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'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTCTCTTTGTATGTTATGACTTAATCCGACCAGACGTGGCTCTAGAACTTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatcctaaccctcaaataaactcttttgattctctgctcaatgaggttggaaccattatttgaacgctatgatgaattctcttcttcctgtcgttttttctttgcag

Basic information

species Arabidopsis thaliana
transcript AT3G08530.1
intron # 28
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 28
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 28
ATGTCTCTTTGTATGTTATGACTTAATCCGACCAGACGTGGCTCTAGAACTTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatcctaaccctcaaataaactcttttgattctctgctcaatgaggttggaaccattatttgaacgctatgatgaattctcttcttcctgtcgttttttctttgcag
 ||||||||| | ||||||||||| |||||  | || || ||||| || ||||| ||||| ||||| ||| |||||||||| ||||| |||||  | |||||    | |     |  |||  |      ||  ||    ||  ||| | | ||    ||  || |    |    |  |  ||   |  |     ||  |              
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtttc--cgttcatgtg----tttggga----ctattcatttacgt----acagttttccata----acaacaaagcttgcttcatgtgcag--------------

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 28
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
ATGTCTCTTTGTATGTTATGACTTAATCCGACCAGACGTGGCTCTAGAACTTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatcctaaccctcaaataaactcttttgattctctgctcaatgaggttggaaccattatttgaacgctatgatgaattctcttcttcctgtcgttttttctttgcag
 ||||||||| | ||||||||||| |||||  | || || ||||| || ||||| ||||| ||||| ||| |||||||||| ||||| |||||  | |||||    | |     |  |||  |      ||  || | |    | |         ||||  || |    |    |  |  ||   |  |     ||  |              
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgtttc--cgttcatgtg----tttgggactattcatttac--------gaacagttttccata----acaacaaagcttgcttcgtgtgcag--------------

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 28
lower sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 26
ATGTCTCTTTGTATGTTATGACTTAATCCGACCAGACGTGGCTCTAGAACTTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatcctaaccctcaaataaactcttttgattctctgctcaatgaggttggaaccattatttgaacgctatgatgaattctcttct-tcctgtcgttttttctttgcag
 || |||||  | || || ||| | ||||| ||||| |||||||| || ||||| ||||| ||||| ||| ||||||||||||||||||| ||  | |||||                  | |||  ||| |  ||  ||    | | |    |  |   |   |||     | ||  | |  ||||| || | || |     | | |  ||||
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCAGATGTGGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtacgt--------------agtaatttctgtccatgttcgtgccgacgtctatttacatacagttta----ccatagtaacatctctactgtgctatgtgactgtgtgcgcag

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 28
lower sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 13
ATGTCTCTTTGTATGTTATGACTTAATCCGACCAGACGTGGCTCTAGAACTTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatcctaaccctcaaataaactcttttgattctctgctca-atgaggttggaaccattatttgaacgctatgatgaattctcttcttcctgtcgttttttctttgcag
 || |||||  | || || ||| | ||||| || || || ||||| || ||||| ||||| ||||| ||| ||||||||||||||||||| ||  | |||||      |  |||         |   ||         ||| || | ||   |||   |   | |  |     || || |   |     ||| |                    
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgta---cgtagtaatttctgtccatgttcgcgccgacgtctacttacatacagttaccatagtaacatccctactgtgctatgtgactgtctgcgcag----------------

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 28
lower sequence: GRMZM2G115138_T01 (Zea mays), 5'ss of exon 12
ATGTCTCTTTGTATGTTATGACTTAATCCGACCAGACGTGGCTCTAGAACTTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatcctaaccctcaaataaactcttttgattctctgctca-atgaggttggaaccattatttgaacgctatgatgaattctcttcttcctgtcgttttttctttgcag
 || |||||  | || || ||| | ||||| || || || ||||| || ||||| ||||| ||||| ||| ||||||||||||||||||| ||  | |||||      |  |||         |   || |       |||  | | ||   |||   |   | |  |     || || |   |     | | |                    
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgta---cgtagtaatttctgtccatgttcgtgccgacgtctatttacatacagttaccatagtaacatccctactgtgctatgtgactgtgtgcgcag----------------

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 28
lower sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 13
ATGTCTCTTTGTATGTTATGACTTAATCCGACCAGACGTGGCTCTAGAACTTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatcctaaccctcaaataaactcttttgattctctgctca-atgaggttggaaccattatttgaacgctatgatgaattctcttcttcctgtcgttttttctttgcag
 || |||||  | || || ||| | ||||| || || || ||||| || ||||| ||||| ||||| ||| ||||||||||||||||||| ||  | |||||      |  |||   |     |   ||         |||  | | ||   |||   |||||  |   | | |||  |||    |                            
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgta---cgtagtaatttttgtccatgttcgcgccgacgtctatttacatacagttt--accatagtaacatccctactatgtgcgcag--------------------------

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 28
lower sequence: GRMZM2G091121_T01 (Zea mays), 5'ss of exon 8
ATGTCTCTTTGTATGTTATGACTTAATCCGACCAGACGTGGCTCTAGAACTTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatcctaaccctcaaataaactcttttgattctctgctca-atgaggttggaaccattatttgaacgctatgatgaattctcttcttcctgtcgttttttctttgcag
 || |||||  | || || ||| | ||||| || || || ||||| || ||||| ||||| ||||| ||| ||||||||||||||||||| ||  | |||||      |  |||         |   || | |     |||  | | ||   |||   |   | |  |     || || |   |     | | |                    
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgta---cgtagtaatttctgtccatgttcgtgtcgacgtctatttacatatagttaccatagtaacatccctactgtgctatgtgactgtgtgcgcag----------------

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 28
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 27
ATGTCTCTTTGTATGTTATGACTTAATCCGACCAGACGTGGCTCTAGAACTTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatcctaaccctcaaataaactcttttgattctctgctcaatgaggt-tggaaccattatttgaacgctatgatgaattctcttcttc---ctgtcgttttttctttgcag---------
 ||||| ||||| || ||||| || |||||  ||||| | ||||| ||| | |||||||| ||||||||||| |||||||||||||| |||||||| |||||      ||||      |   | |  | | ||  ||       ||  ||  | |   |    | ||| |||  | |    | | || || ||       | || || |  || |           
-TGTCTATTTGTTTGCTATGATTTGATCCGGGCAGACATTGCTCTTGAATTGGCCTGGATGAACAATATGATTGACTTTGCCTTCCCATATCTCCTGCAGGtttgtattccttctgtgctgcttacttttattacttaaacatacatcgacatgtattatttctttttcaacattttatctagtgcttttttttaattaattgtcttcttctttcgctgatgtagt

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 28
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 27
ATGTCTCTTTGTATGTTATGACTTAATCCGACCAGACGTGGCTCTAGAACTTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatcctaaccctcaaataaactcttttgattctctgctcaatgaggttggaaccattatttgaacgctatgatgaattctcttcttcc-tgtcgttttttctttgcag---
 ||||| ||||| || ||||| || |||||  ||||| | ||||| ||  | |||||||| ||||||||||| |||||||||||||| |||||||| |||||      ||||      |   | | || | ||  ||       ||  ||  |      | || |    | | ||||  |     ||||   |  | |  |||||||  ||  |   
GTGTCTATTTGTTTGCTATGATTTGATCCGGGCAGACATTGCTCTTGAGTTGGCCTGGATGAACAATATGATTGACTTTGCCTTCCCATATCTCCTGCAGgtttgtattccttctgtgctgcttacctttattacttaaacatacatcgacatgtatgtctttttcatcatgttatgtagtgcgttctttcactatcttcttttttcgctgttgtag

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 28
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 28
ATGTCTCTTTGTATGTTATGACTTAATCCGACCAGACGTGGCTCTAGAACTTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatcctaaccctcaaataaactcttttgattctctgctcaatgaggttggaaccattatttgaacgctatgatgaattctcttcttcctgtcgttttttctttgcag-
 || |||||||| || || |||||||| || |||||| | ||||| |||||||||||||| ||||||||| | ||||||||||| || |||||  | |||||||||| |      | ||         ||| | ||||||      ||    | ||||   |     | |   ||   ||     |   |  ||||| |   ||| || |    
TTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACTTTGCCTTGCCATATCTGTTGCAGgtgatctgtttgcttcttc--------ccttgtcattctc------atatattaggaattttaggagggaaattagcttgcgactttcccagcctgtgggccttttttagagct

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|164147644|gb|ES075842.1|ES075842
EST:     TTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAG                         TTTATCCGAGA
genomic: TTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatc ... ttctttgcagTTTATCCGAGA
EST: gi|47829444|gb|CK119128.1|CK119128
EST:     TTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAG                         TTTATCCGAGAGTACTCTGGCAAAGTGGATGAGCTAATAAAGGACAAGCTT
genomic: TTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatc ... ttctttgcagTTTATCCGAGAGTACTCTGGCAAAGTGGATGAGCTAATAAAGGACAAGCTT
EST: gi|116468291|gb|EG510883.1|EG510883
EST:     TTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAG                         TTTATCCGAGAGTACTCTGGCAAAGTGGATGAGCTAATAAAGGACAAGCTT
genomic: TTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatc ... ttctttgcagTTTATCCGAGAGTACTCTGGCAAAGTGGATGAGCTAATAAAGGACAAGCTT
EST: gi|86083413|gb|DR379172.1|DR379172
EST:     TTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAG                         TTTATCCGAGAGTACTCTGGCAAAGTGGATGAGCTAATAAAGGACAAGCTT
genomic: TTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatc ... ttctttgcagTTTATCCGAGAGTACTCTGGCAAAGTGGATGAGCTAATAAAGGACAAGCTT
EST: gi|47828467|gb|CK118151.1|CK118151
EST:     TTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAG                         TTTATCCGAGAGTACTCTGGCAAAGTGGATGAGCTAATAAAGGACAAGCTT
genomic: TTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatc ... ttctttgcagTTTATCCGAGAGTACTCTGGCAAAGTGGATGAGCTAATAAAGGACAAGCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTCTCTTTGTATGTTATGACTTAATCCGACCAGACGTGGCTCTAGAACTTGCCTGGATCAACAATATGATGGACTTTGCCTTCCCGTATCTCCTCCAGgtgatctatcctaaccctcaaataaactcttttgattctctgctcaatgaggttggaaccattatttgaacgctatgatgaattctcttcttcctgtcgttttttctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC