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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttttcttcttcttttcataagtacctcattgtctcgacaatacatatccgcttatttatacaaacaagctcaactgtctgatttggctgttgtgctagGTTGTGAGGTATACAACCTGGGAACCGGAAAAGGAACAACAGTGTTGGAGATGGTTGATGCATTTGAGAAAGCTTCTGGAATG

Basic information

species Arabidopsis thaliana
transcript AT1G64440.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G64440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os09g15420.1 (Oryza sativa), 3'ss of exon 6
gtatgcttttcttcttcttttcataagtacctcattgtctcgacaatacatatccgcttatttatacaaacaagctcaactgtctgatttggctgttgtgctagGTTGTGAGGTATACAACCTGGGAACCGGAAAAGGAACAACAGTGTTGGAGATGGTTGATGCATTTGAGAAAGCTTCTGGAATG
      |      ||  ||   |     |     |||  |   ||  || | ||   || |||  |     || ||    | |   ||||   | |  |   ||| ||| | | ||||||||| ||||| ||||| |||||| |||||||||| || ||| ||||||||||||||| |||||||| |
---aattacagcactgtttagaactcaaatagtgttggatgctcagaac-tgtcactttgttttgatgttaaatcttttttctaaaatttatttctacttgcagGATGTCAAGCATACAACCTTGGAACAGGAAAGGGAACATCAGTGTTGGAAATAGTTAATGCATTTGAGAAAGTTTCTGGAAAG

upper sequence: AT1G64440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G138410_T01 (Zea mays), 3'ss of exon 6
-gtatgcttttcttcttctttt-cataagtacctcattgtctcgacaatacatatccgcttatttatacaaacaagctcaactgtctgatttggctgttgtgctagGTTGTGAGGTATACAACCTGGGAACCGGAAAAGGAACAACAGTGTTGGAGATGGTTGATGCATTTGAGAAAGCTTCTGGAATG
  | || |   |   ||||| | |||| |   |||||    ||   |  || ||  |  | | || |  |    |       |  |  ||||  ||||| |   ||| ||||| | ||||||||| |||||||||||||||||| ||||||||||||| ||  ||||||||||||| |||||||||| |
tttttgttgaacagtttcttgtacatatgatgctcataaagtc---agaacgta--cagtaagttttgtagttgaatcttgtt-ccaaatttaactgttcttgcagGATGTGAAGCATACAACCTTGGAACCGGAAAAGGAACATCAGTGTTGGAGATAGTCAATGCATTTGAGAAGGCTTCTGGAAAG

upper sequence: AT1G64440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G469523_T02 (Zea mays), 3'ss of exon 1
gtatgcttttcttcttcttttcataagtacctcattgtctcgacaatacatatccgcttatttatacaaacaagctcaactgtctgatttggctgttgtgctagGTTGTGAGGTATACAACCTGGGAACCGGAAAAGGAACAACAGTGTTGGAGATGGTTGATGCATTTGAGAAAGCTTCTGGAATG
    |  | | | | | ||||| ||  | ||||||   |  |    |  ||       | ||| |||     |     | | |   |||||    |  |   ||| ||||| |  |||||||| |||||||||| ||| ||| | ||| ||||||| ||| | ||||||||||| |||||||| | |
---ggtatctgtccatattttc-tatttccctcatgtgcgaggtgtttgattcatttgtgtttgtactttggaatcttattttaaaatttgatactatttgcagGGTGTGAAGCGTACAACCTTGGAACCGGAAGAGGTACATCTGTGCTGGAGATTGTTAAAGCATTTGAGAAGGCTTCTGGGAAG

upper sequence: AT1G64440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G01940.4 (Glycine max), 3'ss of exon 6
-----------gtatgcttttcttcttct-tttcataagtac-------ctcattgtctc---gacaat-acatatccgcttatttatacaaacaagctcaactgtctgatttggctgttgtgctagGTTGTGAGGTATACAACCTGGGAACCGGAAAAGGAACAACAGTGTTGGAGATGGTTGATGCATTTGAGAAAGCTTCTGGAATG-----------------
             ||  | ||| |||||| ||   ||| ||        ||  |  | ||     || | ||||    |   |||||||     ||  |    | |    |||    ||  |   |||||||||||| || ||||||||||| ||||| |||||| |||| ||||||||||||   || |||||||  || ||||||| |                 
gtatcattctaaaattttcttcatcttctattatttaactatgccagttctggtgatttctgaagcagtgacattgtggtgaatttatagtggtaaaattttattttaattttcatggtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTTCGAGCTTTTGAGATGGCATCTGGAAAGGTGAATAGAATAATGTA

upper sequence: AT1G64440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G43540.1 (Glycine max), 3'ss of exon 6
-------------gtatgcttt-tcttcttcttttca-----taagtacc--tcattgtctcgacaat-acatatccgcttatttatacaaacaagctcaactgtctgatttggctgttgtgct---agGTTGTGAGGTATACAACCTGGGAACCGGAAAAGGAACAACAGTGTTGGAGATGGTTGATGCATTTGAGAAAGCTTCTGGAATG
             || | |||| ||||||   ||| |     | ||  |   | |||      ||| | |||     |   |||| ||     ||  |  | |   | ||||   || |||  |   |||||||||||| || ||||||||||| ||||| |||||| |||| ||||||||||||   || ||||| |  || ||||||| |
gtattattctaaagttttctttatcttctatatttaactctgtcagctctggtgatttctgaaacagtgacaatgtggtaaatttgtattggtaaaatttatt--ttaattttcatggtgtatttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTTAGAGCTTTTGAAATGGCATCTGGAAAG

upper sequence: AT1G64440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 6
-----------gtatgcttttcttcttctttt-cataagtac-------ctcattgtctc---gacaat-acatatccgcttatttatacaaacaagctcaactgtctgatttggctgttgtgctagGTTGTGAGGTATACAACCTGGGAACCGGAAAAGGAACAACAGTGTTGGAGATGGTTGATGCATTTGAGAAAGCTTCTGGAATG
             ||  | ||| |||||| ||   ||| ||        ||  |  | ||     || | ||||    |   |||||||     ||  |    | |    |||    ||  |   |||||||||||| || ||||||||||| ||||| |||||| |||| ||||||||||||   || |||||||  || ||||||| |
gtatcattctaaaattttcttcatcttctattatttaactatgccagttctggtgatttctgaagcagtgacattgtggtgaatttatagtggtaaaattttattttaattttcatggtgtttacagGTTGTGAGGTTTATAACCTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTTCGAGCTTTTGAGATGGCATCTGGAAAG

upper sequence: AT1G64440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G02690.2 (Glycine max), 3'ss of exon 6
--gtatgcttttcttcttcttttcataagtacctcattgtctcgacaatacatatccgcttatttatacaaacaagctcaactgtctgatttggctgt-tgtgctagGTTGTGAGGTATACAACCTGGGAACCGGAAAAGGAACAACAGTGTTGGAGATGGTTGATGCATTTGAGAAAGCTTCTGGAATG-----------------
  ||||| |||   |   |      | |  |||| | |||    |   |   |   ||     | |||  |    | | || | | ||   ||  ||  | ||| |||||||||||| || ||| ||||||| ||||| |||||| |||| |||||||||||  | || |||||  | || ||||||| |                 
aagtatgatttatgtaaccgacc--tcatcacct-agtgtgataaggttttgttgtcgtca--tcatattactttggtaaaat-tttgtactgtttgcatatgc-agGTTGTGAGGTTTATAACTTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTAAACGCTTTTGAACAGGCCTCTGGAAAGGTAACAGACTTATAGCT

upper sequence: AT1G64440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G02690.1 (Glycine max), 3'ss of exon 6
--gtatgcttttcttcttcttttcataagtacctcattgtctcgacaatacatatccgcttatttatacaaacaagctcaactgtctgatttggctgt-tgtgctagGTTGTGAGGTATACAACCTGGGAACCGGAAAAGGAACAACAGTGTTGGAGATGGTTGATGCATTTGAGAAAGCTTCTGGAATG
  ||||| |||   |   |      | |  |||| | |||    |   |   |   ||     | |||  |    | | || | | ||   ||  ||  | ||| |||||||||||| || ||| ||||||| ||||| |||||| |||| |||||||||||  | || |||||  | || ||||||| |
aagtatgatttatgtaaccgacc--tcatcacct-agtgtgataaggttttgttgtcgtca--tcatattactttggtaaaat-tttgtactgtttgcatatgc-agGTTGTGAGGTTTATAACTTGGGAACAGGAAAGGGAACATCAGTTTTGGAGATGGTAAACGCTTTTGAACAGGCCTCTGGAAAG

upper sequence: AT1G64440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G36850.1 (Glycine max), 3'ss of exon 6
gtatgcttttcttcttcttttcataagtacctcattgtctcgacaatacatatccgct-tatttatacaaacaagctcaactgtctgatttggctgttgtgctagGTTGTGAGGTATACAACCTGGGAACCGGAAAAGGAACAACAGTGTTGGAGATGGTTGATGCATTTGAGAAAGCTTCTGGAATG
 |     | |  ||    |  |  |  |  || | |||   || ||  | |    | | |  | ||   |    | | || | | ||   ||  |||      |||||||||||| || ||| ||||||| ||||| |||||| | || |||||||||||  | || |||||  | || ||||||| |
-tcgaactgtgatccatgtagctgacctgacttagtgt---gataaggctttgttgttgtcgtcatgttactttggtaaaat-tttgtactgtttgtatatacagGTTGTGAGGTTTATAACTTGGGAACAGGAAAGGGAACATCTGTTTTGGAGATGGTAAACGCTTTTGAACAGGCCTCTGGAAAG

upper sequence: AT1G64440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 6
gtatgcttttcttcttcttttcataagtacctcattgtctcgacaata-catat-ccgcttatttatacaaacaagctcaactgtctgatttggctgttgtgc----tagGTTGTGAGGTATACAACCTGGGAACCGGAAAAGGAACAACAGTGTTGGAGATGGTTGATGCATTTGAGAAAGCTTCTGGAATG
              |   ||||| ||    || |  | | | ||| |  ||||   | |||   || |     |||   |  |||| |  |||  | || ||      ||| ||||| || |||||| ||||||| || ||||||||  |||| |||||||||||||  ||||||||||| || ||||||| |
--------agaacttaagtttcagaacagtcttaaaggc-caacactgtcataaatcacttgagtaaatggg-aaggaaacttgtcagtattgatttttatgaacagcagGGTGTGAAGTGTACAACTTGGGAACTGGGAAAGGAACTTCAGTTTTGGAGATGGTTGCAGCATTTGAGAAGGCATCTGGAAAG

upper sequence: AT1G64440.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 6
-----gtatgcttttcttcttcttttcataagtacctcattgtctcgacaatacatatccgcttatttatacaaacaagctcaactgtctgatttggc-tgttgtgctagGTTGTGAGGTATACAACCTGGGAACCGGAAAAGGAACAACAGTGTTGGAGATGGTTGATGCATTTGAGAAAGCTTCTGGAATG
     | |        |    ||| ||      || |   | |       |||| || | ||| |    |  |||||   |  | | ||  |||||   | |      ||| ||||| || |||||| ||||||| |||||||||||| | || |||||||||||||  ||||||||||| || ||||||| |
ctcgagcaaatggaagtaaaacttgtcg-----acattgattttcatttgatacctaactgctaaaacttgtaaaca---ttgattttc--atttgatatctaactgcagGCTGTGAAGTGTACAACTTGGGAACAGGAAAAGGAACATCGGTTTTGGAGATGGTTGCAGCATTTGAGAAGGCATCTGGAAAG

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|86084442|gb|DR380201.1|DR380201
EST:     AGCAGATGGCCATATATTTGCGCTTCAAAAGCTAGACGATACTGAAATAG                         GTTGTGAGGTATACAACCTGGGAACCGGWAAAGGWACAACAGTGTTGGAGA
genomic: AGCAGATGGCCATATATGTGCGCTTCAAAAGCTAGACGATACTGAAATAGgtatgctttt ... gttgtgctagGTTGTGAGGTATACAACCTGGGAACCGGAAAAGGAACAACAGTGTTGGAGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatccgcttatttatacaaacaagctcaactgtctgatttggctgttgtgctagGTTGTGAGGTATACAACCTGGGAACCGGAAAAGGAACAACAGTGTTGGAGATGGTTGATGCATTTGAGAAAGCTTCTGGAATG
                                gtctgat  putative branch site (score: 4)
        ttatttatacaaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttttcttcttcttttcataagtacctcattgtctcgacaatacatatccgcttatttatacaaacaagctcaactgtctgatttggctgttgtgctagGTTGTGAGGTATACAACCTGGGAACCGGAAAAGGAACAACAGTGTTGGAGATGGTTGATGCATTTGAGAAAGCTTCTGGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG