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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgcgaccatccaatccccaccctctcttaaggaatcacggtatctctgtaaccattgatttatctttgttcttgcagACTACATACGAGAATTTCCGATACAGATATGATCGGCGAAGCAACCCACATAACAAGGGAGTGGTTAATAACTTCAAAGAAACATTTTTTTCCACAATCC

Basic information

species Arabidopsis thaliana
transcript AT3G26935.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G26935.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G05670.2 (Glycine max), 3'ss of exon 4
gtatgttgcgaccatcc-aatccccaccctctcttaaggaatcacggtatctctgtaaccattgatttatctttgttcttgcagACTACATACGAGAATTTCCGATACAGATATGATCGGCGAAGCAACCCACATAACAAGGGAGTGGTTAATAACTTCAAAGAAACATTTTTTTCCACAATCC
||| |    |  | |   ||||| ||  ||||    ||   |   | | | |       |||   |    | || ||||||||||||||||| || || ||| ||||| ||||||||||||||  ||| ||| |||| || |||||| | ||||| |||||||| | ||| |    ||  ||  
gtaagccctgttcgttttaatccacatgctct----agcttttcagatgtatacagcttcatatttgctccattattcttgcagACTACATATGAAAACTTCAGATACCGATATGATCGGCGAGCCAATCCATATAATAAAGGAGTGTTGAATAATTTCAAAGAGATATTCTGCATCAGCATTT

upper sequence: AT3G26935.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G27160.1 (Glycine max), 3'ss of exon 4
gtatgttgcgaccatcc-aatccccaccctctcttaaggaatcacggtatctctgtaaccattgatttatctttgttcttgcagACTACATACGAGAATTTCCGATACAGATATGATCGGCGAAGCAACCCACATAACAAGGGAGTGGTTAATAACTTCAAAGAAACATTTTTTTCCACAATCC
||| |    |  | |   ||||| ||  ||||    ||   |   | | | | ||    |||   |    | || ||||||||||||||||| || || ||| ||||| ||||||||||||||  ||||||| ||||  | |||||| | ||||| |||||||| | ||| |    ||  || |
gtaagcacagttctttttaatccgcatgctct----agctgttcagatgtatatggcttcatatttgctccattattcttgcagACTACATATGAAAACTTCAGATACCGATATGATCGGCGAGCCAACCCATATAATGAAGGAGTGTTGAATAATTTCAAAGAGATATTCTGCATCAGCATTC

upper sequence: AT3G26935.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G07190.1 (Glycine max), 3'ss of exon 4
-------------------------gtatgttgcgaccatccaatccccacc---ctctcttaaggaatcacggtatctctgtaaccattgatttatctttgttcttgcagACTACATACGAGAATTTCCGATACAGATATGATCGGCGAAGCAACCCACATAACAAGGGAGTGGTTAATAACTTCAAAGAAACATTTTTTTCCACAATCC
                          |||  |   |  ||  ||     | |   || || ||  | |     | | || | ||    |   || ||   ||||    ||||||||||| ||||| ||| ||||| |||||||||| ||   ||||||  |||||||||||||| | ||||| |||  ||| | ||| |   |||  || |
gtaatcattcctttttaaaatctttatatagtagtataatttaaagttaagctatctatcctacaggactt--gcaactttatatttgt--gttcattactgtt---acagACTACATATGAGAACTTCAGATACCGATATGATCGACGGGCCAACCCGTATAACAAGGGAGTGTTCAATAATTTCTTAGAGATATTCTGCACCAGCATTC

upper sequence: AT3G26935.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 4
------------------gtatgttgcgaccatccaatccccaccctctcttaaggaatcacgg-tatctctgtaaccattgatttatctt---tgttcttgcagACTACATACGAGAATTTCCGATACAGATATGATCGGCGAAGCAACCCACATAACAAGGGAGTGGTTAATAACTTCAAAGAAACATTTTTTTCCACAATCC
                    ||| |  ||   |  |  |   |   |   | ||   ||   |  || |     ||   |   | | | ||   |  | ||||||||||| || ||||||||| ||||| |||||||||| |||  ||||||  | ||||| ||||||||  | |||||||| || | |||||   |||  ||  
gtaacgggctcatcttcctaatgctatgattctgtagccgaaattttaggtcaaaatattgtgcctaacagcagaattttccttctctattccattcttttgcagACTACCTATGAGAATTTCAGATACCGATATGATCGACGAGCCAACCCCTACAACAAAGGAGTGGTGCAGAACTTCAAGGAGATATTTTGCACCAGCATTT

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|125107188|gb|EL160577.1|EL160577
EST:     TGTTGGTGGCTTAACAGTTTTCCATTTATATCTTCATCAGCACGAACCAG                         ACTACATACGAGAATTTCCGATACAGATATGATCGGCGAAGCAACCCACA
genomic: TGTTGGTGGCTTAACAGTTTTCCATTTATATC-TCATCAGCACGAACCAGgtatgttgcg ... gttcttgcagACTACATACGAGAATTTCCGATACAGATATGATCGGCGAAGCAACCCACA
EST: gi|164140224|gb|ES066599.1|ES066599
EST:     TTGTTGGTGGCTTAACAGTTTTCCATTTATATCTCATCAGCACGAACCAG                         ACTACATACGAGAATTTCCG
genomic: TTGTTGGTGGCTTAACAGTTTTCCATTTATATCTCATCAGCACGAACCAGgtatgttgcg ... gttcttgcagACTACATACGAGAATTTCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcttaaggaatcacggtatctctgtaaccattgatttatctttgttcttgcagACTACATACGAGAATTTCCGATACAGATATGATCGGCGAAGCAACCCACATAACAAGGGAGTGGTTAATAACTTCAAAGAAACATTTTTTTCCACAATCC
                                    tttatctttgttctt  CT-rich tract
                               attgatttatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgcgaccatccaatccccaccctctcttaaggaatcacggtatctctgtaaccattgatttatctttgttcttgcagACTACATACGAGAATTTCCGATACAGATATGATCGGCGAAGCAACCCACATAACAAGGGAGTGGTTAATAACTTCAAAGAAACATTTTTTTCCACAATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA