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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattgtcttgaccacaaacatttttgagtgatttggtttcatatttaaccgcctttatcaactgtacaaaataccacatcagGTAATCACAAGAATATCTTCAATGATGCCAAAGTTCCGTGGTCCGAATACCGCTACTATGATCCAAAAACAATTGGTTTGGATTTTGAGGGAATGATAGC

Basic information

species Arabidopsis thaliana
transcript AT4G31990.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os02g55420.1 (Oryza sativa), 3'ss of exon 6
------------------gtacattgtctt-gaccaca-aacat--ttttgagtgatttggtttcatatttaaccgcctttatcaactgtacaaaataccacatcagGTAATCACAAGAATATCTTCAATGATGCCAAAGTTCCGTGGTCCGAATACCGCTACTATGATCCAAAAACAATTGGTTTGGATTTTGAGGGAATGATAGC
                  || | |  |||| || ||   ||| |  ||||   |      || ||  |||   |   ||||   ||||  |    |||      |||| ||||||||||| || ||||||||||| || || || ||||| || ||||| || || || || || ||  |||| |||||||||||||||||||||||
gtatgtatgtgaattaatgtgcttaatctttgagcattcaacttcatttttcatagcagagtgtctcatt-ggcaaactttg--aactccaatctatattcttacagGCAATCACAAGAACATTTTCAATGATGCAAAGGTACCTTGGTCAGAGTACCGTTATTACGACCCCAAGACTGTTGGCTTGGATTTTGAGGGAATGATAGC

upper sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 6
-------------------------------------------------------gtacattgtcttgaccacaaacatttttgagtga--tttg--gtttcatatttaaccgccttta---tcaactgtacaaaataccacatcagGTAATCACAAGAATATCTTCAATGATGCCAAAGTTCCGTGGTCCGAATACCGCTACTATGATCCAAAAACAATTGGTTTGGATTTTGAGGGAATGATAGC
                                                          ||| ||||||  | |  |   ||||  ||||  ||||  || ||| | |      | | ||   |||    | | |  |   |   ||||||| ||||||||||||||||||||||| |  || || ||||| || ||||| || ||||| || || ||  |||| |||||||||||||||||||||||
gtaagtatgttgatgcaactattcttcatgacttgatgtacctaccaaaatcatgactcatagtcttgggctctcattgtttttggtgaaatttgaagtgtcaaagtggcggacttctaatttcattcattctacttgttaa--cagGTAACCACAAGAATATCTTCAATGATGCTAGGGTACCTTGGTCAGAGTACCGGTATTATGACCCCAAGACTGTTGGGTTGGATTTTGAGGGAATGATAGC

upper sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA14G13480.2 (Glycine max), 3'ss of exon 6
gtacattgtcttgaccacaaacatttttgagt-gatttggtttcatatttaaccgcctttatcaactgtacaa-aataccacat--cagGTAATCACAAGAATATCTTCAATGATGCCAAAGTTCCGTGGTCCGAATACCGCTACTATGATCCAAAAACAATTGGTTTGGATTTTGAGGGAATGATAGC
    ||     ||||  |     |  || | | | |   | | | | |||    |     |    |||   || | ||     |  ||||||||||||||||||| ||||||||||| |  || || ||||| || ||||| || |||||||| || ||| |||| |||||||||||||| ||||||| 
--gtatgtatctgactgcttctctgcttaacttggtcgtgatacttgtttgggagttcaaacatcctgggtaacattattgtcttgcagGTAATCACAAGAATATTTTCAATGATGCTAGTGTCCCATGGTCTGAGTACCGATATTATGATCCCAAGACAGTTGGCTTGGATTTTGAGGGCATGATAGA

upper sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G33050.4 (Glycine max), 3'ss of exon 6
-------gtacattgtcttgaccacaaacatttttgagtgatttggtttcatatttaaccgcctttatcaactgtacaaaataccacatcagGTAATCACAAGAATATCTTCAATGATGCCAAAGTTCCGTGGTCCGAATACCGCTACTATGATCCAAAAACAATTGGTTTGGATTTTGAGGGAATGATAGC
        |  | ||  |     |  ||| |  | | |  ||||| |      || || |  |  |   |||  ||     |  |   | |||||||||||||||||| ||||||||||| |  || || ||||| || ||||| || |||||||| || ||| |||| |||||||||||||| ||||| | 
gtatgcattttactgcttccctgattaacttggtcgtgatatttgttagggagttcaaacatccctggtaacattat----tgtcttgt-agGTAATCACAAGAATATTTTCAATGATGCTAGTGTCCCATGGTCTGAGTACCGATATTATGATCCCAAGACAGTTGGGTTGGATTTTGAGGGCATGATTGA

upper sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv04s0008g06040.t01 (Vitis vinifera), 3'ss of exon 8
gtacattgtcttgaccacaaacatt-tttgagtgatttggtttcatatttaaccgcctttatcaactgtacaaaataccacatcagGTAATCACAAGAATATCTTCAATGATGCCAAAGTTCCGTGGTCCGAATACCGCTACTATGATCCAAAAACAATTGGTTTGGATTTTGAGGGAATGATAGC
           |||  |    | || |||| | |||||| | |||    ||      | |      || |  ||  | |    ||||||||||||||||||| ||||||||||| | |||||| ||||| |||||||| |||||||| ||||||||| |||| ||||||||||| || |||||| |
----------gtgagtattccccttgtttgggagatttg-tgtcaagagtactgatttctcatggttgaa-gaatcatctttgcagGTAATCACAAGAATATTTTCAATGATGCTAGAGTTCCCTGGTCTGAATACCGATACTATGACCCAAAAACAGTTGGCTTGGATTTTGATGGGATGATATC

upper sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S245_98V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------gtacattgtcttgaccacaaacatttttgagt-gatttggtttcatatttaaccgcctttatcaactgta-caaaataccacatcagGTAATCACAAGAATATCTTCAATGATGCCAAAGTTCCGTGGTCCGAATACCGCTACTATGATCCAAAAACAATTGGTTTGGATTTTGAGGGAATGATAGC
                                     ||  ||||  | ||   | | ||    | ||||    |  |  | ||   | |||      ||||  |  | || ||  |||||||||||||| || |||||||||||||||   ||||| |||   || ||||||||||  ||||| || ||  | || |||||||| || || ||||| | 
gtatggatcaaactccagtcgcatacaattcacccttatgttctttccaacgtgcttcttgatctagattctaatctaagtgtatttgtcttctatggctgtggcgcattaacatttcagGTAATCACAAAAACATCTTCAATGATGCCGGTGTTCCATGGAAAGAGTACCGCTACTTCGATCCTAAGACCGTAGGGTTGGATTTCGAAGGCATGATTGA

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|47828582|gb|CK118266.1|CK118266
EST:     AGAGCGTTATTTCCCTGGAGCAAAAGTTGTGATCTCATCACCAACCTGGG                         GTAATCACAAGAATATCTTCAATGATGCCAAAGTTCCGTGGTCCGAATACC
genomic: AGAGCGTTATTTCCCTGGAGCAAAAGTTGTGATCTCATCACCAACCTGGGgtacattgtc ... accacatcagGTAATCACAAGAATATCTTCAATGATGCCAAAGTTCCGTGGTCCGAATACC
EST: gi|125091382|gb|EL149205.1|EL149205
EST:     GCGTTATTTCCCTGGAGCAAAAGTTGTGATCTCATCACCAACCTGGG                         GTAATCACAAGAATATACTTCAATGATGCCAAAGTTCCGTGGTCCGAA
genomic: GCGTTATTTCCCTGGAGCAAAAGTTGTGATCTCATCACCAACCTGGGgtacattgtc ... accacatcagGTAATCACAAGAATAT-CTTCAATGATGCCAAAGTTCCGTGGTCCGAA
EST: gi|124928291|gb|EL005949.1|EL005949
EST:     AGAGCTTTATTTCCCTGGAGCAAAAGTTGTGATCTCATCACCAACCTGGG                         GTAATCACAAGAATATCTTCAATGATGCCAAAGTTCCGTGGTCCGAATACC
genomic: AGAGCGTTATTTCCCTGGAGCAAAAGTTGTGATCTCATCACCAACCTGGGgtacattgtc ... accacatcagGTAATCACAAGAATATCTTCAATGATGCCAAAGTTCCGTGGTCCGAATACC
EST: gi|164029105|gb|ES152243.1|ES152243
EST:     GTTGTTGATCTCATCACCAACCTGGG                         GTAATCACAAGAATATCTTCAATGATGCCAAAGTTCCGTGGTCCGAAATAC
genomic: GTTG-TGATCTCATCACCAACCTGGGgtacattgtc ... accacatcagGTAATCACAAGAATATCTTCAATGATGCCAAAGTTCCGTGGTCCGAA-TAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatttggtttcatatttaaccgcctttatcaactgtacaaaataccacatcagGTAATCACAAGAATATCTTCAATGATGCCAAAGTTCCGTGGTCCGAATACCGCTACTATGATCCAAAAACAATTGGTTTGGATTTTGAGGGAATGATAGC
               atttaac  putative branch site (score: 3)
         tttcatatttaa  TA-rich tract