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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtgcttaagtttgattctgcaaataattttttttttttttgtcaaacattctgcaatttaatctatgttatgaaagtgtacattgactaagattttgaggtgttatacaatgtagACAGTTGAAGCTGAACGGATATCAGTTGATCATGTTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGT

Basic information

species Arabidopsis thaliana
transcript AT5G56280.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os08g39070.1 (Oryza sativa), 3'ss of exon 4
gtctgtgcttaagtttgattctgcaaataattttttttttttttgtcaaacattctgca-atttaatctatgttatgaaagtgtacattgactaagattttgaggtgttatacaatgtagACAGTTGAAGCTGAACGGATATCAGTTGATCATGTTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGT
                           || ||||||| || | |||    | || | || |  |||| | ||||| ||              |||  ||   | || | ||  ||   |||| || || || ||  ||||||| |||||||||||||| ||||| ||||||||||| || ||||| || || || || |
-------------------------gttagtttttttcttgtgtgtgttgctttttccataaataatttttgttaagac------------ttaacgttagtacgtttgatttaa---agACTGTAGAGGCAGAGAGGATATCTGTTGATCATGTTGCCCATCTCAAACCATCTGATGGTGGCTCTGCGGCGACTCAAT

upper sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G028089_T01 (Zea mays), 3'ss of exon 4
gtctgtgcttaagtttgattctgcaaataattttttttttttttgtcaaacattctgcaatttaatctatgttatgaaagtgtacattgactaagattttgaggtgttatacaatgtagACAGTTGAAGCTGAACGGATATCAGTTGATCATGTTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGT
                      | || || ||    || | |||||| |||  | |    |||  |||                       ||| ||||  | |  | ||| ||    ||| || || |||||  ||||||| || || |||||||| ||||| ||||||||||| || || ||||||||||| ||||
----------------------gtaagtatttccccttctgtttgtctaactatatattgttttttct-----------------------taacatttgtatgcttgataaaa----gACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGT

upper sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G080652_T01 (Zea mays), 3'ss of exon 4
gtctgtgcttaagtttgattctgcaaataattttttttttttttgtcaaacattctgcaatttaatctatgttatgaaagtgtacattgactaagattttgaggtgttatacaatgtagACAGTTGAAGCTGAACGGATATCAGTTGATCATGTTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGT
                      | || |        || | |||||| | |  | |   ||||  |  |  |||     || | | ||||  ||                       |||| || || |||||  ||||||| || || |||||||| ||||| ||||| ||||| || |||||||||||||| ||||
----------------------gtaagtgtccccccttgtgtttgtctagctatatatgatttttttaacatta-----gtatgc-ttgatcaa-----------------------agACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCTTCTGATGGTGGCTCAGCAGCAACTCAGT

upper sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 4
gtctgtgcttaagtttgattctgcaaataattttttttttttttg--tcaaacattctgcaatttaatctatgttatgaaagtgtacattgactaagattttgaggtgttatacaatgtagACAGTTGAAGCTGAACGGATATCAGTTGATCATGTTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGT
            ||| |||| |   | |  || | |   ||||    |   | ||       | |||  ||  | ||  |  || |         |   |        |  |    || |||| |||||||| |||||||||||||||||||||||||| |||||||| |||||||| || || ||||| || || || |
------------gttggattttatgacttcttctatcccttttcacattttaaatcactgtttctaaattaattgattgacttggattcccttctatcctcctcctcttgctttgctgaagACTGTTGAAGCAGAACGGATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT

upper sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 4
gtctgtgcttaagtttgattctgcaaataattttttttttttttgtcaaacattctgcaatttaatctatgttatgaaagtgtacattgactaagattttgaggtgttatacaatgtagACAGTTGAAGCTGAACGGATATCAGTTGATCATGTTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGT
   || | || |  |   |||||| |    ||||    ||||   |||    |||| ||||| |||  ||    |   | |      |  ||      |     || | | |  || |||| |||||||| ||||| |||||||||||||||||||| |||||||| |||||||| || || ||||| || || || |
-gttgggtttta--tgacttctgctatcccttttcacattttaaatcactgtttct-caatt-aattgattcacttggattcccttctctctccctcctca---tgctttgc--tgaagACTGTTGAAGCAGAACGAATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAAT

upper sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 4
gtctgtgcttaagtttgattctgcaaataattttttttttttttgtcaaacattctgcaatttaatctatgttatgaaagtgtacattgactaagattttgaggtgttatacaatgtagACAGTTGAAGCTGAACGGATATCAGTTGATCATGTTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGT
                     | | | |   | || |||||||| | || |||      |||| | ||||         | ||| | ||| | |  ||||   || | | |       ||| || ||||| ||| |||| ||||||||||||||||| ||||||||||||||||| ||||| || || ||||| || |
--------------------gttcgacttgctcttctttttttt-ttaatcat------atttcacctatcaccaactggggta-actgaattattttttcttgtttcaaa-------gACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAAT

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|86054010|gb|DR349767.1|DR349767
EST:     TTGATGGAATCCCGCAGCTAATTTTCGCTCATACAAGCTACACAATCGAG                         ACAGTTGAAGCTGAACGGATATCAGTTGATCATGTTGCACATCTTAAACCA
genomic: TTGATGGAATCCCGCAGCTAATTTTCGCTCATACAAGCTACACAATCGAGgtctgtgctt ... tacaatgtagACAGTTGAAGCTGAACGGATATCAGTTGATCATGTTGCACATCTTAAACCA
EST: gi|19876192|gb|AU237023.1|AU237023
EST:     TTGATGGAATCCCGCAGCTAATTTTCGCTCATACAAGCTACACAATCGAG                         ACAGTTGAAGCTGAACGGATATCAGTTGATCATGTTGCACATCTTAAACCA
genomic: TTGATGGAATCCCGCAGCTAATTTTCGCTCATACAAGCTACACAATCGAGgtctgtgctt ... tacaatgtagACAGTTGAAGCTGAACGGATATCAGTTGATCATGTTGCACATCTTAAACCA
EST: gi|86054006|gb|DR349763.1|DR349763
EST:     TTGATGGAATCCCGCAGCTAATTTTCGCTCATACAAGCTACACAATCGAG                         ACAGTTGAAGCTGAACGGATATCAGTTGATCANNNTGCACATCTTAAACCA
genomic: TTGATGGAATCCCGCAGCTAATTTTCGCTCATACAAGCTACACAATCGAGgtctgtgctt ... tacaatgtagACAGTTGAAGCTGAACGGATATCAGTTGATCATGTTGCACATCTTAAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctatgttatgaaagtgtacattgactaagattttgaggtgttatacaatgtagACAGTTGAAGCTGAACGGATATCAGTTGATCATGTTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGT
                    cattgac  putative branch site (score: 3)
                           taagatttt  TA-rich tract