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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATTTGGATCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgtattctagtttagtttattgtttctctctctatcagatgcaagtttctcatttcttccataattacgtaaaccttacctctggtttggcatctgtaaac...

Basic information

species Zea mays
transcript GRMZM2G095348_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095348_T03 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 12
GTCATTTGGATCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgtatt-ctagtttagtttattgtttctctctctatcagatgcaagtttctcatt-tcttccataattacgtaaaccttacctctggtttggcatctgtaaac-
|||||||||||||||| |||| ||||||||||||||||||||||| ||||| || ||||||||||||||||||||||||||||||||||||||||||||||| |  |     | | || | |  | ||  | ||| |  |  |    |   | | |  |   | ||| | | || |    ||||||    | ||     | | 
GTCATTTGGATCTGCATTGGAGTTTGTTTGGTCATCAGAAGGAGAGTATGCTATCAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgtttggcccacattgattgtagcctttccttttatgaatttgatcagtaaaactgtagtgtttcatttcttcaatcaccactctgg---agaatgcaccatct

upper sequence: GRMZM2G095348_T03 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 12
GTCATTTGGATCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgtattctagtttagtttattgtttctctctctatcagatgcaagtttctcatttcttccataattacgtaaacct-tacctctggtttggcatctgtaaac---
 |||||||| || |||||||||||||||||||| ||||| || || |||||  | || ||||||||||| |   | || |||||||| |||   || |||||  |   | ||   ||   ||| ||||    ||   || |   | ||| ||  |     | ||   |  |||||  |  |||   |       |  ||     
ATCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCAGATGGGGAGTATGCTGTAAGAGAAAGTACATCGAAGGTTAAAATTTTCAGCAAAAATTTCCAGgttgt---gcttcactttcagttactcttatcattttatactt-tgtcttatgacgaaagtgatggtgacaacctacaattctaaataatttgttaaaaggata

upper sequence: GRMZM2G095348_T03 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 12
GTCATTTGGATCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgt--attctagtttagtttattgtttctctctcta-tcagatgcaagtttctcatttcttccataattacgtaaaccttacctctggtttggcatctgtaaac
||||||||| || |||||||||||||||||||| || || |||||||||||  | || |||||||||||||  || || |||||||| |||   || |||||   | ||  ||||     ||  ||  ||||||| ||   |||||   |||  ||   |   |||| |   ||    | | |    |||   |   | ||| 
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttgtacttttttaaaaactttgtttcctctctaatctcgtgcaa---tcttgttctgtgtgtaatgaaccaacaagttcttgctatttcttaaaaggaaaa

upper sequence: GRMZM2G095348_T03 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 12
GTCATTTGGATCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgtattctagtttagtttattgtttctctctctatcagatgcaagtt-tctcatttcttccataattacgtaaaccttacctctggtttggcatctgtaaac
||||||||| || |||||||||||||||||||| || || |||||||||||  | || |||||||||||||  || || |||||||| |||   || ||||| || || |||  ||||   ||  | ||      |       ||  |||  ||  ||   |||| |   ||    | | |    |||   |   | ||| 
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgt-ttgtacttttttttaaacttcatttcctctctaatcttgtgtgatcttgttctttgtgtaatgaaccaacaagttcttgctatttcttaaaaggaaaa

upper sequence: GRMZM2G095348_T03 (Zea mays), 5'ss of exon 12
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 12
GTCATTTGGATCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgtattctagtttagtttattgtttctct------ctctatcagatgcaa-gtttctcatttcttccataattacgtaaaccttacctctggtttggcatctgtaaac----------------------------
||||||||| |||| ||||||||||||||||||||| || || || | |||  |||| |||||  ||||||  || || || || || |||   || ||||| |||||  |   ||| |   |  |||       ||| |   |  |    | | |  ||  |   |  ||||   | ||    | |   | | |  || |    |                             
GTCATTTGGTTCTGGACTGGAATTTGTTTGGTCATCCGAGGGGGAGTGTGCGGTTAGAGAAAGCTCATCAAAGATTAAAATATTTAGCAAAAATTTCCAGgt-ttctaaatctttttctctctgatctaagccgttctgttcaaccctgtatctatggttgttggaagtattattgatactggtcatggagatagctatattcggatctggctcattcagaaaatacattttcag

upper sequence: GRMZM2G095348_T03 (Zea mays), 5'ss of exon 12
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 12
GTCATTTGGATCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgtattctagtttagtt-tattgtttctctctctatcagatgcaagttt--ctcatttcttccataattacgtaaaccttacctctggtttggcatctgtaaac-------------------------------
 || ||||| ||||  |||||||||||||||||||| || || |||| |||  |||| |||||  ||||||  |||||||| |||||||||   || ||||| | ||| | |  || |    || |||   ||||    |   ||| |   ||     ||  | || |     |  ||| |    |     ||   |     |                               
ATCTTTTGGGTCTGGCCTGGAATTTGTTTGGTCATCTGAGGGGGAATGTGCGGTTAGAGAAAGCTCATCAAAGATAAAGATATTCAGTAAAAATTTCCAGgtttgctattctcattatggccttactcatactattttgttggagtatgattctagggttgaagaaattgcagatgcttgcaatagagacagctattactggcttattatattaataaaaggtggtgttttcag

upper sequence: GRMZM2G095348_T03 (Zea mays), 5'ss of exon 12
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 12
GTCATTTGGATCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgtattctagtttagtttattgtttctctctctatcagatgcaagtttctcatttcttccataattacgtaaacct-tacctctggtttggcatctgtaaac---
||| ||||| || ||| |||||||||| ||||||||||| || ||||||||  | || |||||||||||||   | ||||||||||||||    || ||||| |    ||    |   ||||||||||||  || |||   |  ||          |  |||  ||  |  |  | |   | ||  |  ||  ||| ||||   
GTCTTTTGGTTCGGCATTGGAATTTGTATGGTCATCAGATGGTGAATATGCTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgt--gtcccctcctttgtttctctctg-atgaga-atagattaggtgcaatatatatatatatatgcatgtgtgtgtgtgtgtgtgctgctgaaaacatt

upper sequence: GRMZM2G095348_T03 (Zea mays), 5'ss of exon 12
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 12
GTCATTTGGATCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgt----attctagtttagtttattgtttctctctctatcagatgcaagtttctcatttcttccataattacgtaaaccttacctctggtttggcatctgtaaac---
 |||||||| || || ||||||||||||||||||||||| | |||||||||  | ||||||||||||||||| || ||||||||||| ||| |||| |||||    || ||     ||||||   | || |    |||  ||||   | || ||  | |   || ||||| | ||  |||  || | |||    |  |||  |    
ATCATTTGGCTCAGCGCTGGAATTTGTTTGGTCATCAGATGCAGAATATGCTGTGAGGGAAAGTACATCAAGGATTAAGATTTTCAGCAAAACATTCCAGgttttgatcctttcaaagtttagattctcacgacttatt-gatgggggcttttc--tccaagca-aatta-gcaatgctt--cttttgttgcaaagttgtttatctt

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|32806679|gb|CD958913.1|CD958913
EST:     CAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAG                         GAGAAGAAAACTATCCGCCCTTCATTTTCAGCAGAGCGTATTTTTGGTGGG
genomic: CAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgtattctagt ... gatttttcagGAGAAGAAAACTATCCGCCCTTCATTTTCAGCAGAGCGTATTTTTGGTGGG




















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: 269

GTCATTTGGATCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgtattctagt ... gatttttcagGAGAAGAAAACTATCCGCCCTTCATTTTCAGCAGAGCGTATTTTTGGTGGGGTATTGTTGGCAATGTGTTCTAGTGATTTCATCTGCTTTTATGACTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 189

GTCATTTGGATCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgtattctagt ... gatttttcagGAGAAGAAAACTATCCGCCCTTCATTTTCAGCAGAGCGTATTTTTGGTGGGGTATTGTTGGCAATGTGTTCTAGTGATTTCATCTGCTTTTATGACTGGG


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

GTCATTTGGATCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgtattctagt ... gatttttcagGAGAAGAAAACTATCCGCCCTTCATTTTCAGCAGAGCGTATTTTTGGTGGGGTATTGTTGGCAATGTGTTCTAGTGATTTCATCTGCTTTTATGACTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 247

GTCATTTGGATCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgtattctagt ... gatttttcagGAGAAGAAAACTATCCGCCCTTCATTTTCAGCAGAGCGTATTTTTGGTGGGGTATTGTTGGCAATGTGTTCTAGTGATTTCATCTGCTTTTATGACTGGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCATTTGGATCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgtattctagtttagtttattgtttctctctctatcagatgcaagtttctcatttcttccataattacgtaaaccttacctctggtttggcatctgtaaac

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