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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttttcatagctgttttataaaggttactggtttgtctatggagttatgtgaatgattcttatttctctctatggggtttggttttattttagGTTCATTCTAGGGGGAAGGCACTCGGTAAAGATGTGGACTTTGACAAGGTTGCCAGAAGGACCCCTGGTTTCACGGGTGCTGACTTACAAAACCTGATGA

Basic information

species Arabidopsis thaliana
transcript AT1G50250.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G50250.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G126361_T01 (Zea mays), 3'ss of exon 1
----gttcttttcatagctgttttataaaggttactggtttgtctatggagttatgtgaatgattcttatttctctctatggggtttggttttatt--ttagGTTCATTCTAGGGGGAAGGCACTCGGTAAAGATGTGGACTTTGACAAGGTTGCCAGAAGGACCCCTGGTTTCACGGGTGCTGACTTACAAAACCTGATGA
     |  | || | |   |   | | |   || |  || |    ||    || |     | ||   ||  |     ||   |  ||  ||||||    ||||| || ||  | || |||||  | |  |||||||| || ||||| ||  |||| |||||||||||||||||||| ||||||||| | |||||||| ||||
cacaatattatttaaaaaagaagtttgatttttcccagtatcctgatttcattttaaatgt-atgtatacatgagcttacaagtcttt-ttttatcaaatagGTCCACTCCCGAGGAAAGGCTTTGGCGAAAGATGTTGATTTTGATAAAATTGCTAGAAGGACCCCTGGTTTCACTGGTGCTGACCTCCAAAACCTCATGA

upper sequence: AT1G50250.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv18s0001g00190.t01 (Vitis vinifera), 3'ss of exon 1
-------gttcttttcatagctgttttataaaggttactggtttgtctatggagttatgtgaatgattcttatttctctctatggggtttggttttattttagGTTCATTCTAGGGGGAAGGCACTCGGTAAAGATGTGGACTTTGACAAGGTTGCCAGAAGGACCCCTGGTTTCACGGGTGCTGACTTACAAAACCTGATGA
         |   || ||    |||   | | | ||  ||||  |   |  |  |  | ||  ||||  |  || |   |  ||   |||   | |||   |||| || || || ||||||||||| |  || ||||| |||||||| ||| |||| ||||||||||| || ||||| || |||||||| || ||||||||||
gaatgaccatacatttatgaaagttcattgatgatttttggtcagagaagagtttcttttggctgataat-gttgcaaccattgatattt--ctgtatgacagGTGCACTCAAGAGGGAAGGCACTAGCCAAGGATGTAGACTTTGAAAAGATTGCGAGAAGGACCCCAGGCTTCACAGGGGCTGACTTGCAGAACCTGATGA

upper sequence: AT1G50250.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S10_192V6.2 (Physcomitrella patens), 3'ss of exon 1
----------------------------------------------------gttcttttcatagctgttttataaaggttactggtttgtctatggagttatgtgaatgattcttatttctctctatggggtttggttttat--tttagGTTCATTCTAGGGGGAAGGCACTCGGTAAAGATGTGGACTTTGACAAGGTTGCCAGAAGGACCCCTGGTTTCACGGGTGCTGACTTACAAAACCTGATGA
                                                     | | |||| |  | | |  ||    |    |     || |    |   || |   || |   || |  ||   || |  |||| | ||    |||||||||| ||| | || ||| || | |  || ||||| |||||||| ||| |||| || ||||| || || ||||| ||||| |||||||||||| ||||||
gtacttcccttggatttttctcagttgtactggtcctcttaccaaattttgcttgcctttcgtcac-gatgcatggttgaccttaaagcgtgttgaaaaccatttttgtgttcaatagtaatccagattgtctttgctcttcccctttagGTTCACTCTCGTGGTAAGACATTGGCCAAGGATGTCGACTTTGAGAAGATTGCAAGGAGGACGCCAGGGTTCACCGGTGCCGACTTACAAAACTTGATGA

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|116471288|gb|EG513880.1|EG513880
EST:     AGGTCACGGTGGATAGGCCTGATGTGGCTGGCAGAGTCAAGATTCTTCAG                         GTTCATTCTAGGGGGAAGGCACTCGGTAAAGATGTGGACTTTGACAAGGTT
genomic: AGGTCACGGTGGATAGGCCTGATGTGGCTGGCAGAGTCAAGATTCTTCAGgttcttttca ... tttattttagGTTCATTCTAGGGGGAAGGCACTCGGTAAAGATGTGGACTTTGACAAGGTT
EST: gi|124968756|gb|EL042692.1|EL042692
EST:     AGAGTCAAGATTCTTCAG                         GTTCATTCTAGGGGGAAGGCACTCGGTAAAGATGTGGACTTTGACAAGGTT
genomic: AGAGTCAAGATTCTTCAGgttcttttca ... tttattttagGTTCATTCTAGGGGGAAGGCACTCGGTAAAGATGTGGACTTTGACAAGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggagttatgtgaatgattcttatttctctctatggggtttggttttattttagGTTCATTCTAGGGGGAAGGCACTCGGTAAAGATGTGGACTTTGACAAGGTTGCCAGAAGGACCCCTGGTTTCACGGGTGCTGACTTACAAAACCTGATGA
                                            ttttatttt  CT-rich tract
                                       tttggttttatttta  TA-rich tract