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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctttactgcatttgatcatgatttatcaactattctacatgtttttagtgcatgtctgaatctaataattgagagtcaagaccataatttaat...

Basic information

species Zea mays
transcript GRMZM2G024151_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024151_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g14860.3 (Oryza sativa), 5'ss of exon 2
GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctttactgcatttgatcatgatttatcaactattctacatgtttttagtgcatgtctgaatctaataattgagagtcaag--accataattt--aat------------------------
||||||||||| || || ||||| || || || || ||||| || |||||||||||||| |||||||||||||  |||||||| || |||||||||| | | | |   |||    |  ||||||   ||| | |   ||| |   |   ||   ||||||  |  | || ||   | |||  | | | ||||  |||                        
GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcctgataccat---gttgtgatttcagaacaaatgc-catctgactgtcgcg-atctgaaattgttcatcgattataaagcaatcttcatttctaattgatattcttggataatcttgcag

upper sequence: GRMZM2G024151_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g14860.4 (Oryza sativa), 5'ss of exon 3
GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctttactgcatttgatcatgatttatcaactattctacatgtttttagtgcatgtctgaatctaataattgagagtcaag--accataatt--taat----------------------------
||||||||||| || || ||||| || || || || ||||| || |||||||||||||| |||||||||||||  |||||||| || |||||||||| | | | |   |||    |  ||||||   ||| | |   ||| |   |   ||   ||||||  |  | || ||   | |||  | | | |||  ||||                            
GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcctgataccat---gttgtgatttcagaacaaatgc-catctgactgtcgcg-atctgaaattgttcatcgattataaagcaatcttcatttctaattgatattcttggataatcttgcagacag
















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|5566746|gb|AI881612.1|AI881612
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
EST: gi|19822195|gb|BQ048219.1|BQ048219
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
EST: gi|32928666|gb|CF033478.1|CF033478
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
EST: gi|32929341|gb|CF034153.1|CF034153
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
EST: gi|32928546|gb|CF033358.1|CF033358
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
EST: gi|26455791|gb|CA827374.1|CA827374
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
EST: gi|5566972|gb|AI881883.1|AI881883
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
EST: gi|6918384|gb|AW399914.1|AW399914
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
EST: gi|61117964|gb|DN558925.1|DN558925
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATT
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
EST: gi|5268665|gb|AI770629.1|AI770629
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
EST: gi|22542189|gb|BU092627.1|BU092627
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
EST: gi|60349962|gb|DN216935.1|DN216935
EST:     GC-CATAATTGTCACCACTACTGGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
genomic: GCACATAATTGTCACCACTACT-GGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
EST: gi|33097218|gb|CF057178.1|CF057178
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
EST: gi|32863940|gb|CF003622.1|CF003622
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
EST: gi|30087106|gb|CB885314.1|CB885314
EST:     GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAG                         ACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC
genomic: GGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctt ... gcatttgcagACAGTGAGCTACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctttactgcatttgatcatgatttatcaactattctacatgtttttagtgcatgtctgaatctaataattgagagtcaagaccataatttaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA