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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttaatctatttatacttacaaatactatttcttagtttcatccatcttgttacatgtgtaatttggacaaacgttatgattgtttctttggtttctgtagATGGACGGCAGTGAGATTGTGTGTGAGGGTCCAAGATGCAGTCTTCGTAGTAAAAAG

Basic information

species Arabidopsis thaliana
transcript AT4G11960.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G11960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G14240.1 (Glycine max), 3'ss of exon 4
gttcttaatctatttatacttacaaatactatttct-tagtttcatccatcttgttacatgtgtaatttggacaaacgtta-tgattgtttctttggtttctgtagATGGACGGCAGTGAGATTGTGTGTGAGGGTCCAAGATGCAGTCTTCGTAGTAAAAAG
  | ||  || | | | | |    ||||| |||    | | || |   | ||   ||  |   |  ||     |    ||| ||||    |   || ||||   |||  || || ||||| ||||||  |||||||||||| |||||||||||||||||||||
--tattggtc-actgaaattagggaatacaattggaattgctttagt-agctgagtatctccctccttcttgtattatttactgatctcataactgttttcc--agAAAGAAGGGAGTGAAATTGTGGCTGAGGGTCCAAGGTGCAGTCTTCGTAGTAAAAAG

upper sequence: AT4G11960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0025g04710.t01 (Vitis vinifera), 3'ss of exon 4
gttcttaatctatttatacttacaaatactatttctta-gttt---catccatcttgttacatgtgtaatttggacaaacgttatgattgtttctttggtttctgtagATGGACGGCAGTGAGATTGTGTGTGAGGGTCCAAGATGCAGTCTTCGTAGTAAAAAG
    ||||| ||  |    | |    |  | |||| |  ||||   ||||||| |  || |   | | |||  |       || | ||   |  |||  ||| | ||||| || || ||||| |||||   ||||||||||||||||||||||||||||||||||
---gttaatttagct---ttcaagtttgttttttcctgtgtttggccatccatataattgctgctattattatgctt--tcttcttatccataattttctttttctagATTGAAGGAAGTGAAATTGTAGTTGAGGGTCCAAGATGCAGTCTTCGTAGTAAAAAG
















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|125013776|gb|EL086045.1|EL086045
EST:     AATGAAACTAAAG                         ATGGACGGCAGTGAGATTGTGTGT
genomic: AATGAAACTAAAGgttcttaatc ... gtttctgtagATGGACGGCAGTGAGATTGTGTGT
EST: gi|116378737|gb|EG421329.1|EG421329
EST:     ATCCAATCTTGAGTGATGAAGAGTATGATAAGCTCAAAATGAAACTAAAG                         ATGGACGGCAGTGAGATTGTGTGTGAGGGTCCAAGATGCAGTCTTCGTAGT
genomic: ATCCAATCTTGAGTGATGAAGAGTATGATAAGCTCAAAATGAAACTAAAGgttcttaatc ... gtttctgtagATGGACGGCAGTGAGATTGTGTGTGAGGGTCCAAGATGCAGTCTTCGTAGT
EST: gi|19877739|gb|AU238570.1|AU238570
EST:     ATCCAATCTTGAGTGATGAAGAGTATGATAAGCTCAAAATGAAACTAAAG                         ATGGACGGCAGTGAGATTGTGTGTGAGGGTCCAAGATGCAGTCTTCGTAGT
genomic: ATCCAATCTTGAGTGATGAAGAGTATGATAAGCTCAAAATGAAACTAAAGgttcttaatc ... gtttctgtagATGGACGGCAGTGAGATTGTGTGTGAGGGTCCAAGATGCAGTCTTCGTAGT
EST: gi|47831512|gb|CK121196.1|CK121196
EST:     ATCCAATCTTGAGTGATGAAGAGTATGATAAGCTCAAAATGAAACTAAAG                         ATGGACGGCAGTGAGATTGTGTGTGAGGGTCCAAGATGCAGTCTTCGTAGT
genomic: ATCCAATCTTGAGTGATGAAGAGTATGATAAGCTCAAAATGAAACTAAAGgttcttaatc ... gtttctgtagATGGACGGCAGTGAGATTGTGTGTGAGGGTCCAAGATGCAGTCTTCGTAGT
EST: gi|116378739|gb|EG421331.1|EG421331
EST:     ATCCAATCTTGAGTGATGAAGAGTATGATAAGCTCAAAATGAAACTAAAG                         ATGGACGGCAGTGAGATTGTGTGTGAGGGTCCAAGATGCAGTCTTCGTAGT
genomic: ATCCAATCTTGAGTGATGAAGAGTATGATAAGCTCAAAATGAAACTAAAGgttcttaatc ... gtttctgtagATGGACGGCAGTGAGATTGTGTGTGAGGGTCCAAGATGCAGTCTTCGTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgttacatgtgtaatttggacaaacgttatgattgtttctttggtttctgtagATGGACGGCAGTGAGATTGTGTGTGAGGGTCCAAGATGCAGTCTTCGTAGTAAAAAG
                                     tttctttggtttct  CT-rich tract
           tgtaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcttaatctatttatacttacaaatactatttcttagtttcatccatcttgttacatgtgtaatttggacaaacgttatgattgtttctttggtttctgtagATGGACGGCAGTGAGATTGTGTGTGAGGGTCCAAGATGCAGTCTTCGTAGTAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG