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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctttgtacattggctgatatagtattcctgttttcatttggttaaaattttctttatggatgtcacagGCCGACAAATTGGAAAAACTAAGAGAAAGGATGGTTAAAGTTCGCGAGCTTTTCCGTGACACAGAGTCAACAGAATTCGTCATTGTCACTATCCCAACG

Basic information

species Arabidopsis thaliana
transcript AT3G10350.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G10350.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os02g51100.1 (Oryza sativa), 3'ss of exon 7
gtaagtctttg--tacattggct---gatatagtattcctgttttcatttggttaaaatttt--ctttatggatgtcac-----agGCCGACAAATTGGAAAAACTAAGAGAAAGGATGGTTAAAGTTCGCGAGCTTTTCCGTGACACAGAGTCAACAGAATTCGTCATTGTCACTATCCCAACG
|||||| ||||  || | |  ||    |  | || || || |   ||| |  |||||  |||   ||| |   | || |     ||||  ||||||||||  | || ||||||||||||||  |||| || || ||||| ||||||||||| ||||| |||||  | ||||| ||||| ||||| 
gtaagtatttgcctaaaattcctctgaacttggtgtttct-tcaccatgtctttaaacctttgaatttgttattctcccccttaagGCAAACAAATTGGAGCAGCTGAGAGAAAGGATGGTCCAAGTGCGAGAACTTTTTCGTGACACAGAATCAACTGAATTTATAATTGTGACTATTCCAACA

upper sequence: AT3G10350.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G105539_T01 (Zea mays), 3'ss of exon 7
--------------gtaagtctttgtacattggctgatatagtattcctgttttcatt-tggttaaaattttct---ttatggatgtc-----acagGCCGACAAATTGGAAAAACTAAGAGAAAGGATGGTTAAAGTTCGCGAGCTTTTCCGTGACACAGAGTCAACAGAATTCGTCATTGTCACTATCCCAACG
                 |||   |||  | |     | ||  |||  || | |||| |  |||| |||  ||||   ||||   | ||     | ||||  ||||||| ||  |||| |||||||||||||| |||||  | ||||||||||| ||||| || |||||||| ||  | || || || |||||||||
gtaggtgttttctgcccagttcctgtgaaatactgtacatcatatgtctttcttcactacggttcaaaccttctaacttatatttctcctcctaaagGCGAACAAATTAGAGCAACTCAGAGAAAGGATGGTCAAAGTAAGAGAGCTTTTCCGCGACACGGAATCAACAGAGTTTATAATCGTGACAATCCCAACG

upper sequence: AT3G10350.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G32200.1 (Glycine max), 3'ss of exon 8
gtaagtctttgtacattg-gctgatatagtattc---ctgttttcatttggttaaaattttctttatggatgtcac--agGCCGACAAATTGGAAAAACTAAGAGAAAGGATGGTTAAAGTTCGCGAGCTTTTCCGTGACACAGAGTCAACAGAATTCGTCATTGTCACTATCCCAACG
|||||  ||| | | | | | |  ||| |  ||     |  | | | ||| | |  ||||  | |||   | |     |||| ||||||||||| ||||| ||||| |||||| | ||||| ||||| || || ||||| || || || || ||||| |||||||| || ||||| |||
gtaaga-tttatgcctggagttagtattgcgtttagtttcatcttaattgttcaccatttattatatctttattgtgtagGCTGACAAATTGGAGAAACTCAGAGAGAGGATGATAAAAGTGCGCGAACTCTTTCGTGATACTGATTCGACCGAATTTGTCATTGTTACAATCCCCACG

upper sequence: AT3G10350.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv13s0019g04590.t01 (Vitis vinifera), 3'ss of exon 8
gtaagtctt-tgtacattg-gctgata-----tagtattcctgttttcatt--tggttaaaattttctttatggatgtcacagGCCGACAAATTGGAAAAACTAAGAGAAAGGATGGTTAAAGTTCGCGAGCTTTTCCGTGACACAGAGTCAACAGAATTCGTCATTGTCACTATCCCAACG
|||||| |  | |  || | |||| ||     |  | |||         |   |    || ||  | ||  |  ||     |||| |||||||| ||   |||||| || || ||||| ||||| || |||||||||||||||||||| || |||||||| ||||| || || ||||| |||
gtaagtttgatttgtatggagctggtaccctatgatgttctaaaaactgtcactaaccaatatacttttgcttcattatgtagGCTGACAAATTAGAGCGACTAAGGGAGAGAATGGTAAAAGTGCGGGAGCTTTTCCGTGACACAGACTCGACAGAATTTGTCATAGTAACAATCCCTACG

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|125321219|gb|EL335304.1|EL335304
EST:     CTTCAGCGATCAAATCAGTTTTTGGGAAAGAAGAAAAGGGGCCTGATGCT                         GCCGACAAATTGGAAAAACTAAGAGAAAGGATGGTTAAAGTTCGCGAGCTT
genomic: CTTCAGCGATCAAATCAGTTTTTGGGAAAGAAGAAAAGGGGCCTGATGCTgtaagtcttt ... gatgtcacagGCCGACAAATTGGAAAAACTAAGAGAAAGGATGGTTAAAGTTCGCGAGCTT
EST: gi|125077216|gb|EL140085.1|EL140085
EST:     CGATCAAATCAGTTTTTGGGAAAGAAGAAAAGGGGCCTGATGCT                         GCCGACAAATTGGAAAAACTAAGAGAAAGGATGGTTAAAGTTCGCGAGCTT
genomic: CGATCAAATCAGTTTTTGGGAAAGAAGAAAAGGGGCCTGATGCTgtaagtcttt ... gatgtcacagGCCGACAAATTGGAAAAACTAAGAGAAAGGATGGTTAAAGTTCGCGAGCTT
EST: gi|116412741|gb|EG455333.1|EG455333
EST:     CTTCAGCGATCAAATCAGTTTTTGGGAAAGAAGAAAAGGGGCCTGATGCT                         GCCGACAAATTGGAAAAACTAAGAGAAAGGATGGTTAAAGTTCGCGAGCTT
genomic: CTTCAGCGATCAAATCAGTTTTTGGGAAAGAAGAAAAGGGGCCTGATGCTgtaagtcttt ... gatgtcacagGCCGACAAATTGGAAAAACTAAGAGAAAGGATGGTTAAAGTTCGCGAGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatatagtattcctgttttcatttggttaaaattttctttatggatgtcacagGCCGACAAATTGGAAAAACTAAGAGAAAGGATGGTTAAAGTTCGCGAGCTTTTCCGTGACACAGAGTCAACAGAATTCGTCATTGTCACTATCCCAACG
 ggctgat  putative branch site (score: 4)
                 ttttcatttggttaaa  TA-rich tract