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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccaaaaacatgtcttaatagtaacatgtcttagtccaaatctttcgaaggggattttgtctatcccgttgaagttttcttagaaacaaaggagcatgcttcatttactactgatagaaatcgtgtttacagttgaaatctagtaagaaccttatggtcttccttttttatctttagACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAG

Basic information

species Arabidopsis thaliana
transcript AT3G01310.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 16
gtaccaaaaacatgtcttaatagtaacatgtcttagtccaaatctttcgaaggggattttgtctatcccgttgaagttttcttagaaacaaaggagcatgcttcatttactactgatagaaatcgtgtttacagttgaaatctagtaagaaccttatggtcttccttttttatctttagACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAG
                                                                         |  | | | ||  |  ||  |      |    |||       ||| |  |  | |    |     | | | | |  ||| ||||      | || | ||| |||||||||| ||| ||||| |||||||| || |||||  |||| |||||||| |||||||| |||||||||||||| ||||| |||
------------------------------------------------------------------------catttctacgtactagtaatagttgccaccagttttttagtctatatatgt-atatgctaatccagagttttgaattaactttat------ctttgtatatatttagACCAGATCGAGAAAGCGATAGTGAGGCTGAAGATGTTGAGCATGCTGAAAAGCTTCGTCAAGTTAAAGCAGTTCTTGAGGAG

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 12
gtaccaaaaacatgtcttaatagtaacatgtcttagtccaaatctttcgaaggggattttgtctatcccgttgaagttttcttagaaacaaaggagcatgcttcatttactactgatagaaatcgtgtttacagttgaaatctagtaagaaccttatggtcttccttttttatctttagACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAG
                                                                             |||||  | |  |        |||  |   |  |   |     |   || |    ||    | | | | |  ||| ||||      | || | ||| |||||||||| ||| |||||||||||||| || |||||  |||| |||||||| |||||||  |||||||||||||| ||||| |||
-------------------------------------------------------------------------gccatttctacgtactagtaatagttgccaccagttttttagtctatatgtgtatgctaagccagagttttgaattaactttat------ctttgtatatatttagACCAGATCGAGAAAGTGATAGTGAGGCTGAAGATGTTGAGCATGCTGAAAAGCTTCATCAAGTTAAAGCAGTTCTTGAGGAG

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 12
gtaccaaaaacatgtcttaatagtaacatgtcttagtccaaatctttcgaaggggattttgtctatcccgttgaagttttcttagaaacaaaggagcatgcttcatttactactgatagaaatcgtgtttacagttgaaatctagtaagaaccttatggtcttccttttttatctttagACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAG
                                                                      |||   ||    | |  |   |     |||  |  |      |||||    ||  | ||   | || ||   |  | | |    ||| | ||   | | |||| |  ||||||| ||| |||||||||||||| || ||||   | || || ||||| ||||| || ||||||||||| ||||||||||||
----------------------------------------------------------------------ttgccattcctgttggcaagtaattttatgggtttt------ctgatcagtatatttttattatttcaagggttttgaaataactatag-ctgtatatattatgt--agACCAGATCGAGAAAGTGATAGTGAGGCTGAAG---TCGAGCACGCTGAAAAGCTCCGTCAAGTTAAAGCTGTCCTTGAAGAG

upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 14
gtaccaaaaacatgtcttaatagtaacatgtcttagtccaaatctttcgaaggggattttgtctatcccgttgaagttttcttagaaacaaaggagcatgcttcatttac-tactgatagaaatcgtgtttacagttgaaatc--tagtaagaaccttatggtcttccttttttatctttagACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAG
                                                                             |  || | ||    |    ||   || |||| | || |||      || | |     | |   ||   |  | |  | || |||       ||  |  | |||||||| ||||| |||||||| ||||| |||||||| ||||| |||||||| || ||||| ||||||||||||||||||||||||
-----------------------------------------------------------------------------taactgaaaatggcaaacacacttttaatttgcatattgac-----tcttatgctaggatagcattaatgattatgaactaatgacaaaatttcatattatttagACCTGGTCGAGAAAGTGACAGTGAAGCAGAAGATCTTGAGCATGCTGAAAAACTTCGTCAAGTTAAAGCAGTCCTTGAAGAG

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|19874907|gb|AU235738.1|AU235738
EST:     CAGTTGCAAGATCTATTAGATGCCACAAGAATGTTAGTTCCCCGTACAAG                         ACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAA
genomic: CAGTTGCAAGATCTATTAGATGCCACAAGAATGTTAGTTCCCCGTACAAGgtaccaaaaa ... ttatctttagACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtttacagttgaaatctagtaagaaccttatggtcttccttttttatctttagACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAG
                                tggtcttcctttttta  CT-rich tract
                                         ttttttatcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccaaaaacatgtcttaatagtaacatgtcttagtccaaatctttcgaaggggattttgtctatcccgttgaagttttcttagaaacaaaggagcatgcttcatttactactgatagaaatcgtgtttacagttgaaatctagtaagaaccttatggtcttccttttttatctttagACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA