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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcatccattcatgcctacattcgcatccatcgataaaactcatatacaattaacacaatcaaagcttttcctaattaataactgcaagcattaaaagtgtagtgtaatcgatcttgtaattacgctctgatctagctacctatatatgagtgatccatggatcgatatatacatatatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACATCTTCGGCGCCTGCTGCGCCACCACCGTGTTCATCCCCTCCTTCCACAAC

Basic information

species Zea mays
transcript GRMZM2G045057_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045057_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 3
gtaatcatccattcatgcctacattcgcatccatcgataaaactcatatacaattaacacaatcaaagcttttcctaattaataactgcaag--cattaaaa-gtgtagtgtaatcgatcttgtaattacgctctgatctagctacctatatatgagtgatccatggatcgatatatacatatatga-gcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACATCTTCGGCGCCTGCTGCGCCACCACCGTGTTCATCCCCTCCTTCCACAAC
                                                                   |     || ||     ||  | ||   ||||| || ||  | | || |     ||| |   |||     |||    |   || |||   || |    |   || || |  |   |||||  ||||||||||||||||||| || ||||| |  |||||| | || |||||||||||||||||||||||||| || || ||||| ||||| || || ||||| || 
-------------------------------------------------------------------gtaaacccaaaaggggaaaggaaaaatcattacaatgtacattatatttctgtttggacagacgaatacatc---atgtatacatactggttaatttttcctcaatttccattgatatgctgcagCAACATCTACTACATAAATGACAATTTCGACAAGAGAACTTGGACGTACATCTTCGGCGCCTGCTGTGCTACGACCGTTTTCATTCCTTCATTCCATAAT

upper sequence: GRMZM2G045057_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 3
gtaatcatccattcatgcctacattcgcatccatcgataaaactcatatacaattaacacaatcaaagcttttcctaattaataactgcaagcattaaaagtgtagtgtaatcgatcttgtaattacgctctgatctagctacctatatatgagtgatcca-tggatcgatatatacatatatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACATCTTCGGCGCCTGCTGCGCCACCACCGTGTTCATCCCCTCCTTCCACAAC
                || |         ||| ||  ||     |   ||| | ||            || |  ||  ||        |  |  ||     | |      | |    || |  || |  |||   | |   ||  | || ||||  ||    || | |     ||     |    |||||||||| || ||||| || || ||    |||||| |||| ||||| ||||||||||| |||||||| |||||||| || || || || || |||||||||
----------------gcatctccctctctccctccctatcctcctcctactactactctctctctctctctctctctttctctgtctcttgttttt----tcttcacccaccacatttttttttcctttctttacaataaacaaagatctgaggcattttctgcaactgggcatgtcgtttgttgcagCAACATATATTACATAAATGATAATCTGGACAAGAGGACATGGACTTACATCTTCGGAGCCTGCTGTGCCACCACAGTCTTTATTCCTTCATTCCACAAC
















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|78112333|gb|DV530727.1|DV530727
EST:     TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|76288759|gb|DV028327.1|DV028327
EST:     TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|71758159|gb|DR956096.1|DR956096
EST:     CATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: CATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|78120350|gb|DV538734.1|DV538734
EST:     TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|74233955|gb|DT641869.1|DT641869
EST:     TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|148934104|gb|EC878118.2|EC878118
EST:     GTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: GTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|76926808|gb|DV171015.1|DV171015
EST:     TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|149082574|gb|EE171769.2|EE171769
EST:     TCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|71767925|gb|DR965862.1|DR965862
EST:     TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|78089315|gb|DV517689.1|DV517689
EST:     TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|76010505|gb|DT937675.1|DT937675
EST:     TCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|78107103|gb|DV525521.1|DV525521
EST:     TGCACTTTCCTCCTCCTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|50327191|gb|CO522317.1|CO522317
EST:     TCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|76010835|gb|DT938005.1|DT938005
EST:     TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|94474307|gb|EB703265.1|EB703265
EST:     TCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|148959931|gb|EE153170.2|EE153170
EST:     TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|88748025|gb|DY532166.1|DY532166
EST:     AGCTCATTGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: AGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|78088592|gb|DV516985.1|DV516985
EST:     TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|78125247|gb|DV543631.1|DV543631
EST:     TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|148966351|gb|EE017338.2|EE017338
EST:     ACTTTCCTCTTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: ACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|149098688|gb|EE184698.2|EE184698
EST:     GCACTTTCCTCCTCTTCCGGCTCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: GCACTTTCCTCCTCTT-CGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|76922170|gb|DV168885.1|DV168885
EST:     CATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGAACGTGGACGTACAT
genomic: CATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|78076145|gb|DV504579.1|DV504579
EST:     TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|76021210|gb|DT948380.1|DT948380
EST:     TCCTCCTCTTGGGGTCCGTCATCCAGCTCATCGCATGGGCAAG                         CAACATCTACTACATCAAGGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|71758786|gb|DR956723.1|DR956723
EST:     CATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: CATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|149095643|gb|EE181265.2|EE181265
EST:     TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|76016574|gb|DT943744.1|DT943744
EST:     CGTCAT-CAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: CGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|86465793|gb|DY232166.1|DY232166
EST:     CCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: CCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|76280995|gb|DV020563.1|DV020563
EST:     ATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: ATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|86470112|gb|DY236482.1|DY236482
EST:     TCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|76010802|gb|DT937972.1|DT937972
EST:     TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: TGCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|71301533|gb|DR786807.1|DR786807
EST:     GCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: GCACTTTCCTCCTCTTCGGCTCCGTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
EST: gi|91050270|gb|EB160688.1|EB160688
EST:     GTCATCCAGCTCATCGCATGTGCAAG                         CAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT
genomic: GTCATCCAGCTCATCGCATGTGCAAGgtaatcatcc ... atatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctagctacctatatatgagtgatccatggatcgatatatacatatatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACATCTTCGGCGCCTGCTGCGCCACCACCGTGTTCATCCCCTCCTTCCACAAC
 ctctgat  putative branch site (score: 4)
                                   atatatacatatatga  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcatccattcatgcctacattcgcatccatcgataaaactcatatacaattaacacaatcaaagcttttcctaattaataactgcaagcattaaaagtgtagtgtaatcgatcttgtaattacgctctgatctagctacctatatatgagtgatccatggatcgatatatacatatatgagcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACATCTTCGGCGCCTGCTGCGCCACCACCGTGTTCATCCCCTCCTTCCACAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC