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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtccacacataacaacctgctgtgtttatgtttcttagatattcatgtcttcttgatcatttgccttaaccatactactcttgactcttttgaatcccttttgcgattttagTTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATATCCATATGAAGAAATTCTAAGGACCTTCCACAATCAGACCAGCATAGTCATGTGCTCAT

Basic information

species Arabidopsis thaliana
transcript AT5G49720.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G49720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g21210.1 (Oryza sativa), 3'ss of exon 3
gtcagtccacacataacaacctgctgtgtttatgtttcttagatattcatgtcttcttgatcatttgccttaaccatactactcttgactcttttgaatcccttttgcgattttagTTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATATCCATATGAAGAAATTCTAAGGACCTTCCACAATCAGACCAGCATAGTCATGTGCTCAT
          |   |  |    || ||   ||    |   | | || ||  |   |   || |   |  ||||| |||  | |    |||  ||| |      | ||  |||  || | || ||||||||||| ||| | ||  | |||||||| |||||||||||||| || || ||||| ||||||||||| || |||||  | |||||||| |
--------ggagggagtacatagcagtagctag---taaaaaaaatccagatgaaca-aataaacggatttaac-atatcaattggtacttatttta---tggtctgtcattacagGTTCTTTTGAGCCGGTTAAGGCTCTTCTTAAGTCCTGGTTATCCATATGAAGAGATCCTCAGGACATTCCACAATCAAACAAGCATTATTATGTGCTCTT

upper sequence: AT5G49720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G003379_T01 (Zea mays), 3'ss of exon 3
gtcagtccacacataacaacctgctgtgtttatgtttcttagatattcatgtcttcttgatcatt---tgccttaaccatactactcttgactcttttgaatcccttttgcgattttagTTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATATCCATATGAAGAAATTCTAAGGACCTTCCACAATCAGACCAGCATAGTCATGTGCTCAT
                    | | | | ||||   |   |||| | | |  | || || | | ||   || | ||    |  |||  |      | ||  ||   | || | |||| || | ||  | |||||||||||| | ||  ||||||||||||||||||||||||| |   | || || |||||||| || || |||||  ||||||| || |
----------------tgggccggtctctttaa--taaatagagagtaacattttgtttaccgttgagtgacatatttgtcttacagtacttattcttttatttgtgttac-atttcagGTTCTTCTAAGCCGGTTGAGGCTTTTCTTGAGTCCTGGATATCCATATGAAGAGACCTTGAGTACATTCCACAACCAAACTAGCATTATCATGTGTTCCT

upper sequence: AT5G49720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G099101_T01 (Zea mays), 3'ss of exon 3
gtcagtccacacataacaacctgctgtgtttatgtttcttagatattcatgtcttcttgatcatttgccttaaccatactactcttgactcttttgaatcccttttgcgattttagTTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATATCCATATGAAGAAATTCTAAGGACCTTCCACAATCAGACCAGCATAGTCATGTGCTCAT
 | | |  | | | |  | | |  ||| |   ||||   |  ||  |  |||         ||||||  |||     | ||||  |    | |||  ||   | || | |||  || | ||  | || ||||||||| | ||  | ||||||||||||||||| ||||| ||  | ||||| ||||||||||| || |||||  ||||||| || |
ataaatagagagaaagtagcattttgtttacttgttgagtgaatgatagtgt-------gacatttgtttta----cagtacttat----cctttttatttatcttac-attccagGTTCTTCTAAGTCGGTTGAGGCTTTTCTTAAGTCCTGGATATCCATACGAAGAGATCTTGAGGACGTTCCACAATCAAACTAGCATTATCATGTGTTCCT

upper sequence: AT5G49720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G02160.1 (Glycine max), 3'ss of exon 3
gtcagtccacacataacaacctgctgtgtttatgtttcttagatattcatg-tcttcttgatcat--ttgccttaaccatactactcttgactcttttgaatccctt--ttgcgattttagTTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATATCCATATGAAGAAATTCTAAGGACCTTCCACAATCAGACCAGCATAGTCATGTGCTCAT
                    ||    ||||  | ||  |     || |||| ||||   | | ||  |    |||   | | |||  ||||||  |||||      |  |   |  ||||| | ||  |||| || |||||||||||  |||||||||| |||||||||||||||||| | |||||||| ||||||||||| |||||| |||||||||| |
-------------------tctttgatgttcctattaat--atcatccatgatcttgcaggttatggtaattttagtgaaaatacatttgactgatttgatctttgtcatcttgtatttagGTTCTTCTGAGTCGTTTGAGGTTGTTCTTGAGTCCTGGGTATCCATATGAAGAAATTTTGAGGACCTTTCACAATCAGACAAGCATAATCATGTGCTCCT

upper sequence: AT5G49720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G00710.1 (Glycine max), 3'ss of exon 1
gtcagtccacacataacaacctgctgtgtttatgtttcttagatattcatgtcttcttga--tcatttgccttaaccatactactcttgactcttttgaatcccttttgcgattttagTTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATATCCATATGAAGAAATTCTAAGGACCTTCCACAATCAGACCAGCATAGTCATGTGCTCAT
                                           || ||     ||||| |  | |    |  ||| || |||| |||  |||  | |       |  |   ||||  ||| ||  | || || ||||||||||| || |||||||| ||||| |||||||||||| |||| || || |||||||||||| |||||||||||||||| |
------------------------------------------gtactctctatttcttcactttaccaacaataaacaaactattct--acttatctcctcttttcattttatttagGTT-CTTCTCAGTCGTTTGAGGTTGTTCCTCAGTCCTGGTTATCCCTATGAAGAAATTTTAAGCACATTTCACAATCAGACCGGCATAGTCATGTGCTCCT

upper sequence: AT5G49720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G40090.1 (Glycine max), 3'ss of exon 1
gtcagtccacacataacaacctgctgtgtttatgtttcttagatattcatgtcttcttgatcatttgccttaaccatactactcttgactcttttgaatcccttttgcgattttagTTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATATCCATATGAAGAAATTCTAAGGACCTTCCACAATCAGACCAGCATAGTCATGTGCTCAT
                              || |   |||  ||  |||  ||      ||  ||   ||| |    | |  || || ||  | |   |  ||| |     ||||| | ||  | || || ||||||||||| ||||||||||| | ||| |||||||| |||||||  || || |||||||||||  |||||||||||||||| |
-----------------------------gtacgcaccttcaattctcaattc-----aatttttaaacttcaagtcatt--tcatgtcttgtct---tgtcttcta----tttagGTTCTTCTCAGTCGTTTGAGGTTGTTCCTGAGTCCTGGTTTTCCCTATGAAGATATTCTAACCACATTTCACAATCAGACAGGCATAGTCATGTGCTCCT

upper sequence: AT5G49720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G13080.1 (Glycine max), 3'ss of exon 3
gtcagtccacacataacaacctgctgtgtttatgtttcttagatattcatgtct-tcttgatcatttgccttaaccatactactcttgactcttttgaatccctt--ttgcgattttagTTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATATCCATATGAAGAAATTCTAAGGACCTTCCACAATCAGACCAGCATAGTCATGTGCTCAT
             ||     ||| | |  ||||| ||  | | |  || ||  | |  || | ||||    ||   | | |||  ||||||  ||||| |    |  |   |  ||||| | ||  |||| || || ||||| ||  ||||||| || |||||||||||||||||| ||| |||||| ||||| ||||| |||||| |||||||||| |
-------------tataggtctggt-taattatgattgct-gctgatcttgcatgttatggtaattt----tagtgaaaatacatttgactgatttgatttttgtcatcttgtatttagGTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAAGAAATTTTAAAGACCTTTCACAACCAGACAAGCATAATCATGTGCTCCT

upper sequence: AT5G49720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv12s0035g02180.t01 (Vitis vinifera), 3'ss of exon 3
gtcagtccacacataacaacctgctgtgtttatgtttcttagatattcatgtcttcttgatcatttgccttaaccatactactcttgactcttttgaatcccttttgcgattttagTTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATATCCATATGAAGAAATTCTAAGGACCTTCCACAATCAGACCAGCATAGTCATGTGCTCAT
           |||    | |   |    ||    || ||   |      |||      | |   || ||    |||  | ||  |   |  |||   |   |||    |||  || ||||  | ||||| ||||| |||||  |||| ||||| |||||||||||||||||||| ||||| || |||||||| ||||||||| | ||||||||||
-------tttgcatgttgatcaaataaaattggaattattgtttgcaagagtca---aaaactcatggctggttcat--tgctgata--tgctttatgtttttttcttaatt--agGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCAT

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|47830557|gb|CK120241.1|CK120241
EST:     GCCCTTACTATGGTGTATTTAGCTGGGACAACAAGCTTGCTGGTGCTCAG                         TTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATATCCATATGAA
genomic: GCCCTTACTATGGTGTATTTAGCTGGGACAACAAGCTTGCTGGTGCTCAGgtcagtccac ... gcgattttagTTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATATCCATATGAA
EST: gi|116458640|gb|EG501232.1|EG501232
EST:     ATTTAGCTGGGACAACAAGCTTGCTGGTGCTCAG                         TTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATATCCATATGAA
genomic: ATTTAGCTGGGACAACAAGCTTGCTGGTGCTCAGgtcagtccac ... gcgattttagTTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATATCCATATGAA
EST: gi|47829810|gb|CK119494.1|CK119494
EST:     GCCCTTACTATGGTGTATTTAGCTGGGACAACAAGCTTGCTGGTGCTCAG                         TTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATATCCATATGAA
genomic: GCCCTTACTATGGTGTATTTAGCTGGGACAACAAGCTTGCTGGTGCTCAGgtcagtccac ... gcgattttagTTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATATCCATATGAA
EST: gi|125199251|gb|EL214205.1|EL214205
EST:     GCCCTTACTATGGTGTATTTAGCTGGGACAACAAGCTTGCTGGTGCTCAG                         TTGCTGTTGAGCCGGTTGAGG
genomic: GCCCTTACTATGGTGTATTTAGCTGGGACAACAAGCTTGCTGGTGCTCAGgtcagtccac ... gcgattttagTTGCTGTTGAGCCGGTTGAGG
EST: gi|124886086|gb|EH964988.1|EH964988
EST:     CAAGCTTGCTGGTGCTCAG                         TTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATAT
genomic: CAAGCTTGCTGGTGCTCAGgtcagtccac ... gcgattttagTTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATAT
EST: gi|124820925|gb|EH905791.1|EH905791
EST:     GCCCTTACTATGGTGTATTTAGCTGGGACAACAAGCTTGCTGGTGCTCAG                         TTGCTGTTGAGCCGG
genomic: GCCCTTACTATGGTGTATTTAGCTGGGACAACAAGCTTGCTGGTGCTCAGgtcagtccac ... gcgattttagTTGCTGTTGAGCCGG
EST: gi|125218290|gb|EL232373.1|EL232373
EST:     CCCTTACTATGGTGTATTTAGCTGGGACAACAAGCTTGCTGGTGCTCAG                         TTGCTGTTGAGCCGGTTGAGGTTGTTTACTGAGTCCTGGATATCCATATGA
genomic: CCCTTACTATGGTGTATTTAGCTGGGACAACAAGCTTGCTGGTGCTCAGgtcagtccac ... gcgattttagTTGCTGTTGAGCCGGTTGAGGTTGTTT-CTGAGTCCTGGATATCCATATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttgccttaaccatactactcttgactcttttgaatcccttttgcgattttagTTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATATCCATATGAAGAAATTCTAAGGACCTTCCACAATCAGACCAGCATAGTCATGTGCTCAT
                     tcttgac  putative branch site (score: 3)
                                     tcccttttgc  putative PPT
                              ttttgaat  TA-rich tract