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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgagaaaaaatcaaaaattgaaacttttttactcagccctaagatctcatgtgttttctttgttgttgttgttaatctgattgtggattagATGTGGAGATGATGAAGGAGAGATTTGCAAAGTTGTTACTTGGTGAAGATATGTCAGGTTCTGGTAAAGGTGTGTGTACGGCTTTAGCTATCTCCAACGC

Basic information

species Arabidopsis thaliana
transcript AT5G05940.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G05940.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G41980.1 (Glycine max), 3'ss of exon 1
----gttagtgagaaaaaatcaaaaat-tgaaacttttttactcagccctaagatctcatgtgttttctttgttgttgttgttaatctgattgtggattagATGTGGAGATGATGAAGGAGAGATTTGCAAAGTTGTTACTTGGTGAAGATATGTCAGGTTCTGGTAAAGGTGTGTGTACGGCTTTAGCTATCTCCAACGC
     ||  |   || | || |||| | |     |  |    | ||   | ||   | || || ||  | | |   |  ||  ||  | ||  ||||| ||   | ||    |||||||| || |||||||| ||  | ||||| |||||||||||||| ||||| ||||| ||||| |  ||||| || ||||| || ||
gtttatttttctcaatacattaaaactatagtggtagtgggtttagttattagtatttatttggttgttgtctaactactgggaaa-taatgatggatcagGAATTGATGCAATGAAGGAAAGGTTTGCAAAATTACTGCTTGGGGAAGATATGTCAGGATCTGGGAAAGGAGTGTGCAGTGCTTTGGCCATCTCTAATGC

upper sequence: AT5G05940.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0019g02710.t01 (Vitis vinifera), 3'ss of exon 1
gttagtgagaaaaaatcaaaaattgaaacttttttactca------gccctaagatctcat-gtgttttctttgttgttgttgttaatctgattgtggattagATGTGGAGATGATGAAGGAGAGATTTGCAAAGTTGTTACTTGGTGAAGATATGTCAGGTTCTGGTAAAGGTGTGTGTACGGCTTTAGCTATCTCCAACGC
 | ||  |||     |   |  |       ||  ||||||      |   |   || |  |  | ||||||||||  |      |||    |   || |  |||  | ||||||||||||||||| ||| | ||  |||| ||||||||||| |||||||| ||||| ||||| || ||||| ||||| || || || || ||
-tcagatagatcctgtttgaggtctgccgattcatactcattagcggttttgtaatttagttatattttctttgtcttaaaaaataaaaaaa--atgaaacagAGATTGAGATGATGAAGGAGAGGTTTTCGAAACTGTTGCTTGGTGAAGACATGTCAGGGTCTGGAAAAGGGGTTTGTACAGCTTTGGCCATTTCAAATGC

upper sequence: AT5G05940.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S58_274V6.1 (Physcomitrella patens), 3'ss of exon 2
------gttagtgagaaaaaatcaaaaattgaaacttttt-tactcagccc-taagatctcatgtgttttctttgttgttgttgttaatctgattgtggattagATGTGGAGATGATGAAGGAGAGATTTGCAAAGTTGTTACTTGGTGAAGATATGTCAGGTTCTGGTAAAGGTGTGTGTACGGCTTTAGCTATCTCCAACGC
        || |       | |  |  ||  | |  |  | ||| | ||   |  |||    |    | | ||   || |  |||   |||| |  ||    ||| |||||||||||||||||||| ||||||||  | || |||||||||||||||||||||   || ||||| || || || || || ||||| || || ||
tgcattactattcgagtgcattttatgatgcatatgtcgtgtacacggctagtgtgatgctgtaatatgtgttgcctgattgtgtct-tctgttcttg---cagAGGTGGAGATGATGAAGGAGAGGTTTGCAAAACTATTGCTTGGTGAAGATATGTCAGGTGGGGGCAAAGGGGTTTGCACAGCGTTGGCTATATCGAATGC

upper sequence: AT5G05940.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S34_404V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------gttagtgagaaaaaatcaaaaattgaaacttttttactcagccctaagatctcatgtgttttctttgttgttgttgtt--aatctgattgtggattagATGTGGAGATGATGAAGGAGAGATTTGCAAAGTTGTTACTTGGTGAAGATATGTCAGGTTCTGGTAAAGGTGTGTGTACGGCTTTAGCTATCTCCAACGC
                                                         | | |   |    |||  |   || |     |||   ||    |    |   |  ||    |  |||  |   || |  || ||| |  |     ||| ||||||||||||||||||| |||||||||| |||| || || |||||||||||||||   |||||||| || || || || |||||||| || || ||
gtcggtaaacgttatcatcaaaacaaatttctccacaaattcaataagaaatttgactgaatttaagcgcatcgtatgatgcattggctttctccacgtttggactgatagatgcaagcgctgtgttaactgattgaacctgttgcttctacagAAGTGGAGATGATGAAGGAGAAATTTGCAAAGCTGTTGCTCGGGGAAGATATGTCAGGTGGGGGTAAAGGAGTTTGCACAGCATTAGCTATATCGAATGC

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|164228496|gb|ES088899.1|ES088899
EST:     AACCCTTCACGATGATTCTGGGTTTAAAGCGAAAGAGATGAATTCTGCAG                         ATGTGGAGATGATGAAGGAGAGATTTGCAAAGTTGTTACT
genomic: AACCCTTCACGATGATTCTGGGTTTAAAGCGAAAGAGATGAATTCTGCAGgttagtgaga ... tgtggattagATGTGGAGATGATGAAGGAGAGATTTGCAAAGTTGTTACT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctaagatctcatgtgttttctttgttgttgttgttaatctgattgtggattagATGTGGAGATGATGAAGGAGAGATTTGCAAAGTTGTTACTTGGTGAAGATATGTCAGGTTCTGGTAAAGGTGTGTGTACGGCTTTAGCTATCTCCAACGC
                 ttttcttt  TA-rich tract