Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccctcatcctaatctcttttctgcgcagaatttcgagttctggaagtcatagttacgagataattgtttgattgaattttgtacgataatttgtgggaattcggcaattttgttgatagtttttgcgttttgtactgatccagGTGTTTACAACAGCTGGTGTACCAATTGAGTGGGAAGAACACTATGTTGGGACTGAGATAGATCCGAGAACACAGAGTTTCTTGACATGGGAAAGTCTCG

Basic information

species Arabidopsis thaliana
transcript AT5G03290.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 3
gtccctcatcctaatctcttttctgcgcagaatttcgagttctggaagtcatagttacgagataattgtttgattgaattttgtacgataatttgtgggaattcggca-attttgttgatagtttttgcgttttgtactgatccagGTGTTTACAACAGCTGGTGTACCAATTGAGTGGGAAGAACACTATGTTGGGACTGAGATAGATCCGAGAACACAGAGTTTCTTGACATGGGAAAGTCTCG
                                               ||   |  | |    | ||  |    |   | | |||| | |  ||  |  | |||    | || ||  |   |  |||| | |||    ||| | ||||| || |     || || |||||||| || |||||||||||||||||||| || ||  | ||||| |||||| |||||||  |||| ||||||||  | |
-----------------------------------------------gtgccaagtgccttctgatcatgctttctgactatgta-gctcgttcttatgtatttattatatcttagtttgaacttttcctttt---gctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG

upper sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g16900.1 (Oryza sativa), 3'ss of exon 2
gtccctcatcctaatctcttttctgcgcagaatttcgagttctggaagtcatagttacgagataattgtttgattgaattttgtacgataatttgtgggaattcggca-attttgttgatagtttttgcgttttgtactgatccagGTGTTTACAACAGCTGGTGTACCAATTGAGTGGGAAGAACACTATGTTGGGACTGAGATAGATCCGAGAACACAGAGTTTCTTGACATGGGAAAGTCTCG
                                               ||   |  | |    | ||  |    |   | | |||| | |  ||  |  | |||    | || ||  |   |  |||| | |||    ||| | ||||| || |     || || |||||||| || |||||||||||||||||||| || ||  | ||||| |||||| |||||||  |||| ||||||||  | |
------------------------------------------aaatggtgccaagtgccttctgatcatgctttctgactatgta-gctcgttcttatgtatttattatatcttagtttgaacttttcctttt---gctgtttcagGTATTCAATGTTGCAGGGGTACCAATAGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTCTGACTTGGGAAAGCTTGG

upper sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G404855_T01 (Zea mays), 3'ss of exon 2
gtccctcatcctaatctcttttctgcgcagaatttcgagttctggaagtcatagttacgagataattgtttgattgaattttgtacgataatttgtgggaattcggcaat--tttg--ttgatagtttttgcgttttgtactgatccagGTGTTTACAACAGCTGGTGTACCAATTGAGTGGGAAGAACACTATGTTGGGACTGAGATAGATCCGAGAACACAGAGTTTCTTGACATGGGAAAGTCTCG
                                          ||  | | |  |     || | |||| |  ||   ||     | | ||  | ||     |||  ||||   |||  || ||| |||||  | | ||  ||  | ||||| || |     || || ||||||||||| |||||||||||||||||||| || ||  | ||||| |||||| ||||||| ||||| |||||||| || |
------------------------------------------tgttaattagtggatgaagttcattgatgcatgatatccgagaaggtagctcgt-----ttctacaatgtcttgacttaatattttttttgctctgcgct--ttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTTGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTTTGACTTGGGAAAGCCTGG

upper sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 2
gtccctcatcctaatctcttttctgcgcagaatttcgagttctggaagtcatagttacgagataattgtttgattgaattttgtacgataatttgtgggaattcggcaattttgttgatagtttttgcgttttgtactgatccagGTGTTTACAACAGCTGGTGTACCAATTGAGTGGGAAGAACACTATGTTGGGACTGAGATAGATCCGAGAACACAGAGTTTCTTGACATGGGAAAGTCTCG
                                   | | |  ||  |   |  ||    || | |||| |  ||   || |   | | |   ||||     |||    || |  || ||| ||||   |||||||  |  | ||||| || |     || || ||||||||||| ||||||||||||||||| || || ||  | ||||| |||||| ||||||| ||||| |||||||| || |
----------------------------------gctactgttgttaactagtgtatgaagttcattgatgcatgatatctgagaaggttgcttgt-----ttctatgatgtc-ttaatattttt---gttttgtgat--ttcagGTATTCAATGTTGCAGGGGTACCAATTGAATGGGAAGAACACTATGTCGGTACAGAAGTTGATCCCAGAACAGAGAGTTTTTTGACTTGGGAAAGCCTGG

upper sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G20790.1 (Glycine max), 3'ss of exon 1
gtccctcatcctaatctcttttctgcgcagaatttcgagttctggaagtcatagttacgagataattgtttgattgaattttgtacgataatttgtgggaattcggcaattttgttgatagtttttgcgttttgtactgatccagGTGTTTACAACAGCTGGTGTACCAATTGAGTGGGAAGAACACTATGTTGGGACTGAGATAGATCCGAGAACACAGAGTTTCTTGACATGGGAAAGTCTCG
                                    |  |  || | || ||   || ||  |   ||||  || ||| ||     | |   |||    || ||      | ||   ||  ||  ||| | || ||||     || | ||   | |||||| ||| ||||| || |||||||| |||||||| || ||||| || || || ||||| || |||||  |||||||||||||| | |
------------------------------------gtttgttgcatgttatg--ta-gatttgtatgttc-atagaaattgacgtgcttggttgaattaaatctaatgctgtgccaattattgctgc-tgttatact----tagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGAACTGAAATTGACCCTAGAACCCAAAGTTTTCTGACATGGGAAAGTTTGG

upper sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G06590.2 (Glycine max), 3'ss of exon 1
gtccctcatcctaatctcttttctgcgcagaatttcgagttctggaagtcatagttacgagataattgtttgattgaattttgtacgataatttgtgggaattcggcaattttgttgatagtttttgcgttttgtactgatccagGTGTTTACAACAGCTGGTGTACCAATTGAGTGGGAAGAACACTATGTTGGGACTGAGATAGATCCGAGAACACAGAGTTTCTTGACATGGGAAAGTCTCG
                                       || ||    |  |  |   ||  |   | ||  || ||| ||     | |   |||    || ||      | |||   |  ||  ||    ||||| | |   || | ||   | |||||| ||| ||||| || |||||||| |||||||| || ||||| || || || ||||| ||||| ||  |||||||||||||| | |
---------------------------------------ttttgtttcttgttatgtagatttgtatattc-atagaaattgacttgcttggttgaattaaatctaatgctctgtcatttattactg----ttgtaat-acttagATATTCCAAGCAGCTGATGTCCCAATAGAATGGGAAGAGCACTATGTAGGAACTGAAATTGACCCTAGAACGCAGAGCTTTCTGACATGGGAAAGTTTAG

upper sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv08s0040g01700.t01 (Vitis vinifera), 3'ss of exon 1
gtccctcatcctaatctcttttctgcgcagaatttcgagttctggaagtcatagttacgagataattgtttgattgaattttgtacgataatttgtgggaattcggcaattttgttgatagtttttgcgttttgtactgatccagGTGTTTACAACAGCTGGTGTACCAATTGAGTGGGAAGAACACTATGTTGGGACTGAGATAGATCCGAGAACACAGAGTTTCTTGACATGGGAAAGTCTCG
                                          | | |  |||       ||||  ||||||  ||| |||    |   | ||||  |   | |   ||| || ||  | |  |||||   |||  |||  | ||||| |||| | ||||||  || |||||||| ||||| ||||||||||| |||    | |||||||| ||||| ||||||||  | |||||||||||||| |
------------------------------------------tagtaa-catcacattaagatgcttgtttt-ttgtattgatgatacttatttaagatgaattttcaagtt-gtgaagaacttttgtcatttacactattacagGTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGGGACCAAATAGATCCAAGAACCCAGAGTTTTCTCACATGGGAAAGTCTAG

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|86073176|gb|DR368933.1|DR368933
EST:     TCTTCCCTGGCGATGGGATCGGTCCCGAGATCGCCGAATCTGTCAAAAAG                         GTGTTTACAACAGCTGGTGTACCAATTGAGTGGGAAGAACACTATGTTGGG
genomic: TCTTCCCTGGCGATGGGATCGGTCCCGAGATCGCCGAATCTGTCAAAAAGgtccctcatc ... actgatccagGTGTTTACAACAGCTGGTGTACCAATTGAGTGGGAAGAACACTATGTTGGG
EST: gi|86073175|gb|DR368932.1|DR368932
EST:     TCTTCCCTGGCGATGGGATCGGTCCCGAGATCGCCGAATCTGTCAAAAAG                         GTGTTTACAACAGCTGGTGTACCAATTGAGTGGGAAGAACACTATGTTGGG
genomic: TCTTCCCTGGCGATGGGATCGGTCCCGAGATCGCCGAATCTGTCAAAAAGgtccctcatc ... actgatccagGTGTTTACAACAGCTGGTGTACCAATTGAGTGGGAAGAACACTATGTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgtgggaattcggcaattttgttgatagtttttgcgttttgtactgatccagGTGTTTACAACAGCTGGTGTACCAATTGAGTGGGAAGAACACTATGTTGGGACTGAGATAGATCCGAGAACACAGAGTTTCTTGACATGGGAAAGTCTCG
                                            tactgat  putative branch site (score: 2)
                 aattttgtt  TA-rich tract