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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtatctcattagctgaaaggttttgtttttttttttttttactgtatgttcgctgatttttttcttttctcattatagTCACTTAGCAGAATGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATCCGGGAAAATGATATCCTATACTTTGTGTTTGAGTACATG

Basic information

species Arabidopsis thaliana
transcript AT5G45430.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G45430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g02555.1 (Oryza sativa), 3'ss of exon 3
gtactgtatctcattagctgaaa--ggttttgtttttttttttttttactgtatgttcgctgatttttttcttttct---cattatagTCACTTAGCAGAATGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATCCGGGAAAATGATATCCTATACTTTGTGTTTGAGTACATG
|| || |||      |  || ||     |||| |  |  | | | |||   |   ||     |||||||| || | |   |||   ||||  |  | || ||||| ||||| ||||||||||| || |||||||||||  |||| ||||||||  ||| |||||| ||||| ||||||
gtgctttattatgcaacatgtaatcaagtttgatcatgatatctattatacttcattaatatattttttttttgtgtgcgcatcccagTCTTTGCGAAGGATGAACCATCCGAACATTGTGAAACTCAAGGAAGTCATAAGGGAGAATGATATGTTATTCTTTGTTTTTGAATACATG

upper sequence: AT5G45430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 6
gtactgtatctcattagctgaaaggttttgtttttttttttttttactgtatgttcgctgatttttttc----ttttctcattatagTCACTTAGCAGAATGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATCCGGGAAAATGATATCCTATACTTTGTGTTTGAGTACATG
     |||| | |  | | |  | ||||| || |  ||   | |||   | | |   ||||  ||| |     || | |  ||  ||||  |  |  | ||||||||||| |||||||||||||| || || || ||||| |||||||||||  |||||||  |  | || ||||||
-----gtattttag-accagcgatgtttttttatcattccctgttatgttctttcaactgacatttcttgttattattttgttgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATG

upper sequence: AT5G45430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 7
gtactgtatctcattagctgaaaggttttgtttttttttttttttactgtatgtt--cgctgatttttttcttttctcattatagTCACTTAGCAGAATGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATCCGGGAAAATGATATCCTATACTTTGTGTTTGAGTACATG
||| | ||   || | | ||     |||    || | | |||| | || |  | |     |  |||| || || | | |||  ||||  |  |  | ||||||||||| |||||||||||||| || || || ||| |||||||||||||  |||||||  |  | || ||||||
gtattttagaccagtgg-tgttctttttatcattctctgttttgttctttcagctgatatttcttttattgttattttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATG

upper sequence: AT5G45430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S479_13V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------------------------gtactgtatctcattagctgaaaggttttgttttttttt---ttttttactgtatgttcgctgatttttttcttttctcat------tat-agTCACTTAGCAGAATGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATCCGGGAAAATGATATCCTATACTTTGTGTTTGAGTACATG
                                                              ||   |||| | | |  |    | |||        ||||   ||||||    | ||   || |||| |||  |   |  ||      | | |||| || || |   ||||||||||||| ||||||||| ||||||| || ||| | ||||| |||   ||||  |||||||| |||||||||
gtatgttatccttagttcgagtgcgaactggtctttgagaaggcgtccgtgcggttttcaccgtttagtatgtaagtctcaacgatgttcaaccagcttttggattttttgaattttgcatgccgattatttgatcggcgaatgtggtttgtcagTCTCTGAGGAAGCTGAATCATCCAAATATTGTGAAGTTGAAGGAGGTTATCAGAGAAAACGATGAACTATTTTTTGTGTTCGAGTACATG

upper sequence: AT5G45430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S173_136V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------gtactgtatctcatta-gctgaaaggttttgttttttttttttt---ttactgtatgttcgctgatttttttcttttc-------tcattatagTCA-------CTTAGCAGAA--TGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATCCGGGAAAATGATATCCTATACTTTGTGTTTGAGTACATG
                                | ||||||   |||  | ||  |||| || ||| |  ||  ||         | |||  || | |  |     |            ||| | ||         ||| || |||  |||||||||| ||||| |||||||||||||| || ||||| ||||| |||   || |  || || |||||||| |||
gtatgaatccggcatattcgtacacaatttgatcctgtataaaattctggtgggaggtattctttgtggttgcttggccggtcatttgtgggcaggtgctccaagtgctaaaacagcaattgtggttttaacagTCTTTGCGGAAGCTGAATCATCCTAACATCGTGAAGCTGAAGGAGGTTATCCGTGAAAACGATGAACTGTTTTTCGTTTTTGAGTATATG

upper sequence: AT5G45430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S34_221V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------gtactgtatctcattagctgaaaggttttgtttttttttt-----tttttactgt-atgttcgctgatttttttcttttctcattatagTCACTTAGCAGAATGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATCCGGGAAAATGATATCCTATACTTTGTGTTTGAGTACATG
                                                       |  ||   ||    || |    |  |||| ||| |  |||     | || | ||  |||| |    |        | |  |  | | |||| ||  | |   |||| || || |||||||||||| |||||||||||||||| ||||| |||   || |  ||||| || ||||| |||
gtaaagatttgccattttcgtttgcatataggtcatcgagaatttctatgcggaaggtcttcgtcgagatatccttgacattttatttatcctttacaaatcttgattgagatgtgcctcaaaaaacagttgtggttttgacagTCTCTGCGAAAGTTGAAGCACCCCAACATTGTGAAGTTGAAGGAAGTCATCCGAGAAAACGATGAACTTTTTTTTGTTTTCGAGTATATG

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|86059416|gb|DR355173.1|DR355173
EST:     AGAAGAAGTATTTCTCTTGGGAAGAGTGTGTGAATCTAAGAGAAGTGAAG                         TCACTTAGCAGAATGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATC
genomic: AGAAGAAGTATTTCTCTTGGGAAGAGTGTGTGAATCTAAGAGAAGTGAAGgtactgtatc ... ctcattatagTCACTTAGCAGAATGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATC
EST: gi|116444408|gb|EG487000.1|EG487000
EST:     AGAAGAAGTATTTCTCTTGGGAAGAGTGTGTGAATCTAAGAGAAGTGAAG                         TCACTTAGCAGAATGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATC
genomic: AGAAGAAGTATTTCTCTTGGGAAGAGTGTGTGAATCTAAGAGAAGTGAAGgtactgtatc ... ctcattatagTCACTTAGCAGAATGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATC
EST: gi|116444419|gb|EG487011.1|EG487011
EST:     AGAAGAAGTATTTCTCTTGGGAAGAGTGTGTGAATCTAAGAGAAGTGAAG                         TCACTTAGCAGAATGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATC
genomic: AGAAGAAGTATTTCTCTTGGGAAGAGTGTGTGAATCTAAGAGAAGTGAAGgtactgtatc ... ctcattatagTCACTTAGCAGAATGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATC
EST: gi|124802491|gb|EH891330.1|EH891330
EST:     AGAAGAAGTATTTCTCTTGGGAAGAGTGTGTGAATCTAAGAGAAGTGAAG                         TCACTTAGCAGAA
genomic: AGAAGAAGTATTTCTCTTGGGAAGAGTGTGTGAATCTAAGAGAAGTGAAGgtactgtatc ... ctcattatagTCACTTAGCAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttttttttttttttactgtatgttcgctgatttttttcttttctcattatagTCACTTAGCAGAATGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATCCGGGAAAATGATATCCTATACTTTGTGTTTGAGTACATG
                           cgctgat  putative branch site (score: 4)
                         ttcgctgatttttttc  CT-rich tract
     ttttttttttttactg  TA-rich tract