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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgcctttctactccctgatacaaaaatgtgaagtggcattgttggttctagaagatgagatttaatagtcgctccactttttttcttttcgatattaatgatgtatgatttgttactcagGTGTCCCCAAACTCAAAAGATCTGAGATTGAAGCTGCCTGTGAAGATTTTAGTAATGTCATTGGGTCTTGCCCCATTGGTACATTGTTCAAAGGGACGCT

Basic information

species Arabidopsis thaliana
transcript AT3G56050.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G56050.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G02850.1 (Glycine max), 3'ss of exon 6
gtaattgcctttctactccctgatacaaaaatgtgaagtggcattgttggttctagaagatgagatttaatagtcgc-tccactttttttcttttcg-atattaatgatgtatgatttgttactcagGTGTCCCCAAACTCAAAAGATCTGAGATTGAAGCTGCCTGTGAAGATTTTAGTAATGTCATTGGGTCTTGCCCCATTGGTACATTGTTCAAAGGGACGCT
                             | ||     | ||| |       ||     |||  | |||    | || |  |   ||| |   | || | ||  ||||   |   ||   |  |||||||| || || || || ||||| ||| ||||||| || |||||||||||||||||||| |||||  |||   ||||||||||| ||| |||||||||  |
---------------------------tgattgcagtattgcactcccttgactgagctatgttacttatgtattgcatataagatttctgcctccgtacatgtatgacagaattttacattttcagGTGTGCCAAAGCTAAAGAGATCAGAGCTTGAAGCAGCATGTGAAGATTTTAGTAATGTAATTGGTACTTCATCCATTGGTACAGTGTACAAAGGGACTTT

upper sequence: AT3G56050.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G35570.1 (Glycine max), 3'ss of exon 5
gtaattgcctttctactccctgatacaaaaatgtgaagtggcattgttggttctagaagatgagatttaatagtcgctc--cactttttttcttttcgatattaatgatgtatgatttgt-tactcagGTGTCCCCAAACTCAAAAGATCTGAGATTGAAGCTGCCTGTGAAGATTTTAGTAATGTCATTGGGTCTTGCCCCATTGGTACATTGTTCAAAGGGACGCT
                             | ||     | ||| |       |      |||  | |||    | ||     |  ||| | | | |    ||  ||||   |   ||    |  |||||||| || || || || ||||| ||| ||||||| || |||||||||||||||||||| |||||  |||   ||||||||||| | | |||||||||  |
----------------------------gattgcagtattgcaatcccttgaccgagcaatgttacttatgtattgcatataagatttctgcctctgttcatgtatgacagaattttaacattttcagGTGTGCCAAAGCTAAAGAGATCAGAGCTTGAAGCAGCATGTGAAGATTTTAGTAATGTAATTGGCACTTCATCCATTGGTACAGTTTACAAAGGGACTTT

upper sequence: AT3G56050.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G43150.1 (Glycine max), 3'ss of exon 7
gtaattgcctttctactccctgatacaaaaatgtgaagtggcattgttggttctagaagatg-agatttaatagtcgc-tccac-tttttttcttttcgatattaatgatgtatgatttgttactcagGTGTCCCCAAACTCAAAAGATCTGAGATTGAAGCTGCCTGTGAAGATTTTAGTAATGTCATTGGGTCTTGCCCCATTGGTACATTGTTCAAAGGGACGCT
                               ||     | |||||      |||   || |  |  | | ||  |  | |  |  |||| | | | |  | ||  ||||   |   ||   |  |||||||  |  || || |  ||||| ||  ||||||| || |||||||||||||||||||| |||||  |||  ||||| |||||| ||| |||||| ||  |
----------------------------ctttgaatgattgcattcccatgtctttgagctatatttctcatgcttacatgtatgttttctgcctatgtacatgcatgacagagtcttacattttcagGTGCGCAAAAGCTAAGGAGATCAGATCTTGAAGCAGCATGTGAAGATTTTAGTAATGTAATTGGTACTTCACCCATCGGTACACTGTACAAAGGAACTTT

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|125273087|gb|EL287172.1|EL287172
EST:     TCCCTGGCGTACAGGTCTTAGTGGACAACTTCAGAAAGTGTTCATAACTG                         GTGTCCCCAAACTCAAAAGATCTGAGATTGAAGCTG
genomic: TCCCTGGCGTACAGGTCTTAGTGGACAACTTCAGAAAGTGTTCATAACTGgtaattgcct ... tgttactcagGTGTCCCCAAACTCAAAAGATCTGAGATTGAAGCTG
EST: gi|124817284|gb|EH902150.1|EH902150
EST:     GGTCTTAGTGGACAACTTCAGAAAGTGTTCATAACTG                         GTGTCCCCAAACTCAAAAGATCTGAGATTGAAGCCGCCTGTGAAGATTTTA
genomic: GGTCTTAGTGGACAACTTCAGAAAGTGTTCATAACTGgtaattgcct ... tgttactcagGTGTCCCCAAACTCAAAAGATCTGAGATTGAAGCTGCCTGTGAAGATTTTA
EST: gi|86054312|gb|DR350069.1|DR350069
EST:     TTCAGAAAGTGTTCATAACTG                         GTGTCCCCAAACTCAAAAGATCTGAGATTGAAGCTGCTTGTGAAGATTTTA
genomic: TTCAGAAAGTGTTCATAACTGgtaattgcct ... tgttactcagGTGTCCCCAAACTCAAAAGATCTGAGATTGAAGCTGCCTGTGAAGATTTTA
EST: gi|86054311|gb|DR350068.1|DR350068
EST:     TTCAGAAAGTGTTCATAACTG                         GTGTCCCCAAACTCAAAAGATCTGAGATTGAAGCTGCTTGTGAAGATTTTA
genomic: TTCAGAAAGTGTTCATAACTGgtaattgcct ... tgttactcagGTGTCCCCAAACTCAAAAGATCTGAGATTGAAGCTGCCTGTGAAGATTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtcgctccactttttttcttttcgatattaatgatgtatgatttgttactcagGTGTCCCCAAACTCAAAAGATCTGAGATTGAAGCTGCCTGTGAAGATTTTAGTAATGTCATTGGGTCTTGCCCCATTGGTACATTGTTCAAAGGGACGCT
                           tattaat  putative branch site (score: 2)
            tttttttcttttcgat  TA-rich tract