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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGATTGTTTCATCAATCATTATCTTCCACACTCCTGTCCGCGCTGTCAATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggctgcttcagttttttcatgtggttgggcttttcctctatatactgaaacgatcactttcttctgaattggggaggcaaaatggaatttatc...

Basic information

species Zea mays
transcript GRMZM2G180720_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180720_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os08g08840.2 (Oryza sativa), 5'ss of exon 5
AGTGATTGTTTCATCAATCATTATCTTCCACACTCCTGTCCGCGCTGTCAATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggctgcttcagttttttcatgtggttgggcttttcctctatatactg-aaacgatcactttcttctgaattggggaggcaaaatggaatttatc
 ||||||||||| |||||||||||||||||||| ||||||||| ||||||||||||| ||||||||||||||||||||||||||||||||||| |||||||||| ||   |||||   | ||||  | | |  | ||||  ||| | ||||||  |||| | |  | | |||       | || | |  |     | ||| 
TGTGATTGTTTCGTCAATCATTATCTTCCACACACCTGTCCGCCCTGTCAATGCACTAGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTATTCTCAGgtaaattc-ttgctttgatattttactttagccgtgcttgccctgtgtatacttcaaacaaactttcttttccctgcacgagaaggatgacattttgtata

upper sequence: GRMZM2G180720_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT5G54800.1 (Arabidopsis thaliana), 5'ss of exon 4
AGTGATTGTTTCATCAATCATTATCTTCCACACTCCTGTCCGCGCTGTCAATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaa-------cttggctgcttcagttttttcatgtggttgggcttttcctctatatactgaaacgatcactttcttctgaattggggaggcaaaatggaatttatc
 || ||||| || || ||||||||||||| |||||| ||||   | |||||||| || ||||| |||||||| |||||||| || ||| |||| || |||||||       |||  ||    ||   |   | | |  |     |  |     ||| |   |||   ||   | | ||    |        ||  |||  |      
CGTCATTGTCTCCTCCATCATTATCTTCCGCACTCCAGTCCAGCCCGTCAATGCTCTTGGAGCAGCCATTGCTATCCTTGGAACCTTCTTGTATTCCCAGgtaaacataaccttaccttgaccaaaatacccttattatccatatcatatatgataaataaaaagcgtcttctgcatc-acttcacacccacatgatgaga------

upper sequence: GRMZM2G180720_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv19s0177g00300.t01 (Vitis vinifera), 5'ss of exon 4
AGTGATTGTTTCATCAATCATTATCTTCCACACTCCTGTCCGCGCTGTCAATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggctgcttcagttttttcatgtggttgggcttttcctctatatactgaaacgatcactttcttctgaattggggaggcaaaatggaatttatc---
 || || || || |||||||| ||||||||||| || ||||   |  ||||||| || ||||||||||| || |||||||| || ||| |||| |||||||||  || |||  |||  ||  |  ||   |   || || | |        ||||||  || |  |   | |  | |    |     ||   ||||| |    
TGTCATAGTCTCCTCAATCATCATCTTCCACACACCCGTCCAGCCCATCAATGCTCTTGGAGCTGCCATCGCAATCCTTGGAACTTTCTTGTATTCTCAGgta--tttgctcattcccttcatgaattgaggatggtttattcagagctgtctgaaaaaat-aaatcaatatatactaataataaggaaaataatttgtttgt

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|76908644|gb|DV163027.1|DV163027
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|60396004|gb|DN228874.1|DN228874
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|60345607|gb|DN212580.1|DN212580
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|76923750|gb|DV169643.1|DV169643
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTTTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTTTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|211235246|gb|FL454385.1|FL454385
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|71440959|gb|DR822009.1|DR822009
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|4827719|gb|AI668411.1|AI668411
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|211039687|gb|FL176198.1|FL176198
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|84976998|gb|DW475420.1|DW475420
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|71595794|gb|DR906545.1|DR906545
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACAAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|14208320|gb|BG841998.1|BG841998
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTTTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|60348620|gb|DN215593.1|DN215593
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|45567584|gb|CK985642.1|CK985642
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|44900140|gb|CK826685.1|CK826685
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|16925074|gb|BM078142.1|BM078142
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|88752571|gb|DY536712.1|DY536712
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTTTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|33771219|gb|CF273398.1|CF273398
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|60344400|gb|DN211373.1|DN211373
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|4647070|gb|AI622145.1|AI622145
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAG
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAG
EST: gi|60353891|gb|DN220864.1|DN220864
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|67040435|gb|CO466690.1|CO466690
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAN                         GCAAAGGCGTGAGGGCGG-CCATGATGACGAACGTCTGCAGAATCAGTAGC
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGG-CGGGCCATGATGACGAACGTCTGCAGAATCAGTAGC
EST: gi|16918835|gb|BM073919.1|BM073919
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|211039689|gb|FL176200.1|FL176200
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|29947343|gb|CB816605.1|CB816605
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|14245627|gb|BG874209.1|BG874209
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|78084229|gb|DV512622.1|DV512622
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|211039688|gb|FL176199.1|FL176199
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGTGTGAGGCGGGCCATGATGA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGA
EST: gi|8930246|gb|BE225010.1|BE225010
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|32920065|gb|CF024877.1|CF024877
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
EST: gi|91868370|gb|EB400011.1|EB400011
EST:     ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAG                         GCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA
genomic: ATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggc ... tctgatgcagGCAAAGGCGTGAGGCGGGCCATGATGACGAACGTCTGCAGAATCAGTAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTGATTGTTTCATCAATCATTATCTTCCACACTCCTGTCCGCGCTGTCAATGCACTGGGAGCTGCCATTGCCATCCTTGGCACATTCCTGTACTCTCAGgtaacttggctgcttcagttttttcatgtggttgggcttttcctctatatactgaaacgatcactttcttctgaattggggaggcaaaatggaatttatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC