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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatagcacattggttcttgttaaattttgatgttgaaaactttttacctttttgcttacaattttaacttaacttgcagATTACACATACACTTTCTGTCTCACTCAATAAAATAGGAGATCTAAAATATTATGACGAAGATCTACAAGCTGCAAGGTCGTATTATGATAGAGCTTTAA

Basic information

species Arabidopsis thaliana
transcript AT3G54360.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G54360.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G47010.1 (Glycine max), 3'ss of exon 5
--------gttatagcacattggttcttgttaaattttgatgttgaaaactttttaccttttt---gcttacaattttaacttaact----tgcagATTACACATACACTTTCTGTCTCACTCAATAAAATAGGAGATCTAAAATATTATGACGAAGATCTACAAGCTGCAAGGTCGTATTATGATAGAGCTTTAA
        | | |   | |||      ||  ||||  | ||    | | | ||||   ||||      |||    || || || | |    | |||||||| |||||||||||||| ||||| || ||||| |||||||| ||||||||||| ||||| || ||||||||||| || || |||  || | |||| |
gttatttcgcttttctagattatggagtgaaaaatcataattgcaacatcatttttttttttgtcaatttatttcttgaaatttattttcctacagATTACCCATACACTTTCTGTTTCACTTAACAAAATTGGAGATCTTAAATATTATGATGAAGACCTTCAAGCTGCAAGATCTTACTATTTTAAATCTTTGA

upper sequence: AT3G54360.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G15130.1 (Glycine max), 3'ss of exon 5
-------------------gttatagcacattggttcttgttaaattttgatgttgaaaactt-tttacctttttgcttacaattttaacttaactt---------gcagATTACACATACACTTTCTGTCTCACTCAATAAAATAGGAGATCTAAAATATTATGACGAAGATCTACAAGCTGCAAGGTCGTATTATGATAGAGCTTTAA
                   | | |   | | |      ||  ||||  | ||    | | |   |||   | |||| |  | ||||   ||| ||||          |||||||| |||||||||||||| || || || ||||| |||||||| |||||||| || | ||| || ||||||||||| || || |||  || | |||| |
gttatttcattggaaccttgcttttttagactacggagtgaaaaatcataattgcaacatcacgtttttttgtttgttctctatttattcttgacttttttgtcccacagATTACCCATACACTTTCTGTTTCTCTTAACAAAATTGGAGATCTTAAATATTACGATGGAGACCTTCAAGCTGCAAGATCTTACTATTTTAAATCTTTGA

upper sequence: AT3G54360.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv13s0047g00170.t01 (Vitis vinifera), 3'ss of exon 5
----------------------gttatagcacattggttcttgttaaattttgatgttgaaaactttttacctttttgcttacaattttaacttaacttgcagATTACACATACACTTTCTGTCTCACTCAATAAAATAGGAGATCTAAAATATTATGACGAAGATCTACAAGCTGCAAGGTCGTATTATGATAGAGCTTTAA
                      |  ||| |  ||   || |||   || | ||    | |    |||  |||||||| |        |||| ||  ||  ||||| |||||||| ||||||||||||||||||||||| |||||||| ||||||||||| |  || ||  |||||||||| || || |||     | ||||  
gttactgcttcataaccattaaggcatatcctatacatttttggataaatgtggccctaattgttttgaaccttttttccc-----cttaatttctct-acagATCACACATACCCTTTCTGTCTCACTCAATAAAATTGGAGATCTCAAATATTATGATGGGGACCTTGAAGCTGCAAGATCTTACTATTCCCAATCTTTGG

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|124954039|gb|EL029170.1|EL029170
EST:     TTGAAGAGAGTGTTGAATTCCTTATGAAACTGCCGTTGAATGATTTGGAG                         ATTACACATACACTTTCTGTCTCAC
genomic: TTGAAGAGAGTGTTGAATTCCTTATGAAACTGCCGTTGAATGATTTGGAGgttatagcac ... taacttgcagATTACACATACACTTTCTGTCTCAC
EST: gi|125017748|gb|EL090017.1|EL090017
EST:     TTGAAGAGAGTGTTGAATTCCTTATGAAACTGCCGTTGAATGATTTGGAG                         ATTACACATACACTTTCTGTCTCACTCAATAAAA
genomic: TTGAAGAGAGTGTTGAATTCCTTATGAAACTGCCGTTGAATGATTTGGAGgttatagcac ... taacttgcagATTACACATACACTTTCTGTCTCACTCAATAAAA
EST: gi|86077534|gb|DR373291.1|DR373291
EST:     TTGAAGAGAGTGTTGAATTCCTTATGAAACTGCCGTTGAATGATTTGGAG                         ATTACACATACACTTTCTGTCTCACTCAATAAAATAGGAGATCTAAAATAT
genomic: TTGAAGAGAGTGTTGAATTCCTTATGAAACTGCCGTTGAATGATTTGGAGgttatagcac ... taacttgcagATTACACATACACTTTCTGTCTCACTCAATAAAATAGGAGATCTAAAATAT
EST: gi|124868755|gb|EH953192.1|EH953192
EST:     AATGATTTGGAG                         ATTACACATACACTTTCTCGTCTCACTCAATAAAATAGGAGATCTAAAAT
genomic: AATGATTTGGAGgttatagcac ... taacttgcagATTACACATACACTTTCT-GTCTCACTCAATAAAATAGGAGATCTAAAAT
EST: gi|125015836|gb|EL088105.1|EL088105
EST:     TTGAAGAGAGTGTTGAATTCCTTATGAAACTGCCGTTGAATGATTTGGAG                         ATTACACATACACTTTCTGTCTCACTCAATAAAAATAGGAGATCTAAAA
genomic: TTGAAGAGAGTGTTGAATTCCTTATGAAACTGCCGTTGAATGATTTGGAGgttatagcac ... taacttgcagATTACACATACACTTTCTGTCTCACTCAATAAAA-TAGGAGATCTAAAA
EST: gi|125037061|gb|EL109330.1|EL109330
EST:     TTGAAGAGAGTGTTGAATTCCTTATGAAACTGCCGTTGAATGATTTGGAG                         ATTACACATACACTTTCTGTCTCACTCAATAAAA
genomic: TTGAAGAGAGTGTTGAATTCCTTATGAAACTGCCGTTGAATGATTTGGAGgttatagcac ... taacttgcagATTACACATACACTTTCTGTCTCACTCAATAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgatgttgaaaactttttacctttttgcttacaattttaacttaacttgcagATTACACATACACTTTCTGTCTCACTCAATAAAATAGGAGATCTAAAATATTATGACGAAGATCTACAAGCTGCAAGGTCGTATTATGATAGAGCTTTAA
                               ttacaattttaactta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatagcacattggttcttgttaaattttgatgttgaaaactttttacctttttgcttacaattttaacttaacttgcagATTACACATACACTTTCTGTCTCACTCAATAAAATAGGAGATCTAAAATATTATGACGAAGATCTACAAGCTGCAAGGTCGTATTATGATAGAGCTTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT