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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