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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattatccactaggaagtgctccttgtaatactatcacaacaaaaacagtttatttgaggttctttgatgaagttttacattagtagatttcgggtacatcgttacagctatctatcttgcagGTAACTCAGCTTGATCTACACCGTTACTTCCATGCTCTTGGCGCTGGAGTTATTGAGGAGGTCCGTGTCCAACGAGACAAAGGCTTTGGTTTCGTGAGAT

Basic information

species Arabidopsis thaliana
transcript AT3G14100.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 10
gtacattatccactaggaagtgctccttgtaa-tactatcacaacaaaaacagtttatttgaggttctttgatgaagttttacattagtagatttcgggtacatcgttacagctatctatcttgcagGTAACTCAGCTTGATCTACACCGTTACTTCCATGCTCTTGGCGCTGGAGTTATTGAGGAGGTCCGTGTCCAACGAGACAAAGGCTTTGGTTTCGTGAGAT
                    |    ||| |   || |||    ||     |  | | |||    ||||      |   ||    ||   |  ||     | |||  | ||   |    |||   ||||||||||| |||||||| || ||  |||||||||||||||| |||||||| || |||||||| || ||||| || || ||||| |||||||| ||||| |
-------------------ttatctcttttggctattatgtatacttgtgcgttatgttttgaattctgcagcaa---ttcctgttgccatttt----attcattatgacctttggtaatcc-acagGTAACTCAACTTGATCTCCATCGCCACTTCCATGCTCTTGGGGCTGGAGTGATGGAGGAGGTTCGGGTCCAGCGTGATAAAGGGTTTGGTTTTGTGAGGT

upper sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 10
gtacattatccactaggaagtgctccttgtaatactatcacaacaaaaacagtttatttgaggttctttgatgaagtttt-----acattagtagatttcgggtacatcgttacagctatctatcttgcagGTAACTCAGCTTGATCTACACCGTTACTTCCATGCTCTTGGCGCTGGAGTTATTGAGGAGGTCCGTGTCCAACGAGACAAAGGCTTTGGTTTCGTGAGAT
                            ||| ||  || |  |   | ||   || |  |  ||| | |  |||| |||      |  |   | |  ||    | |||  | ||   | | ||     |||| |||||| |||||||| || |   |||||||| ||||||| |||||||| ||||||||||| |||||||| || || ||||| |||||||| ||||| |
----------------------------gtagtagaataattatgtatac---ttgtgcgtagttatgttttgaattttgcagcaatttctattgcctttttattcattatgacctttttgtaatccacagGCAACTCAACTTGATCTCCATCACCACTTCCATTCTCTTGGAGCTGGAGTGATTGAGGAGGTTCGTGTCCAGCGTGATAAAGGGTTTGGTTTTGTGAGGT

upper sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 10
gtacattatccactaggaagtgctccttgtaatactatcacaacaaaaacagtttatttgaggttctttgatgaagttttacattagtagatttcgggtacatcgttacagct-atctatcttgcagGTAACTCAGCTTGATCTACACCGTTACTTCCATGCTCTTGGCGCTGGAGTTATTGAGGAGGTCCGTGTCCAACGAGACAAAGGCTTTGGTTTCGTGAGAT
             ||||||    | |    || | | || |     |     ||||||||    | | || |   ||||  |||      |  | | | | ||| ||   | | ||||    ||||||| || ||||||||||| || ||| |||| ||| || |||| ||||| || |||||||| || || || |||||||| || ||||||||||| || ||||
------------gtaggaaacaattcgccaaaaattttccctttttactttatttatttg----tttatgctttggtttggcatctcattaacttgtgaaaatcctttttgttcatctgctatgcagGTGACACAGCTTGATCTCCATCGTCACTTTCATACTTTTGGTGCTGGGGTAATTGAGGAAGTTCGGGTTCAACGAGATAAGGGCTTTGGTTTTGTTAGAT

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|125221069|gb|EL235154.1|EL235154
EST:     AAAATAATTCTCAGTTTACCACTGTTTATGTGGGAAACCTTGCTCCAGAG                         GTAACTCAGCTTGATCTACACCGTTACTTCCATGCTCTTGGCGCTGGAGTT
genomic: AAAATAATTCTCAGTTTACCACTGTTTATGTGGGAAACCTTGCTCCAGAGgtacattatc ... tatcttgcagGTAACTCAGCTTGATCTACACCGTTACTTCCATGCTCTTGGCGCTGGAGTT
EST: gi|116378429|gb|EG421021.1|EG421021
EST:     AAAATAATTCTCAGTTTACCACTGTTTATGTGGGAAACCTTGCTCCAGAG                         GTAACTCAGCTTGATCTACACCGTTACTTCCATGCTCTTGGCGCTGGAGTT
genomic: AAAATAATTCTCAGTTTACCACTGTTTATGTGGGAAACCTTGCTCCAGAGgtacattatc ... tatcttgcagGTAACTCAGCTTGATCTACACCGTTACTTCCATGCTCTTGGCGCTGGAGTT
EST: gi|125001990|gb|EL074259.1|EL074259
EST:     TCTCAGTTTACCACTGTTTATGTGGGAAACCTTGTCTCCAGAG                         GTAACTCAGCTTGATCTACACCGTT-CTTCCATGCTCTTGGCGCTGGAGT
genomic: TCTCAGTTTACCACTGTTTATGTGGGAAACCTTG-CTCCAGAGgtacattatc ... tatcttgcagGTAACTCAGCTTGATCTACACCGTTACTTCCATGCTCTTGGCGCTGGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaagttttacattagtagatttcgggtacatcgttacagctatctatcttgcagGTAACTCAGCTTGATCTACACCGTTACTTCCATGCTCTTGGCGCTGGAGTTATTGAGGAGGTCCGTGTCCAACGAGACAAAGGCTTTGGTTTCGTGAGAT
                                           tctatctt  CT-rich tract
     ttttacatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacattatccactaggaagtgctccttgtaatactatcacaacaaaaacagtttatttgaggttctttgatgaagttttacattagtagatttcgggtacatcgttacagctatctatcttgcagGTAACTCAGCTTGATCTACACCGTTACTTCCATGCTCTTGGCGCTGGAGTTATTGAGGAGGTCCGTGTCCAACGAGACAAAGGCTTTGGTTTCGTGAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG