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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTGgtcagtttctatttccacactcacacatctgttcataactttaaaacaacctatacagttctgaaagaaagatctttcacag

Basic information

species Arabidopsis thaliana
transcript AT1G23190.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 5'ss of exon 13
GTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTGgtcagt--------ttctatttc-----cacactcacacat--ctgttcataactttaaaacaacct-atacagttctgaaagaaagatctttcacag--
|| || || || ||||| |||||||| ||  ||||||||||||| ||||| ||  ||||||| |||||||| ||||| |||||| | |         |  || |      |||| | ||| ||  | ||  ||||  |  |   ||| | || || ||    | |    | || | |     
GTGCCTACTGGGTGGAAATTTTTTGGGAACTTGATGGATGCTGGAATGTGCTCAATTTGTGGTGAAGAAAGCTTTGGCACTGgtaattactatgaacttgatctatggaacacaatgacatatagcagtgaataaaatgcatgtaacttcatgcattttgatatgtggcacctctaattatt

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GRMZM2G109383_T02 (Zea mays), 5'ss of exon 13
GTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTGgtcagtttctatttccacactcacacatc-tgttcataactttaaaacaacctata-cagttctgaaagaaagatctttcacag----------------
|| || || || |||||||||||||| ||| ||||||||||||| ||||| ||  | ||||| |||||||| ||||| |||||| |  |     ||     ||      |  ||   || | ||  | |||  | | |  |    ||  || ||  ||||  |  |                
GTGCCTACTGGATGGAAGTTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatatggcttgtggccttgtgggttgtggctatcatttctatacacacaacagtaaacatgtcagcaacctcttgtattgttatgttagatggata

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GRMZM2G023289_T03 (Zea mays), 5'ss of exon 13
GTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTGgtcagtttctatttcca-----cactcacacatctgttcataacttta--aaacaacctatacagttctgaaagaaagatctttcacag------------
|| || || || ||||| |||||||| ||| ||||||||||||| ||||| ||  | ||||| |||||||| ||||| |||||| |  ||    |||       || |   | |  ||   || ||  ||  |||||    |  ||  |||   |     || ||  |  |            
GTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTGgtaatatttggcttctggctatcatttctatacatgccaatcacagtagtaaacatgtcac-cacctcttgtattgtcatgttagatgggtaaattgtgtt

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA08G04890.1 (Glycine max), 5'ss of exon 13
GTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTGgtcagtttctatttccacact--------cacacatctgttcataactttaaaacaaccta----tacagttctgaaagaaagatctttcacag-------------
|| || || || |||||||| ||||||||| | |||||||||||  | ||||| || ||||| |||||||||||||| ||||||  || | |  |    || |        || |   |   |   |||||||  | ||||||    || | || | |      |||  |||   |             
GTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTGgtatgtgtttgctattgcattaagaggagcaaagtacaactttcaactttattaaaacctagttttaaactttttatcttgtgattattccttgtgcttgtggatag

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA05G34790.1 (Glycine max), 5'ss of exon 13
GTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTGgtcagtttctatttccacactcacac-atctgttcataactttaaaacaacctata---cagttctgaaagaaagatctttcacag-------------
|| || || || |||||||| ||||||||| | |||||||||||  | ||||| || ||||| |||||||||||||| ||||||  || | |  |    || | | |  | |     | |||||| ||      || |    |||| | |      |||  |||   |             
GTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTGgtatgtgtttgctattgcattaagaggagcaaagtacaactttcaactttattaaaacctagtttttatcttgtgattattccttgtgtttgtggatag

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA03G05150.1 (Glycine max), 5'ss of exon 7
GTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTGgtcagtttctatttccacact--------cacacatctgttcataactttaaaacaaccta----tacagttctgaaagaaagatctttcacag-------------
|| || || || |||||||| ||||||||| | ||||||||| |  | ||||| || ||||| |||||||||||||| ||||||  || | |  |    || |        || |   |   |   |||||||  | ||||||    || | || | |      |||  |||   |             
GTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTAGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTGgtatgtgtttgctattgcattaaaaggagcaaagtacaactttcaactttattaaaacctagttttaaactttttatcttgtgattattccttgtgtttgtggatag

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 14
GTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTGgtcagtttc-tatttccacactcacacatctgttcataactttaaaacaacctatacagttctgaaagaaagatctttcacag----------
|| ||||| |||||||| |||||||||||  | |||||||||||  | |||||  ||||||| |||||||||||||||||||||  ||||| |||||      | | |  |||||| || |    | |   |  | || ||     | |    ||||| |   |           
GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTGgtaggtttcatattttgtgtatgaaatttctgttaattatgacatacacatatgtaaag---caatattttgatctgttgtatctacggacag

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: PP1S168_70V6.1 (Physcomitrella patens), 5'ss of exon 14
GTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTGgtc--agtttctatttcca--cactcacacatctgttcataactttaaaacaacctatacagttctgaa----agaaagatctttcacag---------------------------------------------------------------------------------------
|| |||||||| |||||||| |||||||| || |||||||| || ||||| ||||| || || ||||| ||||||||||| ||||  || |  ||    ||   |||   |   || ||  | |    ||     | ||||    ||  ||          | |||| ||                                                                                         
GTACCAACAGGGTGGAAGTTCTTTGGTAACCTCATGGATGCCGGCATGTGCTCTGTGTGCGGTGAAGAGAGTTTTGGAACAGgtctaagctcttaaaaacaattactttaatcacttttagtcaaccaaagttgtcttatatttgtcgtaacctggtgtgcaccttttacgtagtatgcttggatggatgatatttgtgatcttcagaattgtttaccagaaatgttaggttcttaaaaactacccctcggacgtgcag

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: PP1S4_12V6.3 (Physcomitrella patens), 5'ss of exon 14
GTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTGgtcagtttctatttccacactcaca--catctgttcataactttaaaacaacctatacag------ttctgaaagaaagatctttcacag----------------------------------------------------------------------------------------------------------
|| |||||||| |||||||| |||||||| || ||||| || || ||||| || || || || ||||| ||||||||||| ||||       ||| |  | ||||    ||     |   |  || ||||     | |          || | || |     |||||||  |                                                                                                          
GTACCAACAGGATGGAAGTTCTTTGGTAACCTCATGGACGCAGGCATGTGCTCGGTGTGCGGTGAAGAGAGTTTTGGAACAGgtctacgctcattgcatccctcatcgtcaatgccttgcagtttgaaaaagttgtgttggactaatcttattaatggttattctttcatggtttgcttgggttcacgacatttataaactgcgatttatgtacttgagagtagtttaaaaggtttaagtggtgtttttgttttttgaactatggcacggtcttgcag

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: EFJ05270 (Selaginella moellendorffii), 5'ss of exon 12
GTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTGgtcagtttctat-ttccacactcacacatctgttcataactttaaaacaacctatacagttctgaaagaaagatctttcacag
|| || || || |||||||||||||| ||  ||||||||||||| ||||||||  | ||||| ||||||||||| ||||| ||| | | | ||  ||| | | |       ||||   ||  ||          | ||    | || |                 
GTCCCTACTGGATGGAAGTTTTTTGGAAACTTGATGGATGCTGGCATGTGTTCCATCTGTGGTGAAGAAAGTTTCGGAACCGgtaactctttacattcgaaattagtgttcctgtgtgtatattgtgttgcttttgtatttgtttgcag----------------

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: EFJ09195 (Selaginella moellendorffii), 5'ss of exon 12
GTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTGgtcagtttctatttccacactca-cacatctgttcataactttaaaacaacctatacagttctgaaagaaagatctttcacag
|| || || || |||||||||||||| ||  ||||||||||||| ||||||||  | ||||| ||||||||||| ||||| ||| | | | ||  | |  | | |      ||||   ||  ||          | ||   || || |                 
GTCCCTACTGGATGGAAGTTTTTTGGAAACTTGATGGATGCTGGCATGTGTTCCATCTGTGGTGAAGAAAGTTTCGGAACCGgtaactctttacattcggaattagtgttcctgtgtgtatattgtgttgcttttgtatttttttgcag----------------

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|124846888|gb|EH931325.1|EH931325
EST:     TGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG                         GCTCGGATCATATCCGTGAGAAAGACGGAATATGGGCAGTTCTTGCATGGA
genomic: TGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTGgtcagtttct ... tctttcacagGCTCGGATCATATCCGTGAGAAAGACGGAATATGGGCAGTTCTTGCATGGA
EST: gi|163968996|gb|ES105822.1|ES105822
EST:     GATGGATGCTGGGATGTGTTCTGTT-GTGGAGAAGAAAGTTTTGGAACTG                         GCTCGGATCATATCCGT
genomic: GATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTGgtcagtttct ... tctttcacagGCTCGGATCATATCCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTGgtcagtttctatttccacactcacacatctgttcataactttaaaacaacctatacagttctgaaagaaagatctttcacag

- - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA