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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGTCACTCATGGAGAAAGCAAAGGCCAAAGGTGTCTCTCTCTTGCTCCCAACCGATGTGGTTATTGCTGACAAGTTTGCTCCCGATGCTAACAGCAAGgtaactatcacagtcattgtggttgactctcaatgggccatgtatgaaagtaaaacatttaagcgtctggtctggtctctttaaagctgacacatatgactcttgcag

Basic information

species Arabidopsis thaliana
transcript AT1G79550.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79550.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA08G17600.1 (Glycine max), 5'ss of exon 5
AAAGTCACTCATGGAGAAAGCAAAGGCCAAAGGTGTCTCTCTCTTGCTCCCAACCGATGTGGTTATTGCTGACAAGTTTGCTCCCGATGCTAACAGCAAGgtaactatcacagtcattgtggttgactct-caatgggccatgtatgaaagtaaaacatttaagcgtctggtctggtctctttaaagctgacacatatgactcttgcag
||   ||||  | || || || ||||| ||||| || ||| | ||||| ||||| |||||||| || || |||||||||||| | |||||||||||||||||| ||       |||||   ||||  | |       ||   || |    || || |||  ||     || |    | | | | ||    |  || | |    ||| | 
AACTACACTTCTCGAAAAGGCCAAGGCTAAAGGGGTTTCTTTGTTGCTTCCAACTGATGTGGTCATAGCAGACAAGTTTGCTGCTGATGCTAACAGCAAGgta-ctgcttt--tcattagagttgggtttatggaatgcttcgtttcttggtgaa-catacaaaaaattg-tgcattttatgtgaaa---atccaaaagcagattgga-

upper sequence: AT1G79550.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA15G41550.1 (Glycine max), 5'ss of exon 5
AAAGTCACTCATGGAGAAAGCAAAGGCCAAAGGTGTCTCTCTCTTGCTCCCAACCGATGTGGTTATTGCTGACAAGTTTGCTCCCGATGCTAACAGCAAGgtaactatcacagtcattgtggttgactctcaatgggccatgtatgaaagtaaaacatttaagcgtctggtctggtctctttaaagctgacacatatgactcttgcag
||   ||||  | || || || ||||| ||||| || ||| | ||||| ||||| ||||| || || || |||||||||||| | |||||||||||||||||| ||       |||||   ||||  | |  ||||   |||| ||    |        ||  |     ||   || | ||  | |   |  |  | |    ||| | 
AACTACACTTCTTGAAAAGGCCAAGGCTAAAGGGGTTTCTTTGTTGCTTCCAACTGATGTTGTCATAGCAGACAAGTTTGCTGCTGATGCTAACAGCAAGgta-ctgcttt--tcattagagttgggttt--atgga--atgtttggttctgcggtgagtatacaaaaagttgtgtattttatatgaaaatccgaaagcagattgga-

upper sequence: AT1G79550.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv19s0085g00370.t01 (Vitis vinifera), 5'ss of exon 4
AAAGTCACTCATGGAGAAAGCAAAGGCCAAAGGTGTCTCTCTCTTGCTCCCAACCGATGTGGTTATTGCTGACAAGTTTGCTCCCGATGCTAACAGCAAGgtaactatcacagtcattgtggttg------actctcaatgggccatgtatgaaagtaaaacatttaagcgtctggtctggtctctttaaagctgacacatatgactcttgcag-------------------------------
||  |||||  | || || || ||| ||||||||||||| ||  | |||||  | ||||| || |||||||||||||||||| | |||||||||||||||||   | |    ||| || |  |||      | | ||  ||  |||           |||| ||||          ||   |    |  |   ||| | || ||  |||   ||                               
AACTTCACTTCTTGAAAAGGCCAAGTCCAAAGGTGTCTCACTACTTCTCCCCGCAGATGTTGTGATTGCTGACAAGTTTGCTGCTGATGCTAACAGCAAGgtttgtttgcttgtccttctttttggaaaaaaatttccctgccccaaactctctcagaaaatattttcctcaactatccattgatatgtattatgata-atttgtttctgaaagggttaaaaacttctgttcaatgtttttgcag

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|86080490|gb|DR376247.1|DR376247
EST:     CAACCGATGTGGTTATTGCTGACAAGTTTGCTCCCGATGCTAACAGCAAG                         ATAGTGCCAGCCACTGCCATCCCTGATGGCTGGATGGGTCTAGATATTGGT
genomic: CAACCGATGTGGTTATTGCTGACAAGTTTGCTCCCGATGCTAACAGCAAGgtaactatca ... actcttgcagATAGTGCCAGCCACTGCCATCCCTGATGGCTGGATGGGTCTAGATATTGGT
EST: gi|164039457|gb|ES173249.1|ES173249
EST:     CAACCGATGTGGTTATTGCTGACAAGTTTGCTCCCGATGCTAACAGCAAG                         ATAGTGCCAGCCACTGCCA
genomic: CAACCGATGTGGTTATTGCTGACAAGTTTGCTCCCGATGCTAACAGCAAGgtaactatca ... actcttgcagATAGTGCCAGCCACTGCCA
EST: gi|164221077|gb|ES082155.1|ES082155
EST:     TTGCTGACAAGTTTGCTCCCGATGCTAACAGCAAG                         ATAGTGCCAGCCACTGCCATCCCTGATGGCTGGATGGGTCTAGATATTGGT
genomic: TTGCTGACAAGTTTGCTCCCGATGCTAACAGCAAGgtaactatca ... actcttgcagATAGTGCCAGCCACTGCCATCCCTGATGGCTGGATGGGTCTAGATATTGGT
EST: gi|116403251|gb|EG445843.1|EG445843
EST:     AACCCGATGTGGTTATTGCTGACAAGTTTGCTCCCGATGCTAACAGCAAG                         ATAGTGCCAGCCACTGCCATCCCTGAATGGCTGGATGGGTCTTAGATATTT
genomic: AACC-GATGTGGTTATTGCTGACAAGTTTGCTCCCGATGCTAACAGCAAGgtaactatca ... actcttgcagATAGTGCCAGCCACTGCCATCCCTGA-TGGCTGGATGGGTCT-AGATATT-
EST: gi|47828962|gb|CK118646.1|CK118646
EST:     CAACCGATGTGGTTATTGCTGACAAGTTTGCTCCCGATGCTAACAGCAAG                         ATAGTGCCAGCCACTGCCATCCCTGATGGCTGGATGGGTCT
genomic: CAACCGATGTGGTTATTGCTGACAAGTTTGCTCCCGATGCTAACAGCAAGgtaactatca ... actcttgcagATAGTGCCAGCCACTGCCATCCCTGATGGCTGGATGGGTCT
EST: gi|164135048|gb|ES207229.1|ES207229
EST:     CAACCGATGTGGTTATTGCTGACAAGTTTGCTCCCGATGCTAACAGCAAG                         ATAGTGCCAGCCACTGCCATCCCTGATGGCTGGATGGGTC
genomic: CAACCGATGTGGTTATTGCTGACAAGTTTGCTCCCGATGCTAACAGCAAGgtaactatca ... actcttgcagATAGTGCCAGCCACTGCCATCCCTGATGGCTGGATGGGTC
EST: gi|47831638|gb|CK121322.1|CK121322
EST:     CAACCGATGTGGTTATTGCTGACAAGTTTGCTCCCGATGCTAACAGCAAG                         ATAGTGCCAGCCACTGCCATCCCTGATGGCTGGATGGGTCTAGATATTGGT
genomic: CAACCGATGTGGTTATTGCTGACAAGTTTGCTCCCGATGCTAACAGCAAGgtaactatca ... actcttgcagATAGTGCCAGCCACTGCCATCCCTGATGGCTGGATGGGTCTAGATATTGGT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGTCACTCATGGAGAAAGCAAAGGCCAAAGGTGTCTCTCTCTTGCTCCCAACCGATGTGGTTATTGCTGACAAGTTTGCTCCCGATGCTAACAGCAAGgtaactatcacagtcattgtggttgactctcaatgggccatgtatgaaagtaaaacatttaagcgtctggtctggtctctttaaagctgacacatatgactcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG