Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaataatgaagataacttttcattttctccatgcatgatattgcataataaattctgtgtatagttcaatctttaacttaaatccatatgcagctgccttatagtgcctaattcagattagttttctgattcactgcattattattctttcag

Basic information

species Zea mays
transcript GRMZM2G030902_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030902_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g71770.1 (Oryza sativa), 5'ss of exon 4
GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaataatgaagataacttttcattttctccatgcatgatattgcataataaattctgtgtatagttcaatctttaacttaaatccatatg-cagctgccttatagtgcctaattcagattagttttctgattcactgcattattattctttcag
||||| || ||||| ||||||||||||||||| |||||||| ||| ||||||| || ||||| ||||| ||||     |      |  ||| |  |  ||  ||  || | ||||||| |  | |  ||| | |   | |||||||   |  | |  ||||  || |||                                                         
GAGCGTTCGTCTGGTCGATCTCGTGGGTTTGGTTATGTAACGTTCTCATCAGCTGATGATGCCAAGgtagtaatcctgttctcccagatttgc--tgacttgat--attacattgcatgactagtgttgtattt---taaatcttttgttagagtttatatatcaactgtgaa-----------------------------------------------------
















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|148936779|gb|EC880917.2|EC880917
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
EST: gi|149104347|gb|EE289792.2|EE289792
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
EST: gi|31664299|gb|CD573024.1|CD573024
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGA
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGA
EST: gi|22545757|gb|BU098131.1|BU098131
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
EST: gi|71769697|gb|DR967634.1|DR967634
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
EST: gi|211345125|gb|FL007061.1|FL007061
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAA-G                         AATGTTCTTGATTGCGA
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGA
EST: gi|148955713|gb|EC901400.2|EC901400
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
EST: gi|87156149|gb|DY400938.1|DY400938
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
EST: gi|149096474|gb|EE182216.2|EE182216
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
EST: gi|149000018|gb|EE037116.2|EE037116
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
EST: gi|211345131|gb|FL007067.1|FL007067
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGGCATG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAG-CATG
EST: gi|6564152|gb|AW231774.1|AW231774
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGC
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGC
EST: gi|149104935|gb|EE290405.2|EE290405
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
EST: gi|26558833|gb|CA831068.1|CA831068
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
EST: gi|22473110|gb|BU037590.1|BU037590
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
EST: gi|71304925|gb|DR788593.1|DR788593
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
EST: gi|211345135|gb|FL007071.1|FL007071
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTTGGGAGCCGTACAT
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTT-GGGAGCCGTACAT
EST: gi|31557986|gb|CD527198.1|CD527198
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
EST: gi|211138007|gb|FL213712.1|FL213712
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
EST: gi|32919564|gb|CF024376.1|CF024376
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
EST: gi|149080743|gb|EE169805.2|EE169805
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
EST: gi|21432115|gb|BQ547605.1|BQ547605
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
EST: gi|9952229|gb|BE638812.1|BE638812
EST:     GATCTCGTGTGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
EST: gi|13558465|gb|BG549821.1|BG549821
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
EST: gi|60350487|gb|DN217460.1|DN217460
EST:     GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAG                         AATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG
genomic: GATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaat ... attctttcagAATGTTCTTGATTGCGAGCATGTTCTTGGGAGCCGTACATTAGAAGTGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCGGTCTTCTGGGCGATCTCGTGGGTTTGGCTATGTAACATTCGCATCAGCCGACGATGCAAAGgttgtaaaataatgaagataacttttcattttctccatgcatgatattgcataataaattctgtgtatagttcaatctttaacttaaatccatatgcagctgccttatagtgcctaattcagattagttttctgattcactgcattattattctttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG