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'   		30  
 5'  3'   		31  
 5'  3'   		32  
 5'  3'   		33  
 5'  3'   		34  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggacgacttcctagtttttcttgttcagcagaactgatctcttgggagatagttattaatctcttccatttgtgtgatatgtatgttcttttctttctgcaagGTTACTGGTGTTGGAGTCAACACTGAATGGGGATTGCTGATGGCCAGTATTTCTGAAGACAATGGTGAAGAAACTCCCTTGCAG

Basic information

species Arabidopsis thaliana
transcript AT5G57110.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 11
---------------------------------------------------------------------------------gtaggacgacttcctagtttttcttgttcagcagaactgatctcttgggagata-gttattaatctcttccatttgtgtgatatgtatgttcttttctttctgca-agGTTACTGGTGTTGGAGTCAACACTGAATGGGGATTGCTGATGGCCAGTATTTCTGAAGACAATGGTGAAGAAACTCCCTTGCAG
                                                                                   |  | ||  |  ||   ||       || ||  | ||||  ||   ||| ||  |  ||   |  ||  || | | | | || |   |   ||  |   |||  |||| || |  |||||  | ||||||||||||||| |||| ||||| || |||||||||||   |||||||||||| || ||||||
gtgagttttctgtttactgtctgcgtactcaatgcctcaatggaggggatgcacagctactttcaccttctaaatatatgtacattatgaagtagtaaaattgtagtagcatcaacattgattactgatgagttacatggttttacaatttgatctatctcaaatatgcataaattcttaaatgctcagGTGACCGCAGTTGGCATTAACACTGAATGGGGACTGCTAATGGCAAGCATTTCTGAAGATTCTGGTGAAGAAACACCTTTGCAG

upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G140328_T04 (Zea mays), 3'ss of exon 11
-------gtaggacgacttcctagt-ttttcttgttcagcagaactgatctcttgggagatagttattaatctcttccatttgtgtgatatgtatgttcttttctttctgcaagGTTACTGGTGTTGGAGTCAACACTGAATGGGGATTGCTGATGGCCAGTATTTCTGAAGACAATGGTGAAGAAACTCCCTTGCAG
        || ||    | |||| |   |  ||  | |  || | ||||       |  | |||    |   | |  ||  ||    ||        ||| || |     | |||| |||| |||||||||||||||||||||||| ||||| ||||| || || ||||||||    |||||||| || ||  | |||
tagtttaatatgatatatgcctattacctctttaattactagtagtgatt------ggaacagtgtagagcgtttatcaactgaaccat--------tctgttgtaatgtccagGTAACTGCTGTTGGAGTCAACACTGAATGGGGGTTGCTAATGGCAAGCATATCTGAAGATTCGGGTGAAGAGACACCACTCCAG

upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G391042_T02 (Zea mays), 3'ss of exon 11
-------gtaggacgacttcctagtttttcttgttcagcagaactgatctcttgggagatagttattaatctcttccatttgtgtgatatgtatgttcttttctttctgcaagGTTACTGGTGTTGGAGTCAACACTGAATGGGGATTGCTGATGGCCAGTATTTCTGAAGACAATGGTGAAGAAACTCCCTTGCAG
        || ||    | |||| |   ||||  | | ||  |||| |   |   |  | |||    ||  | |  ||  ||    |||    |||    | |        |||| |||| ||||||| | |||||||||||||| ||||| ||||| || || ||||||||    |||||||| || ||  | |||
tactttcatatgatatatgcctattacctctt--taatcactactggtgatt---ggaacagtgtagaacatttatcaactgaaccatactgttgtaaagtcc--------agGTAACTGCTGTTGGAATTAACACTGAATGGGGGTTGCTAATGGCAAGCATATCTGAAGATTCGGGTGAAGAGACACCACTTCAG

upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 13
gtaggacgacttcctagtttttcttgttcagcagaactgatctcttggg-agatagttattaatctcttccatttgtgtgatatgtatgttcttttctttctgcaagGTTACTGGTGTTGGAGTCAACACTGAATGGGGATTGCTGATGGCCAGTATTTCTGAAGACAATGGTGAAGAAACTCCCTTGCAG
 | |      ||  |  |||||    || ||   | ||| | | |||   | | || |     | | ||||   ||| |  | |||  |||  | || |||  || ||| || | ||||||  | || |||||||||||  | || |||||||| ||||| ||||||||||||||||||||||| ||||||
attgattatatttattcttttttagttttagtccacctgttttattgattaaacagat-----ttttttcctgatgtttctt-tgttggttgctctccttcctca-gGTAACAGCTGTTGGTATTAATACTGAATGGGGGCTTCTAATGGCCAGCATTTCAGAAGACAATGGTGAAGAAACTCCTTTGCAG

upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 10
gtaggacgact-tcctagtttttcttgttc-agcagaactgatctcttggg-agatagttattaatctcttccatttgtgtgatatgtatgttcttttctttctgcaagGTTACTGGTGTTGGAGTCAACACTGAATGGGGATTGCTGATGGCCAGTATTTCTGAAGACAATGGTGAAGAAACTCCCTTGCAG
  |    || | |  |  || || | |||  ||   | ||| | | |||   | | || |     | | ||||   ||| |  | | |  |||  | || |||  || ||| || | ||||||  |||| |||||||||||  | || ||| |||| ||||| ||||||||||| ||||||||||| ||||||
--aaattgattatatttattcttttagttttagtccatctgttttattgattaaacagat-----ttttttcctgatgtttttt-tattggttgctctccttcctca-gGTAACGGCTGTTGGTATCAATACTGAATGGGGTCTTCTAATGACCAGCATTTCCGAAGACAATGGCGAAGAAACTCCTTTGCAG

upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 10
-----gtaggacgacttcctagtttttcttgttcagcagaactgatctcttgggagatagttattaatctcttccatttgtgtgatatgtatgttcttttctttctgcaagGTTACTGGTGTTGGAGTCAACACTGAATGGGGATTGCTGATGGCCAGTATTTCTGAAGACAATGGTGAAGAAACTCCCTTGCAG
     ||      | |   || ||  | |  ||   |  || |  |||||    || |   |||  ||   || || || | |  | | ||| || ||||| |      |||| ||||||||||| ||||| |||||||||||  | || ||||| || || || ||||| | |||||||||||| || ||||||
ttggagtcaataaaatatttatttgatttacttttaccaaatt--tctctcaatagttcagtat--attaatttcacttttttcttgtttat-ttattttcat------agGTCACTGGTGTTGGTGTCAATACTGAATGGGGGCTTCTAATGGCTAGCATCTCAGAAGATACTGGTGAAGAAACACCATTGCAG

upper sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 13
gtaggacgacttcctagtttttcttgttcagcagaactgatctcttgggagatagttattaatctcttccatttgtgtgatatgtatgttcttttctttctgca---agGTTACTGGTGTTGGAGTCAACACTGAATGGGGATTGCTGATGGCCAGTATTTCTGAAGACAATGGTGAAGAAACTCCCTTGCAG
         |   ||| | |  |   || |   | ||    |  |||||     || ||   | | | |   || |  | ||  |    ||   ||| | |||    |||| ||  |||||||  | || ||||||||||||||||| ||||| ||||| || ||||||| ||||||||| || || ||||||
-------ctcaatctaatctaacacatttaaatgtaccttgcatttgggt--ctgtcatatgtttttactgattctaagctaacttccatcacatctatatgctttcagGTAACAAGTGTTGGGATAAATACTGAATGGGGATTGCTCATGGCTAGTATATCAGAAGACACTGGTGAAGAGACGCCATTGCAG

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|124994876|gb|EL067145.1|EL067145
EST:     CATTCTTAATGTCTGGCTGTAAAGTGGCAGATGGAAATGGTTCTATGCTG                         GTTACTGGTGTTGGAGTCAACACT
genomic: CATTCTTAATGTCTGGCTGTAAAGTGGCAGATGGAAATGGTTCTATGCTGgtaggacgac ... tttctgcaagGTTACTGGTGTTGGAGTCAACACT
EST: gi|164031764|gb|ES116883.1|ES116883
EST:     GGCAGATGGAAATGGTTCTATGCTG                         GTTACTGGTGTTGGAGTCAACACTGAATGGGGATTGCTGATGGCCAGTATT
genomic: GGCAGATGGAAATGGTTCTATGCTGgtaggacgac ... tttctgcaagGTTACTGGTGTTGGAGTCAACACTGAATGGGGATTGCTGATGGCCAGTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagttattaatctcttccatttgtgtgatatgtatgttcttttctttctgcaagGTTACTGGTGTTGGAGTCAACACTGAATGGGGATTGCTGATGGCCAGTATTTCTGAAGACAATGGTGAAGAAACTCCCTTGCAG
     tattaat  putative branch site (score: 2)
                                 tatgttcttttctttc  putative PPT
     tattaatct  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggacgacttcctagtttttcttgttcagcagaactgatctcttgggagatagttattaatctcttccatttgtgtgatatgtatgttcttttctttctgcaagGTTACTGGTGTTGGAGTCAACACTGAATGGGGATTGCTGATGGCCAGTATTTCTGAAGACAATGGTGAAGAAACTCCCTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA