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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTCGAAGAACGAAGGTTTCTACAGgtttactttgatatgatggcccctctcctagattcttaggacgcaaattatttgcagtgagcaaggcccatccatatctacattctcacttcttgatcctcaacttttttgcag

Basic information

species Arabidopsis thaliana
transcript AT1G24764.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G24764.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os02g50320.2 (Oryza sativa), 5'ss of exon 7
AGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTCGAAGAACGAAGGTTTCTACAGgtttactttgatatgatggcccctctcctagattcttaggacgcaa--attatttgcagtgagcaaggcccatccatatc-tacattctcacttcttg--atcctcaacttttttgcag
|||||||||||||||   ||| || ||||||||||||||||||| |||||| ||||| |||||||| || || ||||| ||||| || |||||||| |||||  |  | |||||       | |||  | | || ||    | ||   |   ||  |  ||   |    |  | || ||| || ||||    ||  ||  ||    ||  ||| | |||
AGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACAAAGTAATGCCTGTCAAACAGTGGCTTGAAGAGCGCAGGTTTCTGCAGgtaaagat-gatata------cttctgtttgttttttgaagctcatctacggttgtccatgcaaagtcacacttcacatcatatattcaatttttatggcatgacaaatgtttcttcag

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os12g44340.1 (Oryza sativa), 5'ss of exon 7
AGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTCGAAGAACGAAGGTTTCTACAGgt-----------ttactttgatatg----atggcc--cctctcctagattcttaggacgcaaattatt--tgcagtgagca---aggcccatccatatctacattctcacttcttgatcctcaacttttttgcag------------------------------------------
 ||||| ||||||||    ||||| |||||||| ||||||||||| ||||||||||| |||||||| || |||||| | |||||||| ||| || |||| ||           | | ||   ||||    || ||   | | | || |||   ||    | |   | ||  ||||   |         |   |||  |     |  |  | |     ||  |  |  ||||||  |                                          
GGCAAATAGAGTTGCAGTAGTGGTGGCAAATGAATGGAAAGATGGCAATGATAAAGTAATGCCTGTTAAACAATGGTTAGAAGAACGGAGGATTTTACAAgtaagtaatgctatcatttaattatgtgctattgctgacttgttctggatggatacagtgaagccttttaatgcaacaattgttttcacttttccccactcctaaacggagtatactatggttcatctttttggggtctaatttgttgggaattttcttttctttctttcttttgcag

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G017525_T01 (Zea mays), 5'ss of exon 3
AGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTCGAAGAACGAAGGTTTCTACAGgtttactttgatatgatggcccctctcctagattcttaggacgc----aaattatttgcagtgagc-----aaggcccatccatatctacattc--tcacttcttgatcctcaactttttt-gcag
|||||| || |||||    ||||| ||||||||||||||||||||  |||||||||| |||||||| || | ||||||||| || |||||| |||| || ||      ||| || ||  |   ||| ||||  | ||| |  ||     | ||  | |  ||          | |  | ||       |  ||   | | || ||||   |   ||||||| ||||
AGCAAATAGGGTTGCAGTAGTGGTGGCAAATGAGTGGAAAGATGGCGATGATAAAGTAATGCCTGTTAAACGATGGCTCGAGGAGCGAAGGATTCTGCAAgtaag---tgaaat-atatcttttcttctag--ttttaagctgctaccgagttgctcgtggtagatttgtacaagttcttcagcggtgaattttattgatttgttgaatattgtctttttttgcag

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM5G832989_T01 (Zea mays), 5'ss of exon 7
AGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTCGAAGAACGAAGGTTTCTACAGgtttactttgatatgatggcccctctcctagattcttaggacgcaaattatttgcagtgagcaaggcccatccatatctacattctcacttcttgatcctcaacttttttgcag
 ||||| || |||||   |||||| ||||| ||||||||||||| |||||| ||||| |||||||| || || ||||| ||||| |||||||| || |||||    |   | | | ||   | | |     || |  ||        ||||  | || | | ||    |||   |    |  || ||       ||     |    || || ||
TGCAAATAGGGTTGCTGTTGTGGTCGCAAACGAGTGGAAAGATGCTAATGACAAAGTAATGCCTGTTAAACAGTGGCTGGAAGAGCGAAGGTTCCTGCAGgtaggatgctaaa-gctgtttcatatagggcatccacag--------ttatcagtagagtgtaaaatgcattagttctaatgttgtc-------gacaaaaactgcttctgtag

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G008556_T01 (Zea mays), 5'ss of exon 7
AGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTCGAAGAACGAAGGTTTCTACAGgtttact--ttgatatgatggcccctctcctaga------ttcttaggacgcaaattatttgcagtgagcaaggcccatc-catatctacat-tctcacttcttgatcctcaacttttttgcag--------------------------------
|||||||||||||||  |||| || || |||||||||||||||  |||||| || |||||||| || || || ||||| ||||| || |||||  | ||||||   |  || |  |        || | | |        || || | |  ||| |       | |  |||    |  |     | | | || |  ||| |  ||  | |     ||||                                     
AGCAAACAGAGTTGCTTCTGTTGTTGCTAATGAGTGGAAAGATTCTAATGACAAGGTGATGCCAGTTAAACAGTGGCTTGAAGAGCGTAGGTTCTTCCAGgttggatggttaaactagcattttctttaccaatgtacttttttttgtattcaactctgcacaaatatgcatattctttggtgaaacaaaatgtaccacctgctggacatggttcttttcttgagtatcatatgtgatactttcttgtttctacag

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G039325_T01 (Zea mays), 5'ss of exon 7
AGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTCGAAGAACGAAGGTTTCTACAGgtttactttgatatgatggcccctctcctaga--------ttcttaggacgcaaattatttgcagtgagcaaggcccatc-catatctacat-tctcacttcttgatcc-----tcaac----ttttttgcag---------------------------------
||||||||| |||||  |||| || || |||||||||||||||  |||||| || |||||||| || || || ||||| ||||| || |||||  | ||||| |  |  | ||   |||||  | || |           ||  ||| |  ||  |       | |  |||    |  |     | | | || |  ||  | ||| |||     |  ||    || ||||  |                                 
AGCAAACAGGGTTGCTTCTGTTGTGGCCAATGAGTGGAAAGATTCTAATGACAAGGTGATGCCAGTTAAACAGTGGCTTGAAGAGCGTAGGTTCTTGCAGgtctgatg-gttaaactggcctttttctttaccaatgtactttgtagcatccacctctgcaaaaatatgcatattctttggtgaaacaaaatgtaccagctgttggtccgttgttggacacgtttctttgttgaatatcatttgtgataatttcttgtttttacag

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA05G34560.1 (Glycine max), 5'ss of exon 7
AGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTCGAAGAACGAAGGTTTCTACAGgt-----ttactt-tgatat-----gatggcccctctcctagattcttaggacgcaaattatttgcagtgagcaaggcccatccatatctacattctcacttcttgatcctcaact---tttttgcag
|||||||||||| ||    ||||| |||||||| |||||||||| |||||| ||||||||||||||||| |||||||| ||||||||| | ||| | |||||     ||| || ||||       |||     || || | | || ||   | | | ||   || | |          ||      || |   ||     || ||  | |  ||||    | ||  ||
AGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACAAAGTGATGCCTGTGAAACAATGGCTTGAAGAACGACGATTTTTGCAGgtgaatattatttctgattcctttggatttaaactttcgtggttttttttaaagtatatatcttcctgcatttggcttccccttcaatgtggttttcattttgtttttaccaaactacactcttatag

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA08G05100.1 (Glycine max), 5'ss of exon 7
AGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTCGAAGAACGAAGGTTTCTACAGgtttactttgatatgatggcccctctcctagattcttaggacgcaaattatttgcagtgagcaaggcccatccatatctacattctcacttcttgat----cctcaacttttttgcag-----------------
|||||||||||| ||    ||||| |||||||| |||||||||| |||||| ||||||||||||||||| |||||||| ||||||||| | ||  | |||||  |  |   |       ||  |    |  ||  || |  | |   || |||  |   |  |      |||    |  |  |  |  |   |  ||      || | |||||| |                   
AGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACAAAGTGATGCCTGTGAAACAATGGCTTGAAGAACGACGATTCTTGCAGgtggatatcatttctgattcctttggatttaatcttttgtgc-ctttttttttataaaaaaaagtatatatcttcttgcatttggtttcccttcaatacggtttccatttttttaccaaactacacttttattag

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 7
AGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTCGAAGAACGAAGGTTTCTACAGgtt-tactttgatatgatggcccctctcctagattcttaggacgcaaattatttgcagtgagcaaggcccatccatatctacattctcacttcttgatcctca-acttttttgcag------------------------------------------
|||||||||||| ||   |||||| |||||||| ||||||||||  |||||||||||||||||||| || |||||||| ||||||||  | ||  | |||||  || |||  | |  |     |||| | |  |  |  | |   |   |  ||| |||     |   ||||   | | |    |   | |||||  |  |   | |||   |||                                           
AGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCCAATGATAAAGTGATGCCTGTCAAACAATGGCTTGAAGAACGCCGATTCTTGCAGgtaatatttttttgtttta----ctctgccaattcatctgaatttag--tggttg-agtttttgaattccattactctttctgcttatatttcttttttatagtaatttcccgcatctggcttcgctttccacttattattaaattgaattcttatag

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA07G26540.1 (Glycine max), 5'ss of exon 7
AGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTCGAAGAACGAAGGTTTCTACAGgt----ttactttgatatgatggcccctctcctagattcttaggacgcaaattatttgcagtgagcaaggcccatccatatctacattctcacttcttgatcctcaactttt--ttgcag--------------------------------
|||||||||||| ||   |||||| |||||||| |||||||||| ||||||||||||||||||||| || || ||||| ||||||||  | ||  | |||||    ||  |||| | |  |   ||   || |      ||||      | || ||  |    |  |       | | ||| |   ||||    | || ||   | || |||   | |                                  
AGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCTAATGATAAAGTGATGCCTGTCAAACAGTGGCTTGAAGAACGTCGATTCTTGCAGgtaatatttttttgctttactctgccaattcatctgaatttagtggttgagttcttgacttccatgactctttttgcttatatttcttcttttatattaatttcccacatttggcttcgctttccgcttattattaaattgcattcttatag

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 7
AGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTCGAAGAACGAAGGTTTCTACAGgtt--tactttgatatgatggcccctct----cctagattcttaggacgcaaattatttgcagtgagcaaggcc--------catccata-tctacattctcacttcttgatcctcaacttttttgcag---
 |||||||| || ||    || ||||||||||| |||||||||| |||||| || |||||||| || || |||||||| || |||||  | ||  | || ||   |||| |||  |  |      |      | |    | |||         |  ||| |  ||| || | |         | |   || | | ||   |   |  ||| | |  ||   | |||      
TGCAAACAGGGTGGCAGTAGTTGTAGCAAATGAATGGAAAGATGCTAATGACAAGGTGATGCCCGTAAAACAATGGCTAGAGGAACGGCGATTCTTGCAAgtaaatactctgaagttcttattgtttcaaaacttgagctattatttactgtttctttttctttgatcatgactgtgtttggcttttgtagtttccacagtttgtaattgttaccaaaacctcttgttacag

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: PP1S31_77V6.1 (Physcomitrella patens), 5'ss of exon 7
AGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTCGAAGAACGAAGGTTTCTACAGgtttactttgatatgatggcccctctcctagattcttaggacgcaaattatttg-cagtgagcaaggcccatccatatctacattctcacttcttgatcctcaacttttttgcag------------------
||| |||||||||||   ||| || |||||||||||||| ||||  ||||| || || |||||||| ||||| |||||||| ||  | |||||| | ||||||   ||   | ||  | |    |  |  || | |||        |||||  |  |   || ||    || |  | | |   || ||  |||| |||  | |  ||| |                       
AGCTAACAGAGTTGCAGTTGTTGTTGCAAATGAGTGGAAGGATGCAAATGACAAGGTTATGCCTGTCAAGCAGTGGCTCGATGAGAGGAGGTTTATGCAGgttcgtttgattttgcagtctgtacctcctgaatgtta-----tcgattatgaggtaagcagtaaaatacaactttttttcttttttcttttct-gattgtgagttttctgatcattgtcgttacgattacag

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|164000241|gb|ES019332.1|ES019332
EST:     ATGGCCCGAAGAACGAAGGTTTCTACAG                         GGAGAAATGCAGCAACTTCGTGATAAGCTCGCCATAACAGACCGGGCTGCA
genomic: ATGGCTCGAAGAACGAAGGTTTCTACAGgtttactttg ... ttttttgcagGGAGAAATGCAGCAACTTCGTGATAAGCTCGCCATAACAGACCGGGCTGCA




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATAAAGTGATGCCTGTGAAGCAATGGCTCGAAGAACGAAGGTTTCTACAGgtttactttgatatgatggcccctctcctagattcttaggacgcaaattatttgcagtgagcaaggcccatccatatctacattctcacttcttgatcctcaacttttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC