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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttttcccgatgctcgttttttgttttgggaacataaatatgtaagaaacttgatttgattttgctaattatgtcaaatttcagACTGCTGCAAGCTACCATGCCATAGCAATTGCGCTCTCCTTGATGGAGGCATACCATTTAAGTGTTCAGCATGAGCAAACAACCTTAAGAATCCTTCGAG

Basic information

species Arabidopsis thaliana
transcript AT1G01320.2
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G01320.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 18
-------gttcttttcccgat--gctcgttttttgttttgggaacataaatatgtaa----gaaacttgatttgattttgctaattatgtcaaatttcagACTGCTGCAAGCTACCATGCCATAGCAATTGCGCTCTCCTTGATGGAGGCATACCATTTAAGTGTTCAGCATGAGCAAACAACCTTAAGAATCCTTCGAG
       |||    |   ||     ||  ||  || |||    |  |||  || |         |  || ||  | |    || || | |   |||| |||||||||| ||||||||||||||||| ||||| ||||| |||||||| || ||    || ||||||||||||||||||||||||||   ||| ||||| |
agtacaggtttcactgttgactacttcacttaatgctttcatcatttaatgatattgcttgattatctgtttcaactaacatacttgtctgttattttagACTGCTGCGAGCTACCATGCCATAGCCATTGCTCTCTCATTGATGGAAGCTTATTCCTTGAGTGTTCAGCATGAGCAAACAACCTTGCAAATTCTTCGTG

upper sequence: AT1G01320.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 20
--------gttcttttcccgatgctcgttttttgttttgggaa----cataaatatgtaagaa-acttgatttgattttgctaattatgtcaaattt--cagACTGCTGCAAGCTACCATGCCATAGCAATTGCGCTCTCCTTGATGGAGGCATACCATTTAAGTGTTCAGCATGAGCAAACAACCTTAAGAATCCTTCGAG
        |  | | |     || |  || | |||||   |||    |  |  | ||| | || |||| |     |    ||  ||   |||   |   ||||| |||||||| || ||||| |||||||| || ||||| |||||||| ||||| |  || ||||| ||||||||||||||||| ||   ||| || || |
aataataggaacctatgggattgat--ttatatgtttaatgaaacttctcatctttgttataacacttaaacacttgcatcttcttggatcatcctctgcagACAGCTGCAAGTTATCATGCAATAGCAATAGCACTCTCATTGATGGAAGCATATCCATTGAGTGTCCAGCATGAGCAAACAACTTTGCAAATTCTGCGGG

upper sequence: AT1G01320.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 20
---------gttcttttcccgatgctcgtttt--ttgttttgggaacataaatatgtaagaaacttgatttg-attttgctaattatgtcaaattt-cagACTGCTGCAAGCTACCATGCCATAGCAATTGCGCTCTCCTTGATGGAGGCATACCATTTAAGTGTTCAGCATGAGCAAACAACCTTAAGAATCCTTCGAG
          |      |     | | || ||  ||||||   |||  |    || |  |  |    | ||  || ||  |   | | |    | | ||||| |||||||| || ||||| |||||||| || || || |||||||| ||||| |  || ||||| ||||||||||||||||| ||   ||| || || |
actaaaataataggaacctaagggattgtattgtttgtttaatgaaacttctcatctgtgttataacacttacatcttcttggatgtttttcctctgcagACAGCTGCAAGTTATCATGCAATAGCAATAGCACTTTCATTGATGGAAGCATATCCATTGAGTGTCCAGCATGAGCAAACAACTTTGCAAATTCTGCGGG

upper sequence: AT1G01320.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 20
---------gttcttttcccgatgctcgttttttgttttgggaacataaatatgtaagaaactt---gatttgatttt-gctaattatgtcaaatttcagACTGCTGCAAGCTACCATGCCATAGCAATTGCGCTCTCCTTGATGGAGGCATACCATTTAAGTGTTCAGCATGAGCAAACAACCTTAAGAATCCTTCGAG
          |     |   || |       ||  ||| ||  |||    | | ||  |  | |   ||  | ||||       || |       | ||||| || ||||| |||||||| ||||||||||| || || |||||||| ||||||| ||| || |||||||||||||||||||||||   ||| || ||||
gaggatttcatctgaatttagaagggaaaaattattttgggccacacttgtgtatatcattcctttggagctaatttccatctcttttaatgctctccagACAGCAGCAAGTTACCATGCAATAGCAATTGCTCTATCATTGATGGAAGCATACCCTTTGAGCGTTCAGCATGAGCAAACAACCTTGCAAATTCTCCGAG

upper sequence: AT1G01320.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: PP1S73_28V6.1 (Physcomitrella patens), 3'ss of exon 14
gttcttt-tcccgatgctcgttttttgttttgggaacataaat------atgtaagaaacttgatttg--------attttgctaattatgt---caaatttcagACTGCTGCAAGCTACCATGCCATAGCAATTGCGCTCTCCTTGATGGAGGCATACCATTTAAGTGTTCAGCATGAGCAAACAACCTTAAGAATCCTTCGAG
|||| || |  |  |  | |||   | ||||  ||  | || |      || |   | ||||    |         | ||| ||||||  ||       || |||||||||||||| ||||| || || ||||||||||| ||  | |||||||| |||    | |||||||||||||||||||| ||||||   ||  | | | 
gttcgttgtaacactagttgttgaatttttttcgagtacaagtcgtttcatctttaacacttaccctatcactgcaaatttactaattgagtacttctgttgcagACTGCTGCAAGTTACCACGCAATTGCAATTGCGCTTTCACTTATGGAGGCTTACTCCCTCAGTGTTCAGCATGAGCAAACTACCTTACAGATTTTGCAAA

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|116396583|gb|EG439175.1|EG439175
EST:     ACAAAGCTCTCAAGTGTAATCAAAGGTTGCTTGGTCCGGACCATATCCAG                         ACTGCTGCAAGCTACCATGCCATAGCAATTGCGCTCTCCTTGATGGAGGCA
genomic: ACAAAGCTCTCAAGTGTAATCAAAGGTTGCTTGGTCCGGACCATATCCAGgttcttttcc ... caaatttcagACTGCTGCAAGCTACCATGCCATAGCAATTGCGCTCTCCTTGATGGAGGCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaacataaatatgtaagaaacttgatttgattttgctaattatgtcaaatttcagACTGCTGCAAGCTACCATGCCATAGCAATTGCGCTCTCCTTGATGGAGGCATACCATTTAAGTGTTCAGCATGAGCAAACAACCTTAAGAATCCTTCGAG
                                 tgctaat  putative branch site (score: 2)
                                    taattatgtcaaattt  TA-rich tract