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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaagatcaatcattgctacttcctcttaatcgaaaacttctttaagggtttaagtctcattgtttcggtttgtatgaatagGTCGCTGCATATGACAAAACTCAGGGGAAAATGGCCTTCTTTGATCCTTCCAGGTCTCAAGACTTCCTCTTCATATCAGGAACCAAG

Basic information

species Arabidopsis thaliana
transcript AT5G43780.1
intron # 3
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 3
lower sequence: GLYMA20G28980.2 (Glycine max), 3'ss of exon 3
---gttaagatcaatcattgctacttcctcttaatcga--aaacttctttaaggg----tttaagt-----ctcattgtttcggtttgtatgaatagGTCGCTGCATATGACAAAACTCAGGGGAAAATGGCCTTCTTTGATCCTTCCAGGTCTCAAGACTTCCTCTTCATATCAGGAACCAAG--
    || |||     | ||   | ||  | | ||  ||   || |||  | |||     || || |      | ||  |||   ||  | ||   |||| |||||||||||||| |||||||| |||||||| |||||||| ||||| ||| |||| |||||||| ||||||||||| || |||  
gtaattgagaatttgccttctca-ttagtataaactgagtgaagttcacttaggccactttgaaatatgtgttgatcattttcattcatttg--cagGTTGCTGCATATGACAAGACTCAGGGTAAAATGGCATTCTTTGACCCTTCAAGGCCTCAGGACTTCCTGTTCATATCAGGCACAAAGGT

upper sequence: AT5G43780.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G38760.1 (Glycine max), 3'ss of exon 3
---gttaagatcaatcattgctacttcctcttaatcgaaaacttctttaag-------ggtttaagtctcattgtttcggtttgt--atgaatagGTCGCTGCATATGACAAAACTCAGGGGAAAATGGCCTTCTTTGATCCTTCCAGGTCTCAAGACTTCCTCTTCATATCAGGAACCAAG
    || |||     | ||   | |    |        ||  |   ||| |       | | || || |   || |    ||  |  ||  | |||| |||||||||||||| |||||||| |||||||| |||||||| ||||| ||| |||| |||||||| ||||||||||| || |||
gtaattgagaatttgccttctcattaatacactgagtgaagttcacttaggccactttgatatatgtgttgatgatcattttcattcatttacagGTTGCTGCATATGACAAGACTCAGGGTAAAATGGCATTCTTTGACCCTTCAAGGCCTCAGGACTTCCTGTTCATATCAGGCACAAAG

upper sequence: AT5G43780.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G28980.1 (Glycine max), 3'ss of exon 3
---gttaagatcaatcattgctacttcctcttaatcga--aaacttctttaaggg----tttaagt-----ctcattgtttcggtttgtatgaatagGTCGCTGCATATGACAAAACTCAGGGGAAAATGGCCTTCTTTGATCCTTCCAGGTCTCAAGACTTCCTCTTCATATCAGGAACCAAG
    || |||     | ||   | ||  | | ||  ||   || |||  | |||     || || |      | ||  |||   ||  | ||   |||| |||||||||||||| |||||||| |||||||| |||||||| ||||| ||| |||| |||||||| ||||||||||| || |||
gtaattgagaatttgccttctca-ttagtataaactgagtgaagttcacttaggccactttgaaatatgtgttgatcattttcattcatttg--cagGTTGCTGCATATGACAAGACTCAGGGTAAAATGGCATTCTTTGACCCTTCAAGGCCTCAGGACTTCCTGTTCATATCAGGCACAAAG

upper sequence: AT5G43780.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0020g04210.t01 (Vitis vinifera), 3'ss of exon 3
gt-taagatcaatcattgctacttc----ctcttaatcgaaaacttctttaagggtttaagtctcattgtttcg---gttt--gtatgaat--agGTCGCTGCATATGACAAAACTCAGGGGAAAATGGCCTTCTTTGATCCTTCCAGGTCTCAAGACTTCCTCTTCATATCAGGAACCAAG
|| ||  | | ||  | |||  |      |||  ||| |    | | |||||    | || |||    | |||    |||   |||| | |  |||| ||||||||||| |||||||||   |||||||| ||||||||||| || ||| |||||||||||||||||||||| || || |||
gtatataaactattgtagctcttatgaaactcaaaattgctttcctgtttaatttatgaaatctgtaggattcacaagttgaggtataattgcagGTTGCTGCATATGATAAAACTCAGAATAAAATGGCATTCTTTGATCCCTCAAGGGCTCAAGACTTCCTCTTCATATCTGGCACAAAG

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|116454015|gb|EG496607.1|EG496607
EST:     TGCTTAGCATGGCACCAGGACTTGAACGCCTCAACATTCTACCCTTCAAG                         GTCGCTGCATATGACAAAACTCAGGGGAAAATGGCCTTCTTTGATCCTTCC
genomic: TGCTTAGCATGGCACCAGGACTTGAACGCCTCAACATTCTACCCTTCAAGgttaagatca ... gtatgaatagGTCGCTGCATATGACAAAACTCAGGGGAAAATGGCCTTCTTTGATCCTTCC
EST: gi|116377755|gb|EG420347.1|EG420347
EST:     TGCTTAGCATGGCACCAGGACTTGAACGCCTCAACATTCTACCCTTCAAG                         GTCGCTGCATATGACAAAACTCAGGGGAAAATGGCCTTCTTTGATCCTTCC
genomic: TGCTTAGCATGGCACCAGGACTTGAACGCCTCAACATTCTACCCTTCAAGgttaagatca ... gtatgaatagGTCGCTGCATATGACAAAACTCAGGGGAAAATGGCCTTCTTTGATCCTTCC
EST: gi|116454026|gb|EG496618.1|EG496618
EST:     TGCTTAGCATGGCACCAGGACTTGAACGCCTCAACATTCTACCCTTCAAG                         GTCGCTGCATATGACAAAACTCAGGGGAAAATGGCCTTCTTTGATCCTTCC
genomic: TGCTTAGCATGGCACCAGGACTTGAACGCCTCAACATTCTACCCTTCAAGgttaagatca ... gtatgaatagGTCGCTGCATATGACAAAACTCAGGGGAAAATGGCCTTCTTTGATCCTTCC
EST: gi|124721409|gb|EH812811.1|EH812811
EST:     TGCTTAGCATGGCACCAGGACTTGAACGCCTCAACATTCTACCCTTCAAG                         GTCGCTGCATATGACAAAACTCAGGGG
genomic: TGCTTAGCATGGCACCAGGACTTGAACGCCTCAACATTCTACCCTTCAAGgttaagatca ... gtatgaatagGTCGCTGCATATGACAAAACTCAGGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatcgaaaacttctttaagggtttaagtctcattgtttcggtttgtatgaatagGTCGCTGCATATGACAAAACTCAGGGGAAAATGGCCTTCTTTGATCCTTCCAGGTCTCAAGACTTCCTCTTCATATCAGGAACCAAG
 tcttaat  putative branch site (score: 3)
           ttctttaa  TA-rich tract