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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttcagtctcattatatttgtacttctgtaatgagacaaattgacacaaaaatgtagataacgaaagcattgagcatttgatgccttcaggttatcatttaggctataattattaatcgcctttgctttttgcattgcagTTCTTCATCACTTGTGCAAAATGCGATTGGCTTGACAACAAGCATGTTGTCTTTGGG

Basic information

species Arabidopsis thaliana
transcript AT2G38730.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G38730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g59700.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------------gtaatttcagtctcattatatttgtact-tctgtaatgagacaaa---ttgacacaaaaatgtagataacgaaagcattgagcatttgatgccttcaggttatcatttaggctata--attattaa-----tcgcctttgctttttgca-ttgcagTTCTTCATCACTTGTGCAAAATGCGATTGGCTTGACAACAAGCATGTTGTCTTTGGG
                                              | |||   ||    |   |||| | | |  |   || |  |     |||  |    | | |         |   | | |||| |       | |||||| || |||  | || |  |||  | |     |   |||   || ||    ||||||||||| || |||||||||||||| || ||||| |||||||||||||| || ||||||
gtacttcttttgataactgctctattttttttctgtgtggctgtagattttttatccagctggttttgcaatcttcgggctggggtactgttttgggattgtattttgttctctatacaaaattagcaatatccagttccaggtt-tcttttcagttacagtattcctgaaaatattatcttctattcttatgcttgcagTTCTTTATAACTTGTGCAAAATGTGAATGGCTGGACAACAAGCATGTGGTTTTTGGG

upper sequence: AT2G38730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G057329_T01 (Zea mays), 3'ss of exon 5
---------------------------------gtaatttcagtctca-ttatatttg--tacttctgtaatga--gacaaattgacacaaaaatgt---agataacgaaagcattgagcatttgatgccttcaggttatcatttaggctataattattaatcgcctttgctttttgcattgcagTTCTTCATCACTTGTGCAAAATGCGATTGGCTTGACAACAAGCATGTTGTCTTTGGG
                                  ||||  | | |||| | | | |    | | |  | ||||         |  |  ||   ||||   |||  |  |||  | |    || |  | | |  |     |  |||||  || | | || ||  || |   || ||    ||||||||||| || || |||||||| || || |||||||||||||| ||||| || ||||||
gtacgttcgccttctctaaaattgcatgtagccttaatgcctgactcagtcacactcagttgccttggcaatgcctattccttcaagccagtcatgtttaagaacaaaaaatgactagatatct--ttcttgtacaccctgttttagagtaca-tgatgaaaagcttacactcttgtgcttgcagTTCTTTATAACATGTGCAAAGTGTGACTGGCTTGACAACAAACATGTGGTATTTGGG

upper sequence: AT2G38730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G11960.1 (Glycine max), 3'ss of exon 5
gtaatttcagtctcattatatttgtacttctgtaatgagacaaattgacacaaaaatgtagataacgaaagcattgagcatttgatgccttcaggttatcatttaggctataattattaatcg-cctttgctttttgcattgcagTTCTTCATCACTTGTGCAAAATGCGATTGGCTTGACAACAAGCATGTTGTCTTTGGG
                       |||  | | || || | || |||  |||  |  |     |  |     ||||       || |    | |  ||   | | |  || |   |||| ||    |||  ||| |||| ||||||||||| || || ||||||||||| || ||||||||||||||||||||||||||||||
-----------------------gtaactttctagtg-gtcacattctcacttacttcctttt--cctttccattttctcagtggtaatgttaaattggtaat-actcttttcctattgatgaatcttctcttcttgc-ttgcagTTCTTTATAACATGTGCAAAATGTGACTGGCTTGACAACAAGCATGTTGTCTTTGGG

upper sequence: AT2G38730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G26260.1 (Glycine max), 3'ss of exon 5
gtaatttcagtctcattatatttgtacttctgtaatgagacaaattgaca----caaaaatgtagataacgaaagcattgagcatttgatgccttcaggttatcatttaggctataattattaatcgcctttgctttttgcattgcagTTCTTCATCACTTGTGCAAAATGCGATTGGCTTGACAACAAGCATGTTGTCTTTGGG
|||| ||     |  | | |||   ||||   |  |    |    | |||    ||   |  |   |  |     ||||       || |    | |  ||   | | |  || |   |||| ||     ||   || |   ||||||||||| || || ||||||||||| || ||||||||||||||||||||||||||||||
gtaactttccagtggtcacattctcacttacttccttttccgtggtcacattctcacttacttccttttcctttccattttctcagtggtaatgttaaattggtaat-actcttttcctattgatgaatgttctcttcttgcttgcagTTCTTTATAACATGTGCAAAATGTGACTGGCTTGACAACAAGCATGTTGTCTTTGGG

upper sequence: AT2G38730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G37190.1 (Glycine max), 3'ss of exon 5
gtaatttcagtctcattatatttgtacttctgtaatgagacaaattgacacaaaaatgtagataacgaaagcattgagcatttgatgccttcaggttatcatttaggctataattattaatcgcctttgctttttgcattgcagTTCTTCATCACTTGTGCAAAATGCGATTGGCTTGACAACAAGCATGTTGTCTTTGGG
                               ||||     ||  | | ||||   |  |   |  |     | ||  |    || |  | | |  ||   | |    || |   |||| ||     ||   || |   ||||||||||| || || |||||||||||||| ||||||||||| ||||||||||||||||||
-------------------------------gtaactttccag-tggtcacactcacttccttttcctttcccttttgtcagtggtaacgttaaattggtaat-gcccttttcctattgatgaatgttctcttcttgcttgcagTTCTTTATAACATGTGCAAAATGCGACTGGCTTGACAAAAAGCATGTTGTCTTTGGG

upper sequence: AT2G38730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S232_73V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaatttcagtctcattatatttgtacttctgtaatgagacaaattgacacaaaaatgtagataacgaaagcattgagcatttgatgccttcaggttatcatttaggctataattattaatcgcctttgctttttgcattgcagTTCTTCATCACTTGTGCAAAATGCGATTGGCTTGACAACAAGCATGTTGTCTTTGGG
                  |  |||    | |||  ||     |||||  | ||  |       ||| | ||       |||||  ||  || ||||     |||  |||       || |  |  || |  |     ||  |||||||||||||| ||||| || ||||| ||||| |||||||| || ||||| || |||
-----------------ttgcttgagagtttgtt-tgt----aattggtaaaagtac-----caacaagagttc----catttagtggtttgaggt----gtttctgct-------ttgacggggttgg--tggaatatgccagTTCTTCATCACATGTGCCAAGTGCGACTGGCTGGACAACAAACACGTTGTTTTCGGG

upper sequence: AT2G38730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ31848 (Selaginella moellendorffii), 3'ss of exon 5
gtaatttcagtctcattatatttgtacttctgtaatgagacaaattgacacaaaaatgtagataacgaaagcattgagcatttgatgccttcag-gttatcatttaggctataattattaatcgcctttgctttttgcattgcagTTCTTCATCACTTGTGCAAAATGCGATTGGCTTGACAACAAGCATGTTGTCTTTGGG
                                                                                     | | ||  | | | |  | | ||  ||   || | |  |    || | ||||   || ||||||| || ||||| || |||||||| ||||| |||||||||||||| || ||||| 
------------------------------------------------------------------------------------gtactttttgtgatcttctgtgggtgatctatacttacggaagatgttgtttg---tgtagTTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGA

upper sequence: AT2G38730.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ38013 (Selaginella moellendorffii), 3'ss of exon 5
gtaatttcagtctcattatatttgtacttctgtaatgagacaaattgacacaaaaatgtagataacgaaagcattgagcatttgatgccttcag-gttatcatttaggctataattattaatcgcctttgctttttgcattgcagTTCTTCATCACTTGTGCAAAATGCGATTGGCTTGACAACAAGCATGTTGTCTTTGGG
                                                                                     ||| ||  | | | |  | | |   ||   || | |  |     | | ||||   || ||||||| || ||||| || |||||||| ||||| |||||||||||||| || ||||| 
------------------------------------------------------------------------------------gtgctttttgtgatcttctgtggatgatctatacttacggaagacgttgtttg---tgtagTTCTTTATAACTTGCGCCAAATGCGACTGGCTCGACAACAAGCATGTGGTGTTTGGA

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|164165853|gb|ES026564.1|ES026564
EST:     GCAAATAGTGGGCCAAACACAAATGGGTGCCAG                         TTCTTCATCACTTGTGCAA
genomic: GCAAATAGTGGGCCAAACACAAATGGGTGCCAGgtaatttcag ... tgcattgcagTTCTTCATCACTTGTGCAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaggttatcatttaggctataattattaatcgcctttgctttttgcattgcagTTCTTCATCACTTGTGCAAAATGCGATTGGCTTGACAACAAGCATGTTGTCTTTGGG
                         tattaat  putative branch site (score: 2)
                               tcgcctttgcttttt  CT-rich tract
           atttaggctataatta  TA-rich tract