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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttttcgtatgagcctagtcacacattgagatgaatcaggtatctttaatgaagaaacatttataattatttcagGTCATGGACATGCTTGGGCCTAGCCTTTGGGATGTTTGGAATTCTTTGGCTCAATC

Basic information

species Arabidopsis thaliana
transcript AT3G03940.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 5
gtaagcttttcgta--tgagcctagtcacacattgagatgaatc---aggtatctttaatgaagaaacatttataattatttcagGTCATGGACATGCTTGGGCCTAGCCTTTGGGATGTTTGGAATTCTTTGGCTCAATC
|| || ||   | |  | |      |   |   ||  ||| | |   | ||||||| | | ||     | ||| |||| || ||||||||||| |||||||| || |||||||||||||| |||||||| || |  ||  |
gtgagtttactgaagttaataaccattctatgctgccatggagctcaacgtatcttgacttaatct-taattaaaatt-ttccagGTCATGGATATGCTTGGTCCCAGCCTTTGGGATGTGTGGAATTCATTAGGGCAGAC

upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 5
gtaagcttttcgtatgagcctagtcacacattgagatgaatcaggtatctttaatgaagaaacatttataattatttcagGTCATGGACATGCTTGGGCCTAGCCTTTGGGATGTTTGGAATTCTTTGGCTCAATC
    |    |||||| ||| |  ||  |   |  || || ||   | |    ||     ||| |||| |||   |||||||| |||||||| || || ||||| ||||||||||||||||||||| | |  ||  |
----gtcagtcgtataagcattttctaattgtttga-gattcttttcttaacaactgctaaa-atttgtaaccttttcagGTAATGGACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGGCAGAC

upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 5
gtaagcttttcgtatgagcctagtcacacattgagatgaatcaggtatctttaatgaagaaacatttataattatttcagGTCATGGACATGCTTGGGCCTAGCCTTTGGGATGTTTGGAATTCTTTGGCTCAATC
              ||||     | |   | |    |  ||      ||   ||||   |  || |||   || |||||||| ||||| |||||||| || |||||||||||||| ||||||||  |||  ||  |
-------------gtgagttcgattat-tactctatttcattgcagctcaacaatgtttattcacttaactttttttcagGTAATGGATATGCTTGGTCCCAGCCTTTGGGATGTGTGGAATTCGATGGGGCAGGC

upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G110085_T01 (Zea mays), 3'ss of exon 2
gtaagcttttcgtatgagcctagtcacacattgagatgaatcaggtatctttaatgaagaaacatttataattatttcagGTCATGGACATGCTTGGGCCTAGCCTTTGGGATGTTTGGAATTCTTTGGCT-CAATC-------------------------------------------
              ||||     | |   | |    |  ||      ||   ||||   |  || |||   || |||||||| ||||| ||||||||  | |||||||||||||| ||||||||  |||   ||  |                                           
-------------gtgagttcgattat-tactctatttcattgcagctcaacaatgtttattcacttaactttttttcagGTAATGGATATGCTTGGTACCAGCCTTTGGGATGTGTGGAATTCGATGGGGGCAGGCATAAGTATCTTTCATTCTTTTTTATGGTATCTTTTGTCACTCA

upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 5
gtaagcttttcgtatgagcctagtcacacattgagatgaatcaggtatctttaatgaagaaacatttataat-tatttcagGTCATGGACATGCTTGGGCCTAGCCTTTGGGATGTTTGGAATTCTTTGGCTCAATC
|| || | |  || ||| | |   || |     | |||         |||||  ||   |||     | ||| |||||||||||||||||||||||||||| || ||||||||||| ||||||||| | | ||||  
gtgagatatg-gtttgaactttaccatatcagcatatgttgatttgctctttgttgtctaaaggaaaacaatatatttcagGTCATGGACATGCTTGGGCCCAGTCTTTGGGATGTATGGAATTCTGTTGGTCAACA

upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 5
gtaagcttttcgtatgagcctagtcacacattgagat-----gaatcaggtatctttaatgaagaaacatttataattatttcagGTCATGGACATGCTTGGGCCTAGCCTTTGGGATGTTTGGAATTCTTTGGCTCAATC
|| || |||| || |||   |  |||  |||   ||       | | |   ||  |   ||||  ||     ||||  || |||||||||||||||| | ||||| || ||||||||| ||||||||||| | |  ||  |
gtgag-ttttggtttgaaattgttcat-catcaggacttccaaatttacacattgtgcctgaattaaataaaataaacatgtcagGTCATGGACATGTTGGGGCCAAGTCTTTGGGATCTTTGGAATTCTGTAGGCCAGAC

upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------gtaagcttttcgtatgagcctagtcac---acattgagatgaatca---ggtatctttaatgaagaaacatttataattattt----cagGTCATGGACATGCTTGGGCCTAGCCTTTGGGATGTTTGGAATTCTTTGGCTCAATC
                               | |  | ||  || |     | |||        || | |    ||    | | | ||||||       |   |    | || |    ||||||||||| ||||||||||| || || |||||||| ||||| ||||  | |||| |
gtgagtcacctattgaattgttgtagtccaagcagaccttcagttttcatgtggtcgtcttgttttcaaacttttctcatgatttttttaattcgatttcgacttcgttcatatgctgcagGTCATGGATATGCTTGGGCCAAGTCTCTGGGATGTCTGGAACTCTTCAGGTCAAGC

upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------gtaagcttttcgtatgagcctagtcacacattgagat----gaatcaggtatcttt---aatgaag-------aaacatttataattatttcagGTCATGGACATGCTTGGGCCTAGCCTTTGGGATGTTTGGAATTCTTTGGCTCAATC
                                         ||   || | || |  |  || || |   |||| ||    | |  || | ||||    |||  |        |  | || |||  |  | ||||||||||| ||||||||||| || ||||||||||||||||| ||||  |  ||  |
gtgggctattcacagaaaatagatgaatttacacatgctgatagatttcttgtctttgattattcccgatttgaaatttttgtacgagttctcttccgaaatacattttattcacccgttgatatcttgtccagGTCATGGATATGCTTGGGCCAAGTCTTTGGGATGTTTGGAACTCTTCAGGCCAGGC

upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ13521 (Selaginella moellendorffii), 3'ss of exon 4
gtaagcttttcgtatgagcctagtcacacattgagatgaatcaggtatctttaatgaagaaacatttataattatttcagGTCATGGACATGCTTGGGCCTAGCCTTTGGGATGTTTGGAATTCTTTGGCTCAATC
                      |||     | ||| || |    ||  |||  |   | |    |   | | | ||  |||| |||||||||||||||||||||||||||||  ||||||| ||    | |||| |
----------------------gtcggtgttagagttgcactgtgttacttctactgaaagttttaagtgactgttctagGTAATGGACATGCTTGGGCCTAGCCTTTGGGACATTTGGAACTCCACCGGTCAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacattgagatgaatcaggtatctttaatgaagaaacatttataattatttcagGTCATGGACATGCTTGGGCCTAGCCTTTGGGATGTTTGGAATTCTTTGGCTCAATC
                       ctttaat  putative branch site (score: 4)
                                              ttatttc  putative PPT
                    tatctttaatgaagaa  TA-rich tract