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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaacgcagaacccttaaatctctttactttttgatagaaatgcaactttcctactggcatgcttgttataatctggggtacggcttcttctctaatcacatgcattgttaattttaccagCCTGAATGGATGGCTCCAGAAGTTCTACGCAATGAGCCCTCAAATGAAAA

Basic information

species Arabidopsis thaliana
transcript AT1G08720.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA10G30070.1 (Glycine max), 3'ss of exon 11
gtgagaacgcagaacccttaaatctctttactttttgatagaaatgcaactttcctactggcatgcttgt-tataatctggggtacggcttcttctctaatcacatgcattgttaattttaccagCCTGAATGGATGGCTCCAGAAGTTCTACGCAATGAGCCCTCAAATGAAAA
        | ||||      ||  |||||  | ||   |||         ||    ||  ||| || ||| | | |||||   | |  |||| | || | | |||||  |   | | | |   |||| |||||||||||||| |||||||| |||||||||||||||||||| ||
------gtg-agaatttgagaaaatctttgttattctgtagctcatttgtttaggcacatgca-gcatgtgtctgatctgcatttct-cttcatttc-actgacatgattctgtcaatatgttagCCGGAATGGATGGCTCCTGAAGTTCTCCGCAATGAGCCCTCAAATGAGAA

upper sequence: AT1G08720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 11
gtgagaacgcagaacccttaaatctctttactttttgatagaaatgcaactttcctactggcatgcttgttataatctggggtacggcttcttctctaatcacatgcattgttaattttaccagCCTGAATGGATGGCTCCAGAAGTTCTACGCAATGAGCCCTCAAATGAAAA
|||||||      |     || ||| | |  || |     | | ||||  ||   ||    |||||    | |  ||||   | |    ||| |  |   |  |     | |||    |   |||| |||||||||||||| |||||||| |||||||| ||||||||||| ||
gtgagaatatgaga-----aagtctttgttattct-----gtagtgca-tttgtttagacacatgcagcatgtg-tctgatctgcattctctacattccactgacatgattttatcaatgttagCCGGAATGGATGGCTCCTGAAGTTCTCCGCAATGAACCCTCAAATGAGAA

upper sequence: AT1G08720.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv14s0030g01440.t01 (Vitis vinifera), 3'ss of exon 10
----------------------------gtgagaacgcagaacccttaaatctctttactttttgatagaaatgcaactttcctact-ggcatgcttgttataatctggggtacggcttcttctctaatcacatgcattgttaat-------tttaccagCCTGAATGGATGGCTCCAGAAGTTCTACGCAATGAGCCCTCAAATGAAAA
                             |||  | |       ||| | | |||||    |   ||  | |   |||  ||| ||| |       |||  | |||| |  | |  || | | |||       | |||  || |        |||   ||||||| |||||||| ||||||||||| ||||||||    |||||||| ||
gtgagaatctgagacttgcattcaagaattgattatgttactatctttattttctttttcatactatttacaaagaacaatccaacttgatgaatatgtcttgatcttgctttctactccatttctgcatctcttcatgatttaagtttctgtttgttagCCTGAGTGGATGGCCCCAGAAGTTCTCCGCAATGAAAATTCAAATGAGAA

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|116426459|gb|EG469051.1|EG469051
EST:     CTCGCTTAAAGCACAATACTTTTTTATCCTCCAAATCAACTGCTGGAACG                         CCTGAATGGATGGCTCCAGAAGTTCTACGCAATGAGCCCTCAAATGAAAA
genomic: CTCGCTTAAAGCACAATACTTTTTTATCCTCCAAATCAACTGCTGGAACGgtgagaacgc ... attttaccagCCTGAATGGATGGCTCCAGAAGTTCTACGCAATGAGCCCTCAAATGAAAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttataatctggggtacggcttcttctctaatcacatgcattgttaattttaccagCCTGAATGGATGGCTCCAGAAGTTCTACGCAATGAGCCCTCAAATGAAAA
                                        tgttaat  putative branch site (score: 3)
                                              ttttacc  CT-rich tract
                                      attgttaatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaacgcagaacccttaaatctctttactttttgatagaaatgcaactttcctactggcatgcttgttataatctggggtacggcttcttctctaatcacatgcattgttaattttaccagCCTGAATGGATGGCTCCAGAAGTTCTACGCAATGAGCCCTCAAATGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT