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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttttaactttataatctatattgatgatgtagtctgttgtacgagatgcaatctagaggtttctccggtgggactaactaatcattggttgtgtagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTCTCTCTTAAAGATAAGGATTTTGTCGAGGGTCCATGGTCTCAGAACAGTCTCGACAATGGTG

Basic information

species Arabidopsis thaliana
transcript AT4G05420.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 8
ttttttttaactttataatctatattgatgatgtagtctgttgtacgagatgcaatctagaggtttctccgg---tgggactaactaatcattggttgtgtagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTCTCTCTTAAAGATAAGGATTTTGTCGAGGGTCCATGGTCTCAGAACAGTCTCGACAATGGTG
 ||   ||  ||||||    ||||||      | |   || |||     ||  |   |   | |||    ||   ||  ||||  |  ||||   |     |||| || ||||||||||||||||| ||||||||||| ||  | || || ||||| |||||||| || ||||||||||| ||||||| |||||| ||||| |
-ttgcatttcctttatgcaatatatttggttggaaaaatggtgtttagcataaacatttttgattttgatggatttgttactatgttttcatcaatgac--agGATAATAAAGATGCTCGTCATGTTAAAACATATGAGGTTGCACTGAAGGATAAAGATTTTGTTGAAGGTCCATGGTCCCAGAACAATCTCGATAATGGGG

upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 8
-ttttttttaactttataatctatattgatgatgtagtctgttgtacgagatgcaatctagaggtttctccggt-gggactaactaatcattggttgtgtagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTCTCTCTTAAAGATAAGGATTTTGTCGAGGGTCCATGGTCTCAGAACAGTCTCGACAATGGTG
 |   |||    | |  ||| ||| ||| ||    | |    | ||  | |  |||| | ||  ||  |    | |  | ||  |  |||| | |     |||| || ||||||||||||||||| ||||||||||| ||  | || || ||||| |||||| | || ||||||||||| ||||||| ||| || ||||| |
ttgcatttcctttatgcaatatattttgttggaaaaatggtgtttagcataaacaattttgattttgatggatttgttattatgttttcatcgatgac--agGATAATAAAGATGCTCGTCATGTTAAAACATATGAGGTTGCACTGAAGGATAAAGATTTTCTTGAAGGTCCATGGTCCCAGAACAATCTTGATAATGGGG

upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 8
ttttttttaactttataatctatattgatgatgtagtctgttgtacgaga--tgcaatctagaggtttctccggtgggactaactaa---tcattggttg----tgtagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTCTCTCTTAAAGATAAGGATTTTGTCGAGGGTCCATGGTCTCAGAACAGTCTCGACAATGGTG
        |||||      |   | || || |  | | ||| | |  |||  |||| |    ||  |    | |  || || || |       ||| ||     || |||| ||||||||||| |||||||| ||||||||||| ||  || | || |||||||||||||| |||||||| ||| ||||||||| ||| |||||||| |
--------aacttagatggccccactg-tgttccattatgtagcatcagaagtgcattaggaagaataactcagatggcctcaccatgttctcttgattcaaattgcagGATAACAAAGATGCACGTCATGTTAAAACATATGAGGTGGCTTTGAAGGATAAGGATTTTGTTGAGGGTCCTTGGGCTCAGAACAATCTAGACAATGGGG

upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ23079 (Selaginella moellendorffii), 3'ss of exon 8
ttttttttaactttataatctatattgatgatgtagtctgttgtacgagatgcaatctagaggtttctccggtgggactaactaatcattggttgtgtagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTCTCTCTTAAAGATAAGGATTTTGTCGAGGGTCCATGGTCTCAGAACAGTCTCGACAATGGTG
                                ||    | |  | | | || |  |   ||     ||  |       |  ||  ||||| |      |||||||||||||||||||||| ||||||||||| ||  |    || ||||| ||||||||||  ||||| |||||||  ||||| |  ||||||||||| |
--------------------------------gttcggtttccttcaatatccttttaggaaaaaacttggcgaatgtttgct--tcatttg----acagGACAACAAAGATGCTCGTCACGTCAAAACATACGAGATACAACTGAAAGAGAAGGATTTTGGTGAGGGGCCATGGTTGCAGAATAACCTCGACAATGGAG

upper sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ30457 (Selaginella moellendorffii), 3'ss of exon 8
ttttttttaactttataatctatattgatgatgtagtctgttgtacgagatgcaatctagaggtttctccggtgggactaactaatcattggttgtgtagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTCTCTCTTAAAGATAAGGATTTTGTCGAGGGTCCATGGTCTCAGAACAGTCTCGACAATGGTG
                                ||    | |  | | | || |  |   ||     ||  |       |  ||  ||||| |      |||||||||||||||||||||| ||||||||||| ||  |    || ||||| ||||| ||||  ||||| |||||||| ||||| |  ||||||||||| |
--------------------------------gttcggtttccttcaatatccttttaggaaaaaacttggcgaatgtttgct--tcatttg----acagGACAACAAAGATGCTCGTCACGTCAAAACATACGAGATACAACTGAAAGAGAAGGACTTTGGTGAGGGGCCATGGTCGCAGAATAACCTCGACAATGGAG

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|116455518|gb|EG498110.1|EG498110
EST:     TCAAGTTTCTGTTTGGATGTGCAAAGCCCACTATTGCAGTACTATATCAG                         GACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTCTCTCTTAAAGAT
genomic: TCAAGTTTCTGTTTGGATGTGCAAAGCCCACTATTGCAGTACTATATCAGgtattgcaaa ... ggttgtgtagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTCTCTCTTAAAGAT
EST: gi|116382313|gb|EG424905.1|EG424905
EST:     TCAAGTTTCTGTTTGGATGTGCAAAGCCCACTATTGCAGTACTATATCAA                         GACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTCTCTCTTAAAGAT
genomic: TCAAGTTTCTGTTTGGATGTGCAAAGCCCACTATTGCAGTACTATATCAGgtattgcaaa ... ggttgtgtagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTCTCTCTTAAAGAT
EST: gi|116382318|gb|EG424910.1|EG424910
EST:     TCAAGTTTCTGTTTGGATGTGCAAAGCCCACTATTGCAGTACTATATCAA                         GACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTCTCTCTTAAAGAT
genomic: TCAAGTTTCTGTTTGGATGTGCAAAGCCCACTATTGCAGTACTATATCAGgtattgcaaa ... ggttgtgtagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTCTCTCTTAAAGAT
EST: gi|116382315|gb|EG424907.1|EG424907
EST:     TCAAGTTTCTGTTTGGATGTGCAAAGCCCACTATTGCAGTACTATATCAG                         GACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTCTCTCTTAAAGAT
genomic: TCAAGTTTCTGTTTGGATGTGCAAAGCCCACTATTGCAGTACTATATCAGgtattgcaaa ... ggttgtgtagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTCTCTCTTAAAGAT
EST: gi|116456285|gb|EG498877.1|EG498877
EST:     TCAAGTTTCTGTTTGGATGTGCAAAGCCCACTATTGCAGTACTATATCAG                         GACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTCTCTCTTAAAGAT
genomic: TCAAGTTTCTGTTTGGATGTGCAAAGCCCACTATTGCAGTACTATATCAGgtattgcaaa ... ggttgtgtagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTCTCTCTTAAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgagatgcaatctagaggtttctccggtgggactaactaatcattggttgtgtagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTCTCTCTTAAAGATAAGGATTTTGTCGAGGGTCCATGGTCTCAGAACAGTCTCGACAATGGTG
                                 taactaat  TA-rich tract