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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttacgcaatttgttctttcagttaaccaaatcgttatataatacattgcttatttattgatgtgaataatacaagcttgatttatggtttgtaatcaacttgaatacagGTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGATGCCACATACTGTTATGCACTTGGTTATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGA

Basic information

species Arabidopsis thaliana
transcript AT1G12000.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 11
-------------------------------------------------------------------------gtaagttacgcaatttgttct--ttcagtta-accaaa---tcgttatataatacattgcttatttattgatgtgaataa---tacaagcttga-tttatggtttgtaatcaacttgaa---tacagGTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGATGCCACATACTGTTATGCACTTGGTTATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGA
                                                                            ||  ||    ||| ||||  || | ||  |  |||   ||  |  || ||||||    | | |  |  |   ||| |   || | | | || ||| | |||  | |   | || ||   | ||| |||||||| ||||| |||||||| || ||||||||||| || || || ||||| || |||||||| |||||||  |||||  | ||||||||||| |||
gtattttatctaattttgatattattattgaatagtaaattctaatacatattgctgtgaatcaaaaaaactttccagggacaatttttattctcctttacttggattaaagtttctctcgatcatacatgttatgtgtgatctttcaaatgagtttatatgttagagtttgtagttactgactcatttaaaatatgcagTTATGAAGGGAGATGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTATGCTCTGGGTTATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGA

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 11
gtaagttacgcaatttgttctttcagttaaccaaatcgttatataatacattgcttatt--tattgatgtgaataatacaagcttgatttatggtttgtaatcaacttgaata--cagGTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGATGCCACATACTGTTATGCACTTGGTTATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGA
             |||   ||     ||||  || || ||  |  |||||||   || |   ||   | |   |  |   |  |||  |  |    |||| ||   |  ||||  ||| |||||||| ||||| |||||||| || ||||||||| | || ||||| |||||| | |||||||| |||| ||  |||||  | ||||||||||| |||
------------gtttaacctg--gattaa--aattcttttgaccatacatttgctaatggcatctctatctttggttagaatttg--tagtcacctgtactcttttaaaatatgcagCTATGAAGGGAGATGTGGCTTGCCAACTAATTTTGATTCTACTTACTGCTATGCATTGGGTTATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGA

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 11
-----------------------------------------------------------------------------gtaagttacgcaatttgttctttcagttaa--ccaaatcgttat--ataatacattgcttatttattgatgtgaataatacaagcttgatttatggtttgta---atcaacttgaa---tacagGTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGATGCCACATACTGTTATGCACTTGGTTATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGA
                                                                             |  |  | |    | |  || || | ||      ||||   | |  || ||||||    | | |  |  | | ||| |   ||   |   |||  |||||||   |   | || ||   | ||| |||||||| || || |||||||| || ||||||||||| || || || ||||| || |||||||| |||||||  |||||  | ||||||||||| |||
gtaatttatctaattttgatattattattgaatagtaaattctaaaacatattgctgtgaatcaaaaaatctttccagggacatgctttttcttctcctttacttggatttaaatttctctcaatcatacatgttatgtgtgatcttttaaatgacttaa---tatgttagagtttgtactgactcatttaaaatatgcagTTATGAAGGGAGGTGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTATGCTCTGGGTTATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGA

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 9
gtaagttacgcaatttgttctttcagttaaccaaatcgttatataatacattgcttatttattgatgtgaataatacaagcttgatttatggtttgtaatcaacttgaatacagGTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGATGCCACATACTGTTATGCACTTGGTTATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGA
         | | |||   ||   | | ||  ||||  ||  |  |   || || |  ||||   ||   | | |      |  | | ||  | | | |  || |   || ||| |||||||| ||||| |||||||| || ||||||||| | || ||||| |||||| | |||||||| |||| ||  |||||  | ||||||||||| |||
-------ttgaagtttaacctgg-attaaaaaaaatattttgaccactaatggcatcattatctttgcttacagtttgtagtc-actaataatctttta--aaat---atgcagCTATGAAGGGAGATGTGGCTTGCCAACGAATTTTGATTCTACTTACTGCTATGCATTGGGTTATGGTGCTGCAGCCCTCCTTCAAAGTGGGAAGACTGGA

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|116438104|gb|EG480696.1|EG480696
EST:     CAAGCTGGTGCATACAAGGGACAATTCATGGGACAGTCACATTTCTTCGG                         GTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGATGCCACATACTGTTA
genomic: CAAGCTGGTGCATACAAGGGACAATTCATGGGACAGTCACATTTCTTCGGgtaagttacg ... ttgaatacagGTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGATGCCACATACTGTTA
EST: gi|124735397|gb|EH826799.1|EH826799
EST:     CAAGCTGGTGCATACAAGGGACAATTCATGGGACAGTCACATTTCTTCGG                         GTATGAAGGAAGAT
genomic: CAAGCTGGTGCATACAAGGGACAATTCATGGGACAGTCACATTTCTTCGGgtaagttacg ... ttgaatacagGTATGAAGGAAGAT
EST: gi|86088437|gb|DR384196.1|DR384196
EST:     CAAGGGGCATTTCATGGGACAGTCCCATTTTTTGGG                         GTATGAAGGAAGATGCGGCTTCCCCACAAATTTTGATGCCACATACTGTTA
genomic: CAAGGGACAATTCATGGGACAGTCACATTTCTTCGGgtaagttacg ... ttgaatacagGTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGATGCCACATACTGTTA
EST: gi|86060419|gb|DR356176.1|DR356176
EST:     CAAGCTGGTGCATACAAGGGACAATTCATGGGACAGTCACATTTCTTCGG                         GTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGATGCCACATACTGTTA
genomic: CAAGCTGGTGCATACAAGGGACAATTCATGGGACAGTCACATTTCTTCGGgtaagttacg ... ttgaatacagGTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGATGCCACATACTGTTA
EST: gi|125004915|gb|EL077184.1|EL077184
EST:     GTGCATACAAGGGACAATTCATGGGACAGTCACATTTCTTCGG                         GTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGATGCCA
genomic: GTGCATACAAGGGACAATTCATGGGACAGTCACATTTCTTCGGgtaagttacg ... ttgaatacagGTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGATGCCA
EST: gi|125319130|gb|EL333215.1|EL333215
EST:     CAAGCTGGTGCATACAAGGGACAATTCATGGGACAGTCACATTTCTTCGG                         GTATGAAGGAAGATGCGGCTTGCCC
genomic: CAAGCTGGTGCATACAAGGGACAATTCATGGGACAGTCACATTTCTTCGGgtaagttacg ... ttgaatacagGTATGAAGGAAGATGCGGCTTGCCC
EST: gi|163995261|gb|ES177180.1|ES177180
EST:     CAAGCTGGTGCATACAAGGGACAATTCATGGGACAGTCACATTTCTTCGG                         GTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGA
genomic: CAAGCTGGTGCATACAAGGGACAATTCATGGGACAGTCACATTTCTTCGGgtaagttacg ... ttgaatacagGTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGA
EST: gi|86060418|gb|DR356175.1|DR356175
EST:     CAAGCTGGTGCATACAAGGGACAATTCATGGGACAGTCACATTTCTTCGG                         GTATGAAGGRGGATGCGGCTTGCCCACAAATTTTGATGCCACATACTGTTA
genomic: CAAGCTGGTGCATACAAGGGACAATTCATGGGACAGTCACATTTCTTCGGgtaagttacg ... ttgaatacagGTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGATGCCACATACTGTTA
EST: gi|116438054|gb|EG480646.1|EG480646
EST:     CAAGCTGGTGCATACAAGGGACAATTCATGGGACAGTCACATTTCTTCGG                         GTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGATGCCACATACTGATA
genomic: CAAGCTGGTGCATACAAGGGACAATTCATGGGACAGTCACATTTCTTCGGgtaagttacg ... ttgaatacagGTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGATGCCACATACTGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgatgtgaataatacaagcttgatttatggtttgtaatcaacttgaatacagGTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGATGCCACATACTGTTATGCACTTGGTTATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGA
          aataatacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttacgcaatttgttctttcagttaaccaaatcgttatataatacattgcttatttattgatgtgaataatacaagcttgatttatggtttgtaatcaacttgaatacagGTATGAAGGAAGATGCGGCTTGCCCACAAATTTTGATGCCACATACTGTTATGCACTTGGTTATGGCGCTGGAGTACTCCTCAACAGTGGGAAGACCGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA