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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTGTAGAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAGgtcagccccttggccctgacttgtacaacctttatttccaaatatgccactaattatgtctgtcctttag

Basic information

species Zea mays
transcript GRMZM2G067985_T04
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G067985_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g01600.1 (Oryza sativa), 5'ss of exon 2
---TTCTGTAG-AAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAGgtcag-----------ccccttggccctgac--------ttgtacaacctttatttccaaatatgccacta-attatgtct-gtcctttag
   |||||||| |||||||||| |||||||||||||||||||||||||| ||||||||||| ||||||||||||||| |           |   ||  | || ||         ||||   | | |  | |  |||||  || || ||||  | |  || | |||
CTCTTCTGTAGGAAATGGCTGACGGTGAGGACATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAGgtctgattttctttttcttttttactcttacgtaatgtaatgtatgtcgtctcctgctgaatattacattacattacatttcatcatgtag

upper sequence: GRMZM2G067985_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g01600.2 (Oryza sativa), 5'ss of exon 2
TTCTGTAGAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAGgtcag-----------ccccttggccctgactt--------gtacaacctttatttccaaatatgccacta-attatgtct-gtcctttag
       ||||||||||| |||||||||||||||||||||||||| ||||||||||| ||||||||||||||| |           |   ||  | || || |        |||   | | |  | |  |||||  || || ||||  | |  || | |||
-------GAAATGGCTGACGGTGAGGACATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAGgtctgattttctttttcttttttactcttacgtaatgtaatgtatgtcgtctcctgctgaatattacattacattacatttcatcatgtag

upper sequence: GRMZM2G067985_T04 (Zea mays), 5'ss of exon 2
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 5'ss of exon 2
TTCTGTAGAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAGgtcagcc----------ccttggccctgacttgtac-aacctttatttccaaatatg-------ccactaattatgtctgtcctttag------
   || | ||||||| ||||||||||| || ||||| |||||||| |||||||| || |||||||| ||||| ||              | |   |||  | || | ||||||  ||     | |||       | ||| || |||  | |  | ||       
---TG-AAAAATGGCCGATGGTGAGGATATTCAGCCACTTGTCTGTGACAATGGAACTGGAATGGTGAAGgtgagttagactgtttatttagatactgtatggttctaaccttctttgttgtacatgtgtaagactactgatcatgatttttgtatattaacag

upper sequence: GRMZM2G067985_T04 (Zea mays), 5'ss of exon 2
lower sequence: Vv12s0178g00200.t01 (Vitis vinifera), 5'ss of exon 1
--TTCTGTAGAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAGgtcagccccttggccctgacttgtacaac----ctttatttccaaatatgccactaattatgtct-gtcctttag-------------------------
   | |    | ||||| ||||  ||||| |||||||||||||| || |||||||| || ||||||||||||||  | |  ||   | |   |  | |||        ||| |     | |||   |  |||  |   |  ||||||                         
AGGTTTTAGAAGATGGCCGATGCCGAGGATATCCAGCCTCTTGTGTGTGACAATGGAACTGGAATGGTCAAGgtttgtcagttattcttatttatttcaatgagttcatatgtttgtgtctgcacttgtttagataaagggctttagggattttacaaaatgaatttgactc

upper sequence: GRMZM2G067985_T04 (Zea mays), 5'ss of exon 2
lower sequence: PP1S372_38V6.3 (Physcomitrella patens), 5'ss of exon 2
------------TTCTGTAGAAA---TGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAGgtcagccccttggccctg---acttgtacaacctttatttccaaat-----atgccactaattatgtctgtcctttag------------------------------------------------------------------------------------------------
            | |     |||   ||||||||||||||||  |||||||| | || |||||||||||| | |||||||| |||||  ||    |  ||      ||   |  ||   |    | |||||     |||| |  |||   | ||  | |||                                                                                                  
TGGTTGAGCAGGTCCAAACTAAACCATGGCTGATGGTGAGGAAGTCCAGCCTTTGGTGTGCGACAATGGCTCTGGAATGGTTAAGgtatgcatgcttaccgcatatacgactgtaattctcccatgcaaatcgagcatgctaacaatcgcgccttgcatttgctaaggtacattgtctgatcaatcatagtactatatacatatcggtcctctgcataatgcgcaaaatctgaaattaggtctggtttatttggcgcag

upper sequence: GRMZM2G067985_T04 (Zea mays), 5'ss of exon 2
lower sequence: PP1S372_38V6.1 (Physcomitrella patens), 5'ss of exon 2
-----------------------TTCTGTAGAAA---TGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAGgtcagccccttggccctg---acttgtacaacctttatttccaaat-----atgccactaattatgtctgtcctttag------------------------------------------------------------------------------------------------
                       | |     |||   ||||||||||||||||  |||||||| | || |||||||||||| | |||||||| |||||  ||    |  ||      ||   |  ||   |    | |||||     |||| |  |||   | ||  | |||                                                                                                  
GTGTTGCAAAGTGGTTGAGCAGGTCCAAACTAAACCATGGCTGATGGTGAGGAAGTCCAGCCTTTGGTGTGCGACAATGGCTCTGGAATGGTTAAGgtatgcatgcttaccgcatatacgactgtaattctcccatgcaaatcgagcatgctaacaatcgcgccttgcatttgctaaggtacattgtctgatcaatcatagtactatatacatatcggtcctctgcataatgcgcaaaatctgaaattaggtctggtttatttggcgcag

upper sequence: GRMZM2G067985_T04 (Zea mays), 5'ss of exon 2
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 5'ss of exon 3
----TTCTGTAGAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAGgtcagccccttggccctgacttgtacaacctttatttccaaatatg--ccactaattatgtctgtcctttag----------------------------
     | |  |||||||||||| ||||||||  | |||||  | || ||||||||||| || |||||||||||||| ||  |  |   |   |        |      ||||| ||  ||   || |   |       | || ||                             
GTCGGTATTAAGAAATGGCTGACGGTGAGGAAGTACAGCCCTTGGTGTGCGACAATGGAACTGGAATGGTCAAGgtgaggtcactcttctaaaacccagagattaacttttccgaacttggttcattggattcaaggattctataatcttgagcttctgctgaaaaatattcta

upper sequence: GRMZM2G067985_T04 (Zea mays), 5'ss of exon 2
lower sequence: PP1S372_38V6.4 (Physcomitrella patens), 5'ss of exon 2
-TTCTGTAGAAA---TGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAGgtcagccccttggccctg---acttgtacaacctttatttccaaat-----atgccactaattatgtctgtcctttag------------------------------------------------------------------------------------------------
 | |     |||   ||||||||||||||||  |||||||| | || |||||||||||| | |||||||| |||||  ||    |  ||      ||   |  ||   |    | |||||     |||| |  |||   | ||  | |||                                                                                                  
GTCCAAACTAAACCATGGCTGATGGTGAGGAAGTCCAGCCTTTGGTGTGCGACAATGGCTCTGGAATGGTTAAGgtatgcatgcttaccgcatatacgactgtaattctcccatgcaaatcgagcatgctaacaatcgcgccttgcatttgctaaggtacattgtctgatcaatcatagtactatatacatatcggtcctctgcataatgcgcaaaatctgaaattaggtctggtttatttggcgcag

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|211380786|gb|FK990764.1|FK990764
EST:     GTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG                         GCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTT
genomic: GTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAGgtcagcccct ... tgtcctttagGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTT
EST: gi|31355571|gb|CD439928.1|CD439928
EST:     GTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAG                         GCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTT
genomic: GTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAGgtcagcccct ... tgtcctttagGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTT
EST: gi|5928698|gb|AW055915.1|AW055915
EST:     GAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG                         GCTGGTTTTGCTGGCGATGATGCACCAAGGGCGGTTTTCCCTAGCATTGTT
genomic: GAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAGgtcagcccct ... tgtcctttagGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTT

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: 1292

TTCTGTAGAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAGgtcagcccct ... tgtcctttagGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 830

TTCTGTAGAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAGgtcagcccct ... tgtcctttagGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 447

TTCTGTAGAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAGgtcagcccct ... tgtcctttagGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 863

TTCTGTAGAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACCGGAATGGTCAAGgtcagcccct ... tgtcctttagGCTGGTTTTGCTGGGGACGATGCACCAAGGGCGGTTTTCCCTAGCATTGTTGGCCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGACAGAAGGATG