatatcttgtttgat--taggtttaccattattcttggataatgtgttttgtttaat---------------------------

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 25
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 27
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatacagcaaaaagcttatgcttgcattctgattagtaaacacatccaatcatatgtaatgtag
||| |||||||||||||||||||||||||| ||||| ||    |||||||| ||||| | ||||||  ||||  |  | || |||||||||||||| ||||| || |        |   | ||    |||| ||  |   |||| | |||| |    |     | ||| |  |  | |   | ||     |||||  | | |    ||   ||| ||  ||
ATCAAAGAAAGACAACATGTACAAGGACTGTATGGAAACGGCTTCACAATCAGGCGAACATGAACTTGCAGAACAACTACTGGTGTATTTCATTGAACAGgtatgatgatggttaaacat-ttacgagatgcta--gtgctagcca-ttcagtttggttagttgaaaagaattggtccagacgttgaacgtagtatcc-cgtgtcttctgctgttatacag

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 25
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 27
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatat-acagcaaaaagcttatgcttgcattctgattagtaaacacatccaatcatatgtaatgtag
 ||||||||||||||| ||||||| |||   ||||||||   ||| |||||||| |||||||||||  ||||||| ||||| || |||||||||||| ||||      |  |    | |      |||| || ||     || ||||  | ||| | |   |||  | |||    || |   ||   | ||     | || | |                  
GTCGAAGAAAGACAACCTGTACAAAGACGCGATGGAGACTGCCTCGCAATCTGGTGACCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGAAGgt---acccagaatgctagagcaatctgaagacatctctttaactaaagccatagtcttccacaatataaaatcaat-cacacaccttcatgcactagcataac------------------

upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 25
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 27
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcgaaccca-ttgtat-tggctgatgatatgggagtagcta--attcaatactatatacagcaaaaag-cttatgcttgcattctgattagtaaacacatccaatcatatgtaatgtag
 || |||||||||||| | ||||| ||    |||||||||||||| || ||||| || ||||||||  ||||||| ||||| || ||||||||||||||||| ||  ||  |  || |||| | |    | ||| || |   ||   |  ||  ||| ||| |||  |  ||    | |         |||| |||  ||                          
GTCAAAGAAAGACAACCTATACAAAGATGCGATGGAGACATGCTCTCAGTCTGGGGATCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGCAGgtatgagtcatatacacttgtctataaaagctgaaattgagataatcatcatcaaatgctaaatagtgtgaatgttccttcataaattttctaattttta--------------------------

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|160481599|gb|EY254431.1|EY254431
EST:     CTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAG                         GGTAAGAAAGAATGTTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATC
genomic: CTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcg ... tgtaatgtagGGTAAGAAAGAATGTTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATC
EST: gi|67014840|gb|CO443589.1|CO443589
EST:     TGCCGACCGTGAACTGTCANAGGACTTGCCTC-TGTATTTCATTGAGCAG                         GGTAAGAAAGAAAGTTTTGCTTTTTGCCCCCTT-ATTTGCTACGACCTGAT
genomic: GGC-GACCGTGAACTGTCAGAGGACTTGC-TCGTGTATTTCATTGAGCAGgtttggttcg ... tgtaatgtagGGTAAGAAAGAATGTTTTGCTTCTTGCCTC-TTCATTTGCTACGACCTGAT

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: 292

ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcg ... tgtaatgtagGGTAAGAAAGAATGTTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATCCGGCCAGATGTGGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 104

ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcg ... tgtaatgtagGGTAAGAAAGAATGTTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATCCGGCCAGATGTGGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 175

ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcg ... tgtaatgtagGGTAAGAAAGAATGTTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATCCGGCCAGATGTGGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcg ... tgtaatgtagGGTAAGAAAGAATGTTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATCCGGCCAGATGTGGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatacagcaaaaagcttatgcttgcattctgattagtaaacacatccaatcatatgtaatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG