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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttatatttatcttctcttgtttctttgcttggtttcgccatctctgtgtttgattgttcatcatgctgggaataaagagttgaaagttccgcaatgacacatttccgataacttaggtgctgttttgtatatatgacagGGGAATTGCAAGGCACTGTAATTACCTTGGCGACTTGATGCTTGCTCTGTCCTTCAGTTTGCCATGTGGAATAAG

Basic information

species Arabidopsis thaliana
transcript AT3G52940.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G52940.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os01g25189.5 (Oryza sativa), 3'ss of exon 14
gtatgttatatttatcttctcttgtttctttgcttggtttcgccatctctgtgtttgattgttcatcatgctgggaataaagagttgaaagttccgcaatgacacatttccgataacttaggtgctgttttgtatatatgacagGGGAATTGCAAGGCACTGTAATTACCTTGGCGACTTGATGCTTGCTCTGTCCTTCAGTTTGCCATGTGGAATAAG
                          | |  |||| |  |  || | |||   |||   |  |  |||||||     |||| | |       |   |||||  | ||        | | |  | |  ||||  |   |  |||||||||||||||||||||||||||| ||||| ||  |  |||| ||||| || || || || || |||||||  ||
-------------------------atttgagctttgcatgtccctttcttccttta--taatagtcatgcttct--taaatactc------tttacaatgtgaaat--------aatgaaatcccctttt-cacgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG

upper sequence: AT3G52940.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os09g39220.1 (Oryza sativa), 3'ss of exon 11
gtatgttatatttatcttctcttgtttctttgcttggtttcgccatctctgtgtttgattgttcatcatgctgggaataaagagttgaaagttccgcaatgacacatttccgataacttaggtgctgttttgtatatatgacagGGGAATTGCAAGGCACTGTAATTACCTTGGCGACTTGATGCTTGCTCTGTCCTTCAGTTTGCCATGTGGAATAAG
                              |  |||   |   ||  ||  | | |   | |  || |        || | |  |   |||| |     | ||| || |   ||||  |   | |  ||||  ||  |  |||||||||||||||||||||| ||||| ||||| ||  |  |||| ||||| || || || || || |||||||  ||
------------------------------tatttgaacttttcacgtccctttctcgctttagatta--------atcatgcttcttaagtactct--ttaca-atgtgaaataa--tgaatcccctttt-catccaatacagGGGAATTGCAAGGCACTGCAATTATCTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG

upper sequence: AT3G52940.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA13G21450.2 (Glycine max), 3'ss of exon 11
gtatgttatatttatcttctcttgtttctttgcttggtttcgccatctctgtgtttgattgttcatcatgctgggaataaagagttgaaagttccgcaatgacacatttccgataacttaggtgctgttttgtatatatgacagGGGAATTGCAAGGCACTGTAATTACCTTGGCGACTTGATGCTTGCTCTGTCCTTCAGTTTGCCATGTGGAATAAG
                                      || |||||||     ||| |  | | || |       |   |     |  |  ||| |             ||  |||  |   |  | || |   ||| |   ||||| ||||| || |||||||||||||| || || |||||||||||||| ||||| || || |||||||| |||||
-----------------------------------ccatttgccatct-----ttttagagcttatgagagcaacatccatatccttga--ttctgtttctcattgaggccattaatctt--tcttattcttattatgttgaagGGGTATTGCTAGACACTGTAATTACCTAGGGGATTTGATGCTTGCTCTCTCCTTTAGCTTACCATGTGGGATAAG

upper sequence: AT3G52940.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA10G07580.1 (Glycine max), 3'ss of exon 3
gtatgttatatttatcttctcttgtttctttgcttggtttcgccatctctgtgtttgattgttcatcatgctgggaataaagagttgaaagttccgcaatgacacatttccgataacttaggtgctgttttgtatatatgacagGGGAATTGCAAGGCACTGTAATTACCTTGGCGACTTGATGCTTGCTCTGTCCTTCAGTTTGCCATGTGGAATAAG
                                            || | ||| |   | |||   |     | |  ||      ||    ||| | || |||     ||  | |  ||||       | |||| ||| |   ||||| ||||| || | |||||||||||| || || |||||||||||||| ||||| || || |||||||| |||||
-----------------------------------------agaatttatgtttgatactgtctttatcatttgtcatccttgattct--gtttctcattgaagtcattaagctttcttattcttattattgt-tatgttgaagGGGTATTGCTAGACGCTGTAATTACCTAGGGGATTTGATGCTTGCTCTCTCCTTTAGCTTACCATGTGGGATAAG

upper sequence: AT3G52940.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv08s0007g03930.t01 (Vitis vinifera), 3'ss of exon 11
gtatgttatatttatcttctcttgtttctttgcttggtttcgccatctctgtgtttgattgttcatcatgctgggaataaagagttgaaagttccgcaatgacacatttccgataacttaggtgctgttttgtatatatgacagGGGAATTGCAAGGCACTGTAATTACCTTGGCGACTTGATGCTTGCTCTGTCCTTCAGTTTGCCATGTGGAATAAG
                                  || |||    ||  || |   |||||   || | |     |  |  |   ||     |  |      ||  || ||| | || ||        | ||||     ||| |||||||| ||||||||||||||||||||||| |||||| || | || |||||||| ||||| || ||||| |||||
---------------------------------atgattt----atgccttttgctgatttggcaccttctactgttttcatgatttgtcatctcatttaaactgatgtccaaaaattttca-ataatcttgt-----tga-agGGGAATCGCAAGGCACTGTAATTACCTTGGGGACTTGTTGTTGGCACTGTCCTTTAGTTTACCTTGTGGGATAAG

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|86080366|gb|DR376123.1|DR376123
EST:     GGCAAGCCTCCAGTGGTAGTTGGTGGAAAGTTACTGGTTTCAGGCTAYTG                         GGGAATTGCAAGGCACTGTAATTACCTTGGCGACTTGATGCTTGCTCTGTC
genomic: GGCAAGCCTCCAGTGGTAGTTGGTGGAAAGTTACTGGTTTCAGGCTATTGgtatgttata ... tatatgacagGGGAATTGCAAGGCACTGTAATTACCTTGGCGACTTGATGCTTGCTCTGTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttccgcaatgacacatttccgataacttaggtgctgttttgtatatatgacagGGGAATTGCAAGGCACTGTAATTACCTTGGCGACTTGATGCTTGCTCTGTCCTTCAGTTTGCCATGTGGAATAAG
                     cgataac  putative branch site (score: 3)
                                    tgttttgtatatat  TA-rich tract