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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaactttggaacatttgcgctctgcattttttagacttttgatttgatgcttttgacaatgtttttctggtttgtttggtggtttttcagCGGTAATGATTGCTGCTCAAAGTATCCAGTTAGGGATCAATGATGTAGTTGTGGCGGGTGGTATGGAAAGCATGTCTAATACACCAAAATATTTGGCAGA

Basic information

species Arabidopsis thaliana
transcript AT5G48230.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G48230.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 4
gtgagaactt-tggaacatttgcgctctgcattttttagacttttgatttgatgcttttgacaatgtttttctggtttgtttggtggtttttcagCGGTAATGATTGCTGCTCAAAGTATCCAGTTAGGGATCAATGATGTAGTTGTGGCGGGTGGTATGGAAAGCATGTCTAATACACCAAAATATTTGGCAGA
|| | |  |  ||   ||    |  |||  |  || |   |     |||  ||     |||  |||   || |  ||| |||  |  || | |||||  |||| |||| || ||    || |  || || ||||||||| | ||||| || ||||| |||||||||||||||||| | ||||||||  | || ||
gttacagttcatgaggcagc--ctttctataaattctgttcaagaaattatatttacctgatcatgggcttgtt-tttatttcct--ttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGA

upper sequence: AT5G48230.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 4
-------------------------gtgagaact-ttggaacatttgc-gctctgcattttttagacttttgatttg---atgcttttg-acaatgtttttctggtt--tgtttggtggtttttcagCGGTAATGATTGCTGCTCAAAGTATCCAGTTAGGGATCAATGATGTAGTTGTGGCGGGTGGTATGGAAAGCATGTCTAATACACCAAAATATTTGGCAGA
                         ||  | |   |||      |||| | ||    ||||||| || | |||  ||   | |  | ||   |   | |  |   ||  | | ||     | | ||||    ||| | || || ||    || ||| | || ||||||||| | |||||||| ||||| |||||||||||||| ||| | ||||| ||  | || ||
gtctgaagctaattcatctatccatgtttgtataattgatctgcttgctgttcattgttttttacacatgtgaagtgttcaggtgtgtgtgtatcatctgaccaattactctctgcacactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTGTGGCAGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGA

upper sequence: AT5G48230.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 4
gtgagaact---ttggaacatttgcgctc-tgcatttt--ttagactttt--gatttgatgcttttgacaatgtttttctggtttgtttggtggtttttcagCGGTAATGATTGCTGCTCAAAGTATCCAGTTAGGGATCAATGATGTAGTTGTGGCGGGTGGTATGGAAAGCATGTCTAATACACCAAAATATTTGGCAGA
||  |||     ||      | ||  ||  || | | |  | ||| ||    ||  |||    ||     |   |  ||| ||||   |      | | ||||    ||| |||| || ||    || || || || ||||||||| | |||||||| ||||| |||||||||||||| ||| | ||||| ||  | || ||
gtttgaatcgaatttatctgtctgtccttgtgtactctgctcagagttcacagaagtgagagattacctgaccatgctcttgttttcctttcctatatgcagCTACTATGTTTGCAGCACAGTCAATTCAATTGGGTATCAATGATATTGTTGTGGCTGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGA

upper sequence: AT5G48230.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G830250_T01 (Zea mays), 3'ss of exon 2
gtgagaactttggaacatttgcgctctgcatttttt------agacttttgatttgatgcttttgacaatgtttttctggtttgtttggtggtttttcagCGGTAATGATTGCTGCTCAAAGTATCCAGTTAGGGATCAATGATGTAGTTGTGGCGGGTGGTATGGAAAGCATGTCTAATACACCAAAATATTTGGCAGA
                             ||  | |      ||      ||  |||    ||     ||  |  || || || | |      | | ||||    ||| |||| || ||    || ||  | || ||||||||| | |||||||| ||||| |||||||||||||| ||| | ||||| ||  | || ||
nnnnnnnnnnnnnnnnnnnnnnnnnnnnaatactctgctcacaggtcgcagaagtgacagattatctgatcatgctcaggcttttctttcctatatgcagCTACTATGTTTGCAGCACAGTCAATTCAACTGGGTATCAATGATATTGTTGTGGCAGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGA

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|116435447|gb|EG478039.1|EG478039
EST:     CTCTGTTATCTGTACTACAGTTAACAAGGTTTGTGCATCAGGCATGAAAG                         CGGTAATGATTGCTGCTCAAAGTATCCAGTTAGGGATCAATGATGTAGTTG
genomic: CTCTGTTATCTGTACTACAGTTAACAAGGTTTGTGCATCAGGCATGAAAGgtgagaactt ... ggtttttcagCGGTAATGATTGCTGCTCAAAGTATCCAGTTAGGGATCAATGATGTAGTTG
EST: gi|116435458|gb|EG478050.1|EG478050
EST:     CTCTGTTATCTGTACTACAGTTAACAAGGTTTGTGCATCAGGCATGAAAG                         CGGTAATGATTGCTGCTCAAAGTATCCAGTTAGGGATCAATGATGTAGTTG
genomic: CTCTGTTATCTGTACTACAGTTAACAAGGTTTGTGCATCAGGCATGAAAGgtgagaactt ... ggtttttcagCGGTAATGATTGCTGCTCAAAGTATCCAGTTAGGGATCAATGATGTAGTTG
EST: gi|164031831|gb|ES018068.1|ES018068
EST:     CTCTGTTATCTGTACTACAGTTAACAAGGTTTGTGCATCAGGCATGAAAG                         CGGTAATGATTGCTGCTCAAAGT
genomic: CTCTGTTATCTGTACTACAGTTAACAAGGTTTGTGCATCAGGCATGAAAGgtgagaactt ... ggtttttcagCGGTAATGATTGCTGCTCAAAGT
EST: gi|116435448|gb|EG478040.1|EG478040
EST:     CTCTGTTATCTGTACTACAGTTAACAAGGTTTGTGCATCAGGCATGAAAG                         CGGTAATGATTGCTGCTCAAAGTATCCAGTTAGGGATCAATGATGTAGTTG
genomic: CTCTGTTATCTGTACTACAGTTAACAAGGTTTGTGCATCAGGCATGAAAGgtgagaactt ... ggtttttcagCGGTAATGATTGCTGCTCAAAGTATCCAGTTAGGGATCAATGATGTAGTTG
EST: gi|116435459|gb|EG478051.1|EG478051
EST:     CTCTGTTATCTGTACTACAGTTAACAAGGTTTGTGCATCAGGCATGAAAG                         CGGTAATGATTGCTGCTCAAAGTATCCAGTTAGGGATCAATGATGTAGTTG
genomic: CTCTGTTATCTGTACTACAGTTAACAAGGTTTGTGCATCAGGCATGAAAGgtgagaactt ... ggtttttcagCGGTAATGATTGCTGCTCAAAGTATCCAGTTAGGGATCAATGATGTAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttgatttgatgcttttgacaatgtttttctggtttgtttggtggtttttcagCGGTAATGATTGCTGCTCAAAGTATCCAGTTAGGGATCAATGATGTAGTTGTGGCGGGTGGTATGGAAAGCATGTCTAATACACCAAAATATTTGGCAGA
               ttttgac  putative branch site (score: 3)
                                               tttttc  putative PPT
                      aatgttttt  TA-rich tract