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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttttctgaatcttatttctcttgttttccttaacaatgtgtatgaattagtggccatgttgaagtatgagaatatgaatcttatcatttgtgattgattggttgtttttgaaaattgaatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAATCTTCACTCACAGGAATGTTGGAAAGACACTTGTTTCCAGAACTCAGGGT

Basic information

species Arabidopsis thaliana
transcript AT3G04840.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G04840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S80_120V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaagtttttctgaatcttatttctcttgttttccttaacaatgtgtatgaattagtggccatgttgaagta-tgagaatatgaatcttatcatttgtgattgattggttgttttt--------gaaaattgaatgt--tgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAATCTTCACTCACAGGAATGTTGGAAAGACACTTGTTTCCAGAACTCAGGGT
            | | |    | ||  |  ||  ||| |||         |||| |  | | || ||   |  |  || | |   | |     |||||| ||| ||    |  ||         ||   | | ||||  |||||||| ||||||||||| ||||| |||||||||||  | ||||| ||    | |||||| || | |    | || ||||| || ||  |||| ||   ||||
------------gtagcgctctccttctccttctctttacaggaatggctaattcgctgtcctgctgcgctggtttgagtttaggtttcgaggtttgtgtttgtttccacgcattgacgcggaggacggtgggatgtaatgcagTGTCGATCCTTTCTCGAAGAAGGATTGGTATGACATCAAGGCCCCCAACACCTTCACGCAGAAGTCGCTGGGGAAGACCCTGGTGACCAGGACCGCGGGT

upper sequence: AT3G04840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S92_47V6.2 (Physcomitrella patens), 3'ss of exon 1
gtaagtttttctgaatcttatttctcttgttttccttaacaatgtgtatgaattagtggccatgt-tgaagtatgagaatatgaatcttatcatttgtgattgattggttgtttttgaaaattgaatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAATCTTCACTCACAGGAATGTTGGAAAGACACTTGTTTCCAGAACTCAGGGT
                  ||  |||    ||   | |  |  ||||      || ||||   | | ||   | |||| || | || ||  ||||         |||| || ||||||    |    |  |||||||| ||||||||||||||||| || ||||||||| | ||||| ||    |||||||| || | |    | |||||||| |||||  | || |||   || 
-----------------gtacgtctaa-attcaacatggcgttgtgaggtttttggtgggtttttgtgggttgtgagcatttaaaact-gtcat---------attgattttttttgtgcgtc---ttgtgcagTGTCGATCCTTTCTCCAAGAAGGACTGGTATGATATCAAGGCACCCAATATCTTCACGCAAAAGGCGTTGGGAAAGACTCTTGTGACAAGGACTGCCGGC

upper sequence: AT3G04840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S219_50V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------gtaagttttt-ctg-aatcttatttctcttgttttccttaacaatgtgtatgaattagtggccatgt-tgaagtatgagaatatgaatcttatcatt----tgtgattgattggttgtttttga-------------aaattgaatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAATCTTCACTCACAGGAATGTTGGAAAGACACTTGTTTCCAGAACTCAGGGT
             |||  ||| | |||  |  | |   |||   |    ||    | ||| | || | |||  | | ||  ||| |  |  |  | |     |||   |     |||| |  ||  |  | || | |              | ||      |||||||| ||||||||||||||||| || ||||||||  | ||||| ||    | |||||| || | |||| | || ||||| || ||  | || ||   ||| 
gtacttctttccagtacttttctactgtgaattcacggctccactgcgtctgccaagtgtttgtgtactagctgtcttgagtgatggtttggtttctagggtttagtgtgcttgtgtggtatatgcggaggttctaactagagcgacgatgatttttgcactgcagTGTCGATCCTTTCTCCAAGAAGGACTGGTATGACATCAAGGCACCCAACACCTTCACGCAGAAGAATTTGGGGAAGACTCTCGTCACTAGGACCGCGGGA

upper sequence: AT3G04840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S179_15V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaagtttttctgaatcttatttctcttgttttccttaacaatgtgtat-gaattagtggccatgttgaagtatgagaatatgaatcttatcatttgtgattgattggttgtttttgaaaattgaatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAATCTTCACTCACAGGAATGTTGGAAAGACACTTGTTTCCAGAACTCAGGGT
           |  | |||   |  ||||   ||| | ||     ||   | | | || |   ||| |  |  |   ||| |   | | | ||||||   |    |||   | |||||   |||     ||||| || ||||||||||||||||| |||||||||||  | |||||||||   | |||||| || | |    | || ||||| || ||  |||| ||   ||||
----------gtacaccttccctaccttgccctccattacctccagtgccgcacttgtaggtttgt-gttgcttccaaatgttcct-tgagcatttggtctaacatggagatgtttgagtcttg-----tgcagCGTCGATCCTTTCTCCAAGAAGGATTGGTATGACATCAAGGCTCCTAACACCTTCACGCAGAAGTCGTTGGGGAAGACCCTCGTCACCAGGACGGCGGGT

upper sequence: AT3G04840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S174_49V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------gtaagtttttctgaatcttatttctcttgttttccttaacaatgtgtatgaattagtggccatgttgaagtatgagaatatgaatcttatcatttgtgattgattggttgt-ttttgaaaattgaatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAATCTTCACTCACAGGAATGTTGGAAAGACACTTGTTTCCAGAACTCAGGGT
                            |   | | ||     ||   |     | |||  ||   |           | | |||    | ||   || |    || ||  | | |  ||||| |||    |||   | | ||   | |   | |   |||||||||||| ||||||||||| || ||||||||  | || |||||    | |||| | || | |    | |||||||| || ||  |||| ||    |||
gtacgctcccataatctctctctctctctctctctctccctcgctcgctatctctctttctctatcccccccactcacagtggtgcgtttattagggttttg--atgtgtttgtgaggatttgagatgacatggcgatatcttctgagtcctacg---cagTGTTGATCCCTTCTCCAAGAAGGACTGGTATGACATCAAAGCTCCCAACACCTTCCCGCAGAAGTCGCTGGGAAAGACTCTCGTGACCAGGACCGCCGGT

upper sequence: AT3G04840.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ11589 (Selaginella moellendorffii), 3'ss of exon 2
gtaagtttttctgaatcttatttctcttgttttccttaacaatgtgtatgaattagtggccatgttgaagtatgagaatatgaatcttatcatttgtgattgattggttgtttttgaaaattgaatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAATCTTCACTCACAGGAATGTTGGAAAGACACTTGTTTCCAGAACTCAGGGT
                                                                         |  | | |    |  | | ||| ||  || ||| ||  || |          |    |||||| || |||||||||||||| |||||||| ||||| |||||    || |  |||| |    |  |  | || ||||| |||||  | ||||| ||||| 
-------------------------------------------------------------------------gtaagtgtttggcgcagcgttt-tgcctgcttgatttcttct----------ttcctcagTGTCGACCCTTTCTCCAAGAAGGATTGGTACGATGTCAAGGCCATGTCCACTTTCAATGTTCGTCAGATCGGGAAGACGCTTGTGACGAGAACGCAGGGA

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|124920335|gb|EH994060.1|EH994060
EST:     GAAAAACAAGAGAATCTCTAAGGGTAGGAAGGGAGGAAAGAAGAAGGC                         TGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAG
genomic: GAAAAACAAGAGAATCTCTAAGGGTAGGAAGGGAGGAAAGAAGAAGGCgtaagttttt ... aatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAG
EST: gi|125199504|gb|EL214458.1|EL214458
EST:     CTAAGGGTAGGAAGGGAGGAAAGAAGAAGGC                         TGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAAT
genomic: CTAAGGGTAGGAAGGGAGGAAAGAAGAAGGCgtaagttttt ... aatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAAT
EST: gi|125028776|gb|EL101045.1|EL101045
EST:     TAGGAAGGGAGGAAAGAAGAAGGC                         TGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAAT
genomic: TAGGAAGGGAGGAAAGAAGAAGGCgtaagttttt ... aatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAAT
EST: gi|125261408|gb|EL275493.1|EL275493
EST:     GAAAAACAAGAGAATCTCTAAGGGTAGGAAGGGAGGAAAGAAGAAGGC                         TGTTGATCCTTTCT
genomic: GAAAAACAAGAGAATCTCTAAGGGTAGGAAGGGAGGAAAGAAGAAGGCgtaagttttt ... aatgttgcagTGTTGATCCTTTCT
EST: gi|125229013|gb|EL243098.1|EL243098
EST:     GAAAAACAAGAGAATCTCTAAGGGTAGGAAGGGAGGAAAGAAGAAGGC                         TGTTGATCCTTTCTCCAAGAAAGATTGGT
genomic: GAAAAACAAGAGAATCTCTAAGGGTAGGAAGGGAGGAAAGAAGAAGGCgtaagttttt ... aatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGT
EST: gi|124910710|gb|EH984790.1|EH984790
EST:     TAGGAAGGGAGGAAAGAAGAAGGC                         TGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAAT
genomic: TAGGAAGGGAGGAAAGAAGAAGGCgtaagttttt ... aatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAAT
EST: gi|116425121|gb|EG467713.1|EG467713
EST:     GAAAAACAAGAGAATCTCTAAGGGTAGGAAGGGAGGAAAGAAGAAGGC                         TGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAAT
genomic: GAAAAACAAGAGAATCTCTAAGGGTAGGAAGGGAGGAAAGAAGAAGGCgtaagttttt ... aatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAAT
EST: gi|164176346|gb|ES132724.1|ES132724
EST:     GAAAAACAAGAGAATCTCTAAGGGTAGGAAGGGAGGAAAGAAGAAGGC                         TGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCA
genomic: GAAAAACAAGAGAATCTCTAAGGGTAGGAAGGGAGGAAAGAAGAAGGCgtaagttttt ... aatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCA
EST: gi|86033517|gb|DR329270.1|DR329270
EST:     GAAAAACAAGAGAATCTCTAAGGGTAGGAAGGGAGGAAAGAAGAAGGC                         TGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAAT
genomic: GAAAAACAAGAGAATCTCTAAGGGTAGGAAGGGAGGAAAGAAGAAGGCgtaagttttt ... aatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAAT
EST: gi|164229700|gb|EL972316.1|EL972316
EST:     GGAAAGAAGAAGGC                         TGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAAT
genomic: GGAAAGAAGAAGGCgtaagttttt ... aatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAAT
EST: gi|124748295|gb|EH838425.1|EH838425
EST:     CAAGAGAATCTCTAAGGGTAGGAAGGGAGGAAAGAAGAAGGC                         TGTTGATCCTT-CTCCAAGAA
genomic: CAAGAGAATCTCTAAGGGTAGGAAGGGAGGAAAGAAGAAGGCgtaagttttt ... aatgttgcagTGTTGATCCTTTCTCCAAGAA
EST: gi|124767912|gb|EH858042.1|EH858042
EST:     AAGGGAGGAAAGAAGAAGGC                         TGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAAT
genomic: AAGGGAGGAAAGAAGAAGGCgtaagttttt ... aatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAAT
EST: gi|124939240|gb|EL015798.1|EL015798
EST:     TAGGAAGGGAGGAAAGAAGAAGGC                         TGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAAT
genomic: TAGGAAGGGAGGAAAGAAGAAGGCgtaagttttt ... aatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAAT
EST: gi|163986870|gb|ES114624.1|ES114624
EST:     CTAAGGGTAGGAAGGGAGGAAAGAAGAAGGC                         TGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAAT
genomic: CTAAGGGTAGGAAGGGAGGAAAGAAGAAGGCgtaagttttt ... aatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAAT
EST: gi|124866020|gb|EH950457.1|EH950457
EST:     GAAAAACAAGAGAATCTCTAAGGGTAGGAAGGGAGGAAAGAAGAAGGC                         TGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGG
genomic: GAAAAACAAGAGAATCTCTAAGGGTAGGAAGGGAGGAAAGAAGAAGGCgtaagttttt ... aatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGG
EST: gi|124921374|gb|EH994997.1|EH994997
EST:     GGGAAAAACAAGAGAATCTCTAAGGGTAGGAAGGGAGGAAAGAAGAAGGC                         TGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAAT
genomic: GGGAAAAACAAGAGAATCTCTAAGGGTAGGAAGGGAGGAAAGAAGAAGGCgtaagttttt ... aatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgaatcttatcatttgtgattgattggttgtttttgaaaattgaatgttgcagTGTTGATCCTTTCTCCAAGAAAGATTGGTATGATGTTAAGGCTCCTTCAATCTTCACTCACAGGAATGTTGGAAAGACACTTGTTTCCAGAACTCAGGGT
                   gattgat  putative branch site (score: 4)
                                tttttgaaaattgaat  TA-rich tract