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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctttgattgtttgcattctagattcctgatattaggctcagtttgtatgtgatggtagtgatttttgcagagtcctaattcgttcttcacatgcagTGAATACATTATTGATTTAATGGGTGCTCCGGGTGCTCTGATCCCTTCTGAGGTTCCAAGCAGTTTTCTTCCAGTTTCTTGCACAGATACAAGAGTATTT

Basic information

species Arabidopsis thaliana
transcript AT5G11850.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G11850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G34730.1 (Glycine max), 3'ss of exon 3
gtattctttgattgtttgcattctagattcctgatattaggctcagtttgtatgtgatggt--agtgattttt-gcagagtc-ctaattcgttcttcacatgcagTGAATACATTATTGATTTAATGGGTGCTCCGGGTGCTCTGATCCCTTCTGAGGTTCCAAGCAGTTTTCTTCCAGTTTCTTGCACAGATACAAGAGTATTT
    | ||||  |  | || || | |||  |  | |    |  ||| |  ||  | ||| |  |   |||||  | |  ||   ||||| ||| | |  |||||||||||||||||||||| | ||||||||||| ||  |||| || ||| ||||||| || |||||    ||   |       |    | |   || |  | |
--catatttggctaatggcctttt-gataac--acaagcagtacaggtcttactttatgttgaaacaattttaagtactgttattaatttgttgtactgatgcagTGAATACATTATTGATATGATGGGTGCTCCTGGCACTCTTATACCTGCTGAGGTACCCAGCAGCCAGCTCGGAAACAACAGTTTTGCTGTTAGGGGTTGT

upper sequence: AT5G11850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G10790.2 (Glycine max), 3'ss of exon 3
gtattctttgattgtttgcattct-agattcctgatatta-ggctcagtttgtatgtgatggtagtgatttttgcagagtc-ctaattcgttcttcacatgcagTGAATACATTATTGATTTAATGGGTGCTCCGGGTGCTCTGATCCCTTCTGAGGTTCCAAGCAGTTTTCTTCCAGTTTCTTGCACAGATACAAGAGTATTT
    | ||||  |  | || || | | |  ||  | | ||  | ||    | |||||      | |  ||   | |  ||   ||||||||| | |  |||||| ||||||||||||||| | ||||||||||| ||  |||| || ||| ||||||| || |||||    |||  |       |    | |   || |  |  
--catatttggctaatggccttttgataacccaaacagtacaggtcttactttatgttggaacaat--ttcaagtattgttattaattcgttgtactgatgcagCGAATACATTATTGATATGATGGGTGCTCCTGGCACTCTAATTCCTGCTGAGGTACCCAGCAGCCAGCTTGGAAACAACAGTTTTGCTGTTAGGGGTTGC

upper sequence: AT5G11850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0008g01310.t01 (Vitis vinifera), 3'ss of exon 3
-gtattctttgattgtttgcattctagattcctgatattaggctcagtttgtatgtgatggtagtgatttttgcagagtcctaattcgttcttcaca-tgcagTGAATACATTATTGATTTAATGGGTGCTCCGGGTGCTCTGATCCCTTCTGAGGTTCCAAGCAGTTTTCTTCCAGTTTCTTGCACAGATACAAGAGTATTT
 || |  ||||||    |  | || |         |   ||  | |  || |   |      |   |  |    | | |   | |   ||    ||  ||||||||||| || |||||| |||||||||| ||||||||||| || ||| ||||||| || || |||  || || |  || | |   ||||  |||    | |
tgtctgttttgat---ctctaatcaaagcaatcattgagagcttaaagttttccatagaaacaaacaagtcataataatgagactgattttggaactctgcagTGAATATATAATTGATCTAATGGGTGCCCCGGGTGCTCTAATTCCTGCTGAGGTACCCAGTAGTCATCATCAAAATTTTGGACTAGATGTAAGGAGCTGT

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|116416001|gb|EG458593.1|EG458593
EST:     ACTGGAACTGATGATGGGGCTGTGAACTTGATTAAACTAGATGACAAAAG                         TGAATACATTATTGATTTAATGGGTGCTCCGGGTGCTCTGATCCCTTCTGA
genomic: ACTGGAACTGATGATGGGGCTGTGAACTTGATTAAACTAGATGACAAAAGgtattctttg ... tcacatgcagTGAATACATTATTGATTTAATGGGTGCTCCGGGTGCTCTGATCCCTTCTGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtatgtgatggtagtgatttttgcagagtcctaattcgttcttcacatgcagTGAATACATTATTGATTTAATGGGTGCTCCGGGTGCTCTGATCCCTTCTGAGGTTCCAAGCAGTTTTCTTCCAGTTTCTTGCACAGATACAAGAGTATTT
                               tcctaat  putative branch site (score: 2)
                                     ttcgttcttc  CT-rich tract
                 tgattttt  TA-rich tract