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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctctttcactttcttctcttccaagaaacgttactttggatacaaagtgtatttcagatgagctttagattttgatgaattgatattggttgttgattctcgctatggagtgaaaaatgttatattgttgtttcttgatttgaacatgtagGTGTTGGAGGATGGTGTACTGGATCCAGAGACCACTGTAGTCTCTATCTTCCCATCTCCGATGCTATACGCTGGCCCAACTGAGGTTCAATGGCATGCCA

Basic information

species Arabidopsis thaliana
transcript AT5G43780.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G43780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G149952_T01 (Zea mays), 3'ss of exon 2
gtatctctttcactttcttctcttccaagaaacgttactttggatacaaagtgtatttcagatgagctttagattttgatgaattgatattggt-tgttgat--tctcgctatggagtgaa-aaatgttatattgttgt----ttcttgatttgaacatgtagGTGTTGGAGGATGGTGTACTGGATCCAGAGACCACTGTAGTCTCTATCTTCCCATCTCCGATGCTATACGCTGGCCCAACTGAGGTTCAATGGCATGCCA
                                                              ||||   | | | ||  || | ||| || ||| | |||||     | |||     ||   || |  | || |||| |     | |||||||  ||    ||||  | ||||| ||||| ||  | |||||  | ||||| ||  | |||||||| ||||| ||||  || ||||| ||||||||||||||||||||||| |
------------------------------------------------------------attgagtgatggctattcctgtaatgaaataggtgttttgatggcaccactacactatgttcaacttctgtactgttctaacactgttgatttctac---cagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTCCCCTCTCCTATGCATTATGCTGGGCCAACTGAGGTTCAATGGCATGCTA

upper sequence: AT5G43780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G28980.2 (Glycine max), 3'ss of exon 2
gtatctctttcactttcttctcttccaagaaacgttactttggatacaaagtgtatttcagatgagctttagattttgat-gaattgatattggttgttgattctcgctatggagtgaaaaatgttatattgttgtttcttgatttgaacatgtagGTGTTGGAGGATGGTGTACTGGATCCAGAGACCACTGTAGTCTCTATCTTCCCATCTCCGATGCTATACGCTGGCCCAACTGAGGTTCAATGGCATGCCA
                                                   ||| |  |   | |  | |  | ||| || |  |   || |  |  ||||||    | |     | |||| |    | |     |||  |  ||      | |||||  | ||||||||||| || ||||||||||||||||| || || || ||||| ||||| ||||  || ||||| || || ||||| || |||||||| |
------------------------------------------------gcctgtctcccttctaatttatgtagtttcattgtctccctagttatcattgatttgttcaaca---taaaaactcccttgtatcaatttggtctttc-----tttagGTACTTGAGGATGGTGTTCTTGATCCAGAGACCACTGTGGTATCCATATTCCCTTCTCCCATGCACTATGCTGGACCCACGGAGGTGCAGTGGCATGCAA

upper sequence: AT5G43780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G38760.1 (Glycine max), 3'ss of exon 2
gtatctctttcactttcttctcttccaagaaacgttactttggatacaaagtgtatttcagatgagctttagattttgatgaattgatattggttgttgattctcgct-atggagtgaaaaatgttatattgttgtttcttgatttgaacatgtagGTGTTGGAGGATGGTGTACTGGATCCAGAGACCACTGTAGTCTCTATCTTCCCATCTCCGATGCTATACGCTGGCCCAACTGAGGTTCAATGGCATGCCA
                                                   | |   |||  | ||  |||   | || |   ||  | |   |  ||     |   |  |  |    ||||  | |  ||||      ||| | |     | |||||  | ||||||||||| || ||||||||||| ||||| || || || ||||||||||| ||||  || ||||| || || ||||| || |||||||| |
---------------------------------------------------tctccctcacctaag--ttattctgtggtttctttgtctccctaattagcattgatttgttcaacagaaaaactcac-ttgtatcaatttggtctt--tctttagGTACTTGAGGATGGTGTTCTTGATCCAGAGACAACTGTGGTATCCATATTCCCATCTCCCATGCACTATGCTGGACCCACGGAGGTGCAGTGGCATGCAA

upper sequence: AT5G43780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0020g04210.t01 (Vitis vinifera), 3'ss of exon 2
gtatctctttcactttcttctcttccaagaaacgttactttggatacaaagtgtatttcagatgagctttagattttgatgaattgatattggttgttgattctcgctatggagtgaaaaatgttatattgttgtttcttgatttgaacatgtagGTGTTGGAGGATGGTGTACTGGATCCAGAGACCACTGTAGTCTCTATCTTCCCATCTCCGATGCTATACGCTGGCCCAACTGAGGTTCAATGGCATGCCA
                       | || |||  | | || || ||  |  |   | ||   |      |||    |     |   |   |   || |  | |  |  ||         |  | | ||  || |   | ||||           ||||| | || ||||| || || ||||||||||| |||||||| ||||| ||||||||||| ||||  || ||||| ||||||||||| || |||||||| |
----------------------gttcatgaactgatcctatg-atgtattgctcaatttgaaaatcagttatccctctgccagaagg-gtccattatgtaattgccttac----cttcagttctaattctgattaatattgaaaatgttcctcagGTGCTTGAAGATGGGGTTCTTGATCCAGAGACAACTGTAGTTTCTATTTTCCCATCTCCCATGCACTATGCTGGTCCAACTGAGGTGCAGTGGCATGCAA

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|146217030|gb|ES431053.1|ES431053
EST:     CTAAGGCTGATGATGTACCTCTCAGCTGGCGTATGAGACAGCACGAGAAG                         GTGTTGGAGGATG
genomic: CTAAGGCTGATGATGTACCTCTCAGCTGGCGTATGAGACAGCACGAGAAGgtatctcttt ... gaacatgtagGTGTTGGAGGATG
EST: gi|124974901|gb|EL048432.1|EL048432
EST:     ATGATGTACCTCTCAGCTGGCGTATGAGACAGCACGAGAAG                         GTGTTGGAGGATGGTGTACTGGATCCAGAGACCACTGTAGTCTCTATC
genomic: ATGATGTACCTCTCAGCTGGCGTATGAGACAGCACGAGAAGgtatctcttt ... gaacatgtagGTGTTGGAGGATGGTGTACTGGATCCAGAGACCACTGTAGTCTCTATC
EST: gi|145309240|gb|ES323575.1|ES323575
EST:     CTAAGGCTGATGATGTACCTCTCAGCTGGCGTATGAGACAGCACGAGAAG                         GTGTTGGAGGATG
genomic: CTAAGGCTGATGATGTACCTCTCAGCTGGCGTATGAGACAGCACGAGAAGgtatctcttt ... gaacatgtagGTGTTGGAGGATG
EST: gi|116377755|gb|EG420347.1|EG420347
EST:     CTAAGGCTGATGATGTACCTCTCAGCTGGCGTATGAGACAGCACGAGAAG                         GTGTTGGAGGATGGTGTACTGGATCCAGAGACCACTGTAGTCTCTATCTTC
genomic: CTAAGGCTGATGATGTACCTCTCAGCTGGCGTATGAGACAGCACGAGAAGgtatctcttt ... gaacatgtagGTGTTGGAGGATGGTGTACTGGATCCAGAGACCACTGTAGTCTCTATCTTC
EST: gi|116454026|gb|EG496618.1|EG496618
EST:     CTAAGGCTGATGATGTACCTCTCAGCTGGCGTATGAGACAGCACGAGAAG                         GTGTTGGAGGATGGTGTACTGGATCCAGAGACCACTGTAGTCTCTATCTTC
genomic: CTAAGGCTGATGATGTACCTCTCAGCTGGCGTATGAGACAGCACGAGAAGgtatctcttt ... gaacatgtagGTGTTGGAGGATGGTGTACTGGATCCAGAGACCACTGTAGTCTCTATCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctcgctatggagtgaaaaatgttatattgttgtttcttgatttgaacatgtagGTGTTGGAGGATGGTGTACTGGATCCAGAGACCACTGTAGTCTCTATCTTCCCATCTCCGATGCTATACGCTGGCCCAACTGAGGTTCAATGGCATGCCA
                                    tcttgat  putative branch site (score: 4)
                aaaaatgttatattgt  TA-rich tract