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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggattcttgaatttttcaatgttctaagtgttctctctttatagatattaagatgaaagctcatagttgcttgcttctttttgtttttttttagGTTGCTGGTATCCCAAAGAAGTTGGCTCCAACAATCGGAATTTCTGTTGATCACCGACGCAAGAACCGTTCTTTGGAGGGTCTTCAGTCCAATGTCCAAA

Basic information

species Arabidopsis thaliana
transcript AT5G23900.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g37970.1 (Oryza sativa), 3'ss of exon 3
-----gtttggattcttgaatttttcaatgttctaagtgttctctctttatagatattaagatgaaagctcatagttgcttgcttctttttgtttttt---tttagGTTGCTGGTATCCCAAAGAAGTTGGCTCCAACAATCGGAATTTCTGTTGATCACCGACGCAAGAACCGTTCTTTGGAGGGTCTTCAGTCCAATGTCCAAA
     |  ||  ||||||     ||  || ||   |       | |||   |  |||||   || ||  | ||| |||      | || || |  | |      ||| ||| || ||||| |||||||  |||||||| || |||||||| || |||||||| ||||||||||| ||  | ||||| || ||| | |||||||| |
gctttgagtgtgttcttg--ccattacatatttagaaaaaaaacactt-gcatttatta---tgtaactttatatttgtgctgatgttgttctcctataaacacagGCTGCGGGCATCCCCAAGAAGTATGCTCCAACCATTGGAATTTCCGTGGATCACCGCCGCAAGAACCGCTCACTTGAGGGACTCCAGGCTAATGTCCAGA

upper sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G145280_T01 (Zea mays), 3'ss of exon 3
gtttggattcttgaatttt---tcaatgttctaagtgtt-ctctctttatagat-attaagatgaaagctcatagttgcttgcttctttttgtttttttttagGTTGCTGGTATCCCAAAGAAGTTGGCTCCAACAATCGGAATTTCTGTTGATCACCGACGCAAGAACCGTTCTTTGGAGGGTCTTCAGTCCAATGTCCAAA
 | || |||  |   | ||   | |   |  || | ||  | || || || ||| ||     | | | ||    | |    | | || | |   |  ||  ||| |||||| |||||||||||| | |||||||| || || ||||||||||||||||| |||||||||   ||  | ||||| || ||| |||||||||| |
ttctgcatttatccttgttgaattatcttcttatgagtcacacttttcatcgatgatctgtgttatatcttgatgctaaaagttactatgt---tgattgcagGCTGCTGGCATCCCAAAGAAGCTTGCTCCAACCATTGGTATTTCTGTTGATCACCGCCGCAAGAACAAATCCCTTGAGGGACTGCAGGCCAATGTCCAGA

upper sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G17370.2 (Glycine max), 3'ss of exon 2
-------------gtttggattcttgaatttttcaatgttctaagtgttctctctttatagatattaagatgaaagctcatagttgcttgcttctttttgtttttttttagGTTGCTGGTATCCCAAAGAAGTTGGCTCCAACAATCGGAATTTCTGTTGATCACCGACGCAAGAACCGTTCTTTGGAGGGTCTTCAGTCCAATGTCCAAA
                |  ||     |  | |  ||     ||    ||||  |||||||  | ||           || |    |  |  |||||||   | | |  |||| ||| || || || |||||  | |||||||| || || |||||||||||||||||  | ||||| |||||||||||| |||| ||| ||||||| || |
aagttaagacagcaaatacataaaaaagctgtctaaaacattagaaattcttcctttatatcttttc---------ttcctgacagactaattctttta--tatatcctagGCTGCAGGAATTCCCAAGAAACTTGCTCCAACTATTGGGATTTCTGTTGATCACCGCAGAAAGAATCGTTCTTTGGAGAGTCTGCAGGCCAATGTGCAGA

upper sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G14640.2 (Glycine max), 3'ss of exon 3
gtttggattcttgaatttttcaatgttctaagtgttctct-ctttatagatattaagatgaaagctcatagttgcttgc-ttctttttgtttttttttagGTTGCTGGTATCCCAAAGAAGTTGGCTCCAACAATCGGAATTTCTGTTGATCACCGACGCAAGAACCGTTCTTTGGAGGGTCTTCAGTCCAATGTCCAAA
 |||  |   || | || ||  |   |  || | | ||   | | |    |  |   |   | | |  |  |    ||  |||| | | || |    ||||  || || || || || ||| | || |||||||| || ||| |||||||||| || ||||||||||||||||||||  |||| ||  | ||||| || |
attttaagcatttatttattataaaatgaaaatatgctaaacatgagttctgcttttagatatgtttctgatattatgtattctctatattatgccatagGCAGCAGGGATTCCCAAAAAGCTTGCACCAACAATTGGTATTGCTGTTGATCATCGCCGCAAGAACCGTTCTTTGGAAAGTCTGCAAGCTAATGTGCAGA

upper sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G08090.1 (Glycine max), 3'ss of exon 3
-------------gtttggattcttgaatttttcaatgttctaagtgttctctctttatagatattaagatgaaagctcatagttgcttgcttctttttgtttttttttagGTTGCTGGTATCCCAAAGAAGTTGGCTCCAACAATCGGAATTTCTGTTGATCACCGACGCAAGAACCGTTCTTTGGAGGGTCTTCAGTCCAATGTCCAAA
             |     |      || | |  ||     ||    ||||  |||||||  | ||           || |    |  |  |||||||   | | |  |||| ||  || || || |||||  | | |||||| || || |||||||||||||||||  | ||||| |||||||||||| |||| ||| ||||||| || |
gaaagtttagacagcaaatacataaaaactgtgtaaaacattagaaattcttcctttatatcttttt---------ttcctgacagaataattctttta--tatatcctagGCTGTGGGAATTCCCAAGAAACTTGGTCCAACTATTGGGATTTCTGTTGATCACCGGAGAAAGAATCGTTCTTTGGAGAGTCTGCAGGCCAATGTGCAGA

upper sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G34760.2 (Glycine max), 3'ss of exon 3
gtttggattcttgaatttttcaatgttctaagtgttctctctttataga----tattaagatgaaagctcatagttgcttgc-ttctttttgtttttttttagGTTGCTGGTATCCCAAAGAAGTTGGCTCCAACAATCGGAATTTCTGTTGATCACCGACGCAAGAACCGTTCTTTGGAGGGTCTTCAGTCCAATGTCCAAA
   |  |   || | || ||  |   |  || | | |          ||    | ||   |   | | |  |  |    ||  || ||| | || |    ||||  || || || || || ||| | || ||||| || || ||| |||||||||| || ||||||||||||||||||||  |||| ||  | ||||| || |
---ttaagcatttatttattataaaatgaaaatatgcaaaacaagaggagttctgttgttagatatgtttttgatattatgtattttttatattatgccatagGCAGCAGGGATTCCCAAAAAGCTTGCACCAACCATAGGTATTGCTGTTGATCATCGTCGCAAGAACCGTTCTTTGGAAAGTCTGCAAGCTAATGTGCAGA

upper sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0047g01160.t01 (Vitis vinifera), 3'ss of exon 2
-gtttggattcttgaatttttcaatgttctaagtgttctctctt--tatagatattaagatgaaagctcatagttgcttgcttctttttgtttttttttagGTTGCTGGTATCCCAAAGAAGTTGGCTCCAACAATCGGAATTTCTGTTGATCACCGACGCAAGAACCGTTCTTTGGAGGGTCTTCAGTCCAATGTCCAAA
  |    |||  |  |  | | ||| ||     | | || | ||  | ||| |  |  | |   |       |||   |   | ||||  ||  |    |||  || || |||||||||||  |||||||||| ||||| || || |||||||| || || |||||||||||| | ||| | |||||  | |||||||| |
tctgaaaatttgtttagctctgaatttttgttatctccttttttattctagttcctttgttatgataatggtgttaaatatgtatttt-attgataaccagGCAGCAGGCATCCCAAAGAAACTGGCTCCAACCATCGGCATATCGGTTGATCATCGCCGTAAGAACCGTTCTCTAGAGAGCCTTCAAGCAAATGTCCAGA

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|125291948|gb|EL306033.1|EL306033
EST:     AGGATTCACTCTTGAAGAGCTTAAG                         GTTGCTGGTATCCCAAAGAAGTTGGCTCCAACAATCGGAATTTCTGTTGAT
genomic: AGGATTCACTCTTGAAGAGCTTAAGgtttggattc ... ttttttttagGTTGCTGGTATCCCAAAGAAGTTGGCTCCAACAATCGGAATTTCTGTTGAT
EST: gi|164094741|gb|ES118392.1|ES118392
EST:     ATAACATGAAAGTTAGAGCTGGAAAAGGATTCACTCTTGAAGAGCTTAAG                         GTTGCTGGTATCCCAAAGAAGTTGGCTCC
genomic: ACAACATGAAAGTTAGAGCTGGAAAAGGATTCACTCTTGAAGAGCTTAAGgtttggattc ... ttttttttagGTTGCTGGTATCCCAAAGAAGTTGGCTCC
EST: gi|47830737|gb|CK120421.1|CK120421
EST:     GAAAAGGATTCACTCTTGAAGAGCTTAAG                         GTTGCTGGTATCCCAAAGAAGTTGGCTCCAACAATCGGAATTTCTGTTGAT
genomic: GAAAAGGATTCACTCTTGAAGAGCTTAAGgtttggattc ... ttttttttagGTTGCTGGTATCCCAAAGAAGTTGGCTCCAACAATCGGAATTTCTGTTGAT
EST: gi|125112807|gb|EL163852.1|EL163852
EST:     CTCTTGAAGAGCTTAAG                         GTTGCTGGTATCCCAAAGAAGTTGGCTCCAACAATCGGAATTTCTGTTGAT
genomic: CTCTTGAAGAGCTTAAGgtttggattc ... ttttttttagGTTGCTGGTATCCCAAAGAAGTTGGCTCCAACAATCGGAATTTCTGTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagatattaagatgaaagctcatagttgcttgcttctttttgtttttttttagGTTGCTGGTATCCCAAAGAAGTTGGCTCCAACAATCGGAATTTCTGTTGATCACCGACGCAAGAACCGTTCTTTGGAGGGTCTTCAGTCCAATGTCCAAA
                           ttgcttgcttcttttt  CT-rich tract
                                   ttctttttgttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggattcttgaatttttcaatgttctaagtgttctctctttatagatattaagatgaaagctcatagttgcttgcttctttttgtttttttttagGTTGCTGGTATCCCAAAGAAGTTGGCTCCAACAATCGGAATTTCTGTTGATCACCGACGCAAGAACCGTTCTTTGGAGGGTCTTCAGTCCAATGTCCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG