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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtatgaatgcaataaattggctttattggtttattatgttattgacttctgagttctgagggattctgatttttctgtttctcaatgactctttgcagCTGCTGATGTGTTCTTGTGGAGGGATAAAAAACTATCAGGTGCTGTTCTTGGTGTCGCGACTGCTATTTGGGTTCTGTTCGAGCTGGTTGAGTATCATTT

Basic information

species Arabidopsis thaliana
transcript AT2G46170.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G46170.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G359018_T03 (Zea mays), 3'ss of exon 1
ttgtatgaatgcaataaattggctttattggtttattatgttattgacttctgagt-tctgagggatt--ctgatttttctgtttctcaatgactctttgcagCTGCTGATGTGTTCTTGTGGAGGGATAAAAAACTATCAGGTGCTGTTCTTGGTGTCGCGACTGCTATTTGGGTTCTGTTCGAGCTGGTTGAGTATCATTT
     ||| ||   |||  || |  |  ||    | |  |   |  |   ||||   ||||     ||  ||   ||     || |||        ||||||||||||||||||||| |||||||| | |  ||  | || |  |  || |||||||  || || || || ||| | || || ||  || |||  || ||| |
-gacttgattggtgtaa--tgtcaattgtgagacactgagacctaaatacctgatcgtctgtcattttacctaccttactcattactcttctctattttgcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTGGTGGAGCCACAGCAATCTGGATCCTATTTGAATTGCTTGGCTACCATCT

upper sequence: AT2G46170.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G159388_T01 (Zea mays), 3'ss of exon 1
ttgtatgaatgcaataaattggctttattggtttattatgttattgacttctga--gttctgagggattctgatttttctgtttctcaatgact-ctttgcagCTGCTGATGTGTTCTTGTGGAGGGATAAAAAACTATCAGGTGCTGTTCTTGGTGTCGCGACTGCTATTTGGGTTCTGTTCGAGCTGGTTGAGTATCATTT
    ||  ||  | |  || |   | ||  |  |  |  |   |  |   || |  ||         | |  |   | ||  ||  |  |  ||  |||| ||||||||||||||||||||||||| | || ||  | || | ||  || |||||||  || || || || ||| |  | || ||  || |||  || ||| |
---gattgataaacttgatcgatgtaatgagaattgtgagacctaaataccttatcgtctgtcattgtacccacaatactcattaccgttctctattttgtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTGGTGGTGCCACAGCAATCTGGATCTTATTTGAATTGCTTGGCTACCATCT

upper sequence: AT2G46170.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G359018_T02 (Zea mays), 3'ss of exon 1
ttgtatgaatgcaataaattggctttattggtttattatgttattgacttctgagttctgagggattctgatttttctgtttctcaatgactctttgcagCTGCTGATGTGTTCTTGTGGAGGGATAAAAAACTATCAGGTGCTGTTCTTGGTGTCGCGACTGCTATTTGGGTTCTGTTCGAGCTGGTTGAGTATCATTT---------------------------------------------------------
                                                    |   | | |   |   |  |  ||    ||||| ||     ||||||||||||||||||||| |||||||| | |  ||  | || |  |  || |||||||  || || || || ||| | || || ||  || |||  || ||| |                                                         
----------------------------------------------------gtcattttacctaccttactcattactcttctctat-----tttgcagctgctgatgtgttcctgtggaggaacaggaacatctccgccggagtacttggtggagCCACAGCAATCTGGATCCTATTTGAATTGCTTGGCTACCATCTTCTTACTTTTGTTTGCCATGGTCTCATATTCTCTCTGGGTGTTCTCTTTCTCTGGTC

upper sequence: AT2G46170.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G47420.1 (Glycine max), 3'ss of exon 1
ttgtatgaatgcaataaattggctttattggtttattatgttattgacttctgagttctgagggattctgatttttctgtttctca--atgactctttgcagCTGCTGATGTGTTCTTGTGGAGGGATAAAAAACTATCAGGTGCTGTTCTTGGTGTCGCGACTGCTATTTGGGTTCTGTTCGAGCTGGTTGAGTATCATTT
  | |  | || |    ||||    |  |  | ||   || ||        ||   |||||     ||| ||   | ||||| | |  |  |   |||||||||||||||||||| ||||||||| | || ||| | || | ||   | ||||| |  || |||||| |||||||||| || ||| || ||||||||||  |
--ggagaattgtatgcgattgtgagtggttttatagagtgataaatgaagttgcagtctgataatatcttatggctttgtttttgatgacaatattttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATTTCTGCTGGCATGCTTGGCGGAGCCACTGCTGTTTGGGTTCTTTTTGAGTTGCTTGAGTATCACCT

upper sequence: AT2G46170.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G38890.1 (Glycine max), 3'ss of exon 1
ttgtatgaatgcaataaattggctttattggtttattatgttatt--gacttctgagttctgagggattctgatttttctgtttct--caatgactctttgcagCTGCTGATGTGTTCTTGTGGAGGGATAAAAAACTATCAGGTGCTGTTCTTGGTGTCGCGACTGCTATTTGGGTTCTGTTCGAGCTGGTTGAGTATCATTT
    |  | || |    | ||  |||  |  | ||    |  |     | ||      | |||     ||| ||   | ||||| |    || | | |||||||||||||||||||| ||||||||| | || ||| |||| | ||  || ||||| |  || |||||| ||||||| || || ||| || ||||||||||  |
----agaattgtatgcgactgtgtttggttatatagagggagaaaagaagtttcagtctatgatactatcttatggctttgtttttggtgatcattttttgcagCTGCTGATGTGTTATTGTGGAGGAACAAGAAAATATCTGCTGGCGTGCTTGGCGGAGCCACTGCTGTTTGGGTCCTTTTTGAGTTGCTTGAGTATCACCT

upper sequence: AT2G46170.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G03410.2 (Glycine max), 3'ss of exon 1
ttgtatgaatgcaat-aaattggctttattggtttattatgttattgacttctgagtt-ctgagggattctgatttttc-tgtttctcaatgactctttgcagCTGCTGATGTGTTCTTGTGGAGGGATAAAAAACTATCAGGTGCTGTTCTTGGTGTCGCGACTGCTATTTGGGTTCTGTTCGAGCTGGTTGAGTATCATTT
 |   | |||  | | ||||| |  ||| |  ||  ||   || || || | | |    || |  | |  | ||||||  | ||||  |||      ||||||||||||||||| ||||||||||| | || ||  |||| | |  ||| |||||||| || |||||| ||||| |  | || ||| || |||| |||||  |
-tccctaaattaattgaaattagaattact--ttattttaatttttaacctgtaaccaactaactggtctttattttttatttttcctaatcttcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTGGTGTAGCCACTGCTGTTTGGATCTTTTTTGAGTTGCTTGAATATCACCT

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|164068914|gb|ES038069.1|ES038069
EST:     TATGTTTGGCAGAGAGAAGCCTGTTCACAAGGTTCTCGGTGGTGGAAAGC                         CTGCTGATGTGTTCTTG
genomic: TATGTTTGGCAGAGAGAAGCCTGTTCACAAGGTTCTCGGTGGTGGAAAGCgtaagggttt ... ctctttgcagCTGCTGATGTGTTCTTG
EST: gi|164107707|gb|ES073886.1|ES073886
EST:     TATGTTTGGCAGAGAGAAGCCTGTTCACAAGGTTCTCGGTGGTGGAAAGC                         CTGCTGATGTGTTCTTG
genomic: TATGTTTGGCAGAGAGAAGCCTGTTCACAAGGTTCTCGGTGGTGGAAAGCgtaagggttt ... ctctttgcagCTGCTGATGTGTTCTTG
EST: gi|125297091|gb|EL311176.1|EL311176
EST:     TATGTTTGGCAGAGAGAAGCCTGTTCACAAGGTTCTCGGTGGTGGAAAGC                         CTGCTGATGTGTTCTTGTGGAGGGAATAAAAAA
genomic: TATGTTTGGCAGAGAGAAGCCTGTTCACAAGGTTCTCGGTGGTGGAAAGCgtaagggttt ... ctctttgcagCTGCTGATGTGTTCTTGTGGAGGGA-TAAAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacttctgagttctgagggattctgatttttctgtttctcaatgactctttgcagCTGCTGATGTGTTCTTGTGGAGGGATAAAAAACTATCAGGTGCTGTTCTTGGTGTCGCGACTGCTATTTGGGTTCTGTTCGAGCTGGTTGAGTATCATTT
                                             ctctttgc  CT-rich tract
                       tgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtatgaatgcaataaattggctttattggtttattatgttattgacttctgagttctgagggattctgatttttctgtttctcaatgactctttgcagCTGCTGATGTGTTCTTGTGGAGGGATAAAAAACTATCAGGTGCTGTTCTTGGTGTCGCGACTGCTATTTGGGTTCTGTTCGAGCTGGTTGAGTATCATTT

- - - - - -caataaa
- - - - - - - - - - - - - - -ggtttat