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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgtcattatatagcttctagtatttcattctagtttaaagtattgaactttttgatattttgttgtactgaaagtggtttatgttgaattgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT

Basic information

species Arabidopsis thaliana
transcript AT5G54800.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os08g08840.2 (Oryza sativa), 3'ss of exon 2
cttgtcattatatagcttctagtatttcattctagtttaaagtattgaactttttgatat-tttgttgtactgaaagtggtttatgttg---aattgcatat---agGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT
              |    | | || |  |||| |    || ||||    | |||| | |   || |      |   || || || |||   | || | | |   ||||||||||||| || |||||||| ||||| ||||| || |||||||||||||| || || || || ||||| ||||| ||||| ||||  || ||||| |
--------------gtgagtggaatctttttcttggc--aattatttgtatatttgctgtgcctgcttgggcaagcatgattgattttggctattttccttttgaagGTTGCTGTGGCTCATACAATTGGGCATGTTGCTGCGACAGTGAGTATGTCAAAAGTAGCAGTGTCATTCACACACATTATCAAAAGTGCAGAGCCTGCAT

upper sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G431314_T01 (Zea mays), 3'ss of exon 2
cttgtca-ttatatagcttctagtatttcattctagtttaaagtattgaactttttgatattttgttgtactgaaagtggtttatgttgaattgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT
   || | ||   ||  |  |   | |   |  |  ||||   |||  | |||  ||  |   |||   ||||||  ||||    | | || || ||  |||||||||||||||| |||||||| ||||| ||||| || ||||| ||||| ||||| || || || ||||| ||||| || || ||||  |||||||| |
---gtgagttgcttatttcgtgccagtaactcttcttttattttatataccttcctggaaaagtgta--actgaatttggt----gattaactg-atgaagGTTGCTGTGGCACATACAATTGGCCATGTTGCTGCGACAGTGAGCATGTCTAAGGTGGCAGTGTCATTCACACACATAATTAAAAGTGCAGAACCTGCAT

upper sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 2
-cttgtc-attatatagcttctagtatttcattctagtttaaagtattgaactttttgatattttgttgtactgaaagtggtttatgttgaattgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT
    ||  ||||| | | | | ||||  |  || || ||||     || | ||   ||  |   |||   ||||||  ||||    | | || || ||  ||||||||||||| || |||||||| ||||| ||||| || ||||| ||||| ||||| || || || ||||| ||||| || || || |  |||||||| |
gtgagttgattattttg-tgccagtaacttcttttatttta-----tttacctgcctggaaaagtgta--actgaatttggt----gattaactg-atgaagGTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCTAAGGTGGCAGTGTCATTCACACACATAATTAAAAGCGCAGAACCTGCAT

upper sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G27680.1 (Glycine max), 3'ss of exon 1
--cttgtcattatatagcttctagtatttcattctagtttaaagtattgaactttttgatattttgt-tgtactgaaagtggtttatgttgaattgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT
   |      | ||| |     |  ||        ||||| |||||  |||   ||   |   | ||    ||| ||     || |  ||   |||  |  ||||||| ||||||||||||||||| ||||| |||||||| ||||| ||||| |||||||||||||| ||||||||||||||||||||||| || || || |
aagtaacgcgtttatggtggtcaa-atggtgggtgagtttgaagtaaggaaaggttgatttagtagtactcactaaagaaatttcaaatttttttg--tgcagGTTGCGGTGGCACACACAATTGGGCATGTTGCTGCAACTGTGAGCATGTCCAAGGTTGCTGTTTCATTCACTCACATCATCAAGAGTGGAGAGCCAGCTT

upper sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G11270.1 (Glycine max), 3'ss of exon 1
-cttgtcattatatagct-tctagtatttcattctagtttaaagtattgaactttttgatattttgt-tgtactgaaagtggtttatgttgaattgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT
 |    |||| ||| |   || | |  |       ||||| |||||  |||   ||   |   | ||    |||  |     || |  ||  ||||  |  ||||||| ||||||||||||||||| ||||| |||||||| ||||| ||||| |||||||||||||| ||||||||||||||||||||||| || || || |
gcaatgcatt-tatggtggtcaaatggtgtgagtgagtttgaagtaaggaaaggttgattgagtagtactcacttgagaaatttcaaattttattg--tgcagGTTGCGGTGGCACACACAATTGGGCATGTTGCTGCAACTGTGAGCATGTCCAAGGTTGCTGTTTCATTCACTCACATCATCAAGAGTGGAGAGCCAGCTT

upper sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G25290.1 (Glycine max), 3'ss of exon 2
cttgtcattatatagcttctagt--attt---cattctagtttaaagtattgaactttttgatattttgttgtactgaaagtggtttatgttgaattgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT
 ||||    | | || |  |  |  ||||   ||||||  ||| |  |||   | ||||  ||   |  |     |     | |||| | ||   |  | |  |||||||||| ||||| |||||||| ||||| || ||||| || || |||||||| ||||| || || ||||| ||||| |||||||||||||||||||| |
gttgtttcaaaaaagttattgatcaatttagccattctccttttat-tatcatatttttgaatggatgatgactttagttttcgttt-tatt---tctccttcagGTTGCTGTTGCACATACAATTGGACATGTAGCGGCAACAGTTAGCATGTCAAAAGTTGCGGTATCATTCACACACATTATCAAGAGTGGTGAACCTGCTT

upper sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G12080.1 (Glycine max), 3'ss of exon 2
-cttgtcattatatagcttctagtatttcattc---tagtttaaagtattgaactttttgatattttgttgtactgaaagtggtttatgttgaattgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT
  |  |  ||  | |  |  || |  |  |||     | | |    |||| | | ||||||     || || |||  |  |  ||| | |||  |  | |  |||||||||| ||||| ||||| || ||||| || ||||| || ||||||||||| ||||| || || || || || || ||||||||||||||||||||  
aataattgtttcaaaaatgttattgatcaatttagtcattctcctttatttatcattttgaatggatgatg-actttagtt--tttgttttgtttctccttcaGGTTGCTGTTGCACATACAATAGGACATGTAGCGGCAACAGTTAGTATGTCAAAAGTTGCGGTATCGTTTACACATATTATCAAGAGTGGTGAACCTGCT-

upper sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G38830.1 (Glycine max), 3'ss of exon 1
cttgtcattatatagcttctagtatttcattctagtttaaagtattgaactttttgatattttgttgtactgaaagtggtttatgttgaattgca--tatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT
      ||  || ||    |||    | |    | |   ||   |  | | ||   || |    | ||||| || | ||  | ||     |||    |  |||| || |||  ||| |||||||| ||||| || || |||||||||||||| || ||||| ||||| || || ||||||||||||||||  |||||||| |
ggcaaaatagtaaagagattagggggtaaaagaaatcataatcgtcaagcatt--aatgtcaattagtactcaatggggaatttgaaactttgggagtgcagGTCGCGGTGTTACATACAATTGGGCATGTTGCAGCTACGGTGAGTATGTCCAAAGTTGCAGTTTCATTTACCCACATCATCAAGAGTGCAGAACCTGCAT

upper sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G01890.1 (Glycine max), 3'ss of exon 1
cttgtcattatatagcttctagtatttcattctagtttaaagtattgaactttttgatattttgttgtactgaaagtggtttatgttgaattgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT
      ||  |  ||    |||    | |    | ||  ||   |  ||| ||    |   ||  |         |   |||    |     |  |  ||||||| |||  ||| |||||||| ||||| || || || ||||||||||| || ||||| ||||| || || ||||||||||||||||  || ||||| |
tacaaaatagtgaagagattagggggtaaaagaaattataatagtcaaacattaatctcaattaatacttattgggaaatttgaaattttgggagtgcagGTTGCGGTGTTACATACAATTGGGCATGTTGCAGCTACCGTGAGTATGTCCAAAGTTGCAGTTTCATTTACCCACATCATCAAGAGTGCAGAGCCTGCAT

upper sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 1
cttgtcattatatagcttcta----gtatttcattctagtttaaagtattgaactttttgatattttgttgtactgaaagtggtttatgttgaattgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT
  |    |    | |||| ||    | ||| | ||    ||    | |   ||      | |   |||| | | | | | |   |    ||  ||    | |||||||||||||| || |||||||| |||||||||||||| ||||||||||| |||||||| || ||||| |||||||| |||||||||||||| ||||| |
--taaattggagttgcttttaaaatggattcccttagttttctcggcagccaaacaga-gctggattgt-gaatttataatcaatctgattttatgttttgtagGTTGCTGTGGCTCATACAATTGGGCATGTGGCTGCAACAGTGAGTATGTCCAAGGTTGCGGTGTCTTTTACTCACATAATCAAGAGTGGTGAGCCTGCAT

upper sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 2
cttgtcattatatagcttctagtatt--tcattctagtttaaagtattgaactttttgatattttgttgtactgaaagtggtttatgttgaattgcatata-gGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT
 |  |    || | |  | | || ||  | |  || |     | |  | | |||| | | | |  | |||| |  ||    ||||||         ||  | ||| ||  |||| ||||| ||||| || ||||| || || ||||||||||| ||||| || || || ||||| |||||||||||||| |  ||||| ||||
gtatttgcaatgtgggat-tggtgttggtaacactggca-gcactgcttatctttgt-acactgggatgtattctaacgtttttatgaaatgcacaatggaagGTGGCATTGGCGCACACGATTGGACACGTGGCAGCGACTGTGAGTATGTCCAAGGTCGCAGTATCCTTCACGCACATCATCAAGAGCGCAGAACCCGCGT

upper sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S143_174V6.1 (Physcomitrella patens), 3'ss of exon 1
---cttgtcattatatagcttctagtatttcattctagtttaaagtattgaactttttgatattttgttgtactgaaagtggtttatgttgaattgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT
   |       | |  ||  |    |  | | || |    |  || | | | |  ||| ||     | ||| || |   |    |   |||       |  |||| ||  |||| ||||| ||||| || ||||| || || ||||||||||| |||||||| || || ||||| |||||||||||||| |  ||||| || |
cggcaaacgtgtgtgcagtgttcgttggtgc-ttgtgagatcgagcact-agcagttttattgggggctgttctaaccttttcatggtttgtgcaat-tgaagGTGGCATTGGCGCACACGATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCAGAACCCGCAT

upper sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S190_76V6.1 (Physcomitrella patens), 3'ss of exon 2
----cttgtcattatatagcttctagtatttcattc-tagtttaaagtattgaactttttgatattttgttgtactgaaagtggtttatgttgaattgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT
    |||||   | |  || |||  || |    ||| |      ||| | ||    | || ||    | |||| |||||  |         || |     | ||||  ||  |||| ||||||||||| || ||||| || || ||||||||||| |||||||| || || ||||| |||||||||||||| |  ||||| || |
tcagcttgtg--tgtgcag-ttcaggtttggtgttcatgagactaagcactgggaatctt-atcgagtattgttctgaacttctcacgaaatgtacattgt-tagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCGGAACCCGCAT

upper sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S241_24V6.1 (Physcomitrella patens), 3'ss of exon 1
cttgtcattatatagcttctagtatttcattctagtttaaagtattgaactttttgatattttgttgtactgaaagtggt-ttatgttgaattgc-atatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT
   |  |   | |   || || |  ||  |||||| |||||   ||| |  | |   |||    |||   |||| ||  |  |   | |     | ||  |||| ||  | ||||| ||||||||||||||||| || || ||||| ||||| |||||||| || |||||||| ||||||||||| |||  ||||||||| |
-caggaaaggtttctgttttaattattttttctagattaaaaatttggagatatgtctatgagcttg-gttgaatgtattactgaatcggtgcactatgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCGAAGGTTGCAGTATCTTTCACACACATCATCAAAAGTTCTGAACCTGCAT

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|94331425|gb|AM111154.1|AM111154
EST:     TCGTTGAGACTCCCAAGACGGATTTTGATTTCTGGAAAACTCTTTTTCCG                         GTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCA
genomic: TCGTTGAGACTCCCAAGACGGATTTTGATTTCTGGAAAACTCTTTTTCCGgtaagtgagt ... ttgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCA
EST: gi|94331410|gb|AM111139.1|AM111139
EST:     TCGTTGAGACTCCCAAGACGGATATTGATTTCTGGAAAACTCTTTTTCCG                         GTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCA
genomic: TCGTTGAGACTCCCAAGACGGATTTTGATTTCTGGAAAACTCTTTTTCCGgtaagtgagt ... ttgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCA
EST: gi|164132890|gb|EL970344.1|EL970344
EST:     GACGGATTTTGATTTCTGGAAAACTC-TTTTCCG                         GTTGCTGTGGCACACACAATTGGTCATGTGGCTGC
genomic: GACGGATTTTGATTTCTGGAAAACTCTTTTTCCGgtaagtgagt ... ttgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGC
EST: gi|94331524|gb|AM111253.1|AM111253
EST:     TCGTTGAGACTCCCAAGACGGATTTTGATTTCTGGAAAACTCTTTTTCCG                         GTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCA
genomic: TCGTTGAGACTCCCAAGACGGATTTTGATTTCTGGAAAACTCTTTTTCCGgtaagtgagt ... ttgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCA
EST: gi|164148299|gb|EL972720.1|EL972720
EST:     GACGGATTTTGATTTCTGGAAAACTCTTTTTCCG                         GTTGCTGTGGCACACACAATTGGTCATGTGGCTGC
genomic: GACGGATTTTGATTTCTGGAAAACTCTTTTTCCGgtaagtgagt ... ttgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGC
EST: gi|116467722|gb|EG510314.1|EG510314
EST:     CGTTGAGACTCCCAAGACGGATTTTGATTTCTGGAAAACTCTTTTTCCCG                         GTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTC
genomic: CGTTGAGACTCCCAAGACGGATTTTGATTTCTGGAAAACTCTTTTT-CCGgtaagtgagt ... ttgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTC
EST: gi|94331545|gb|AM111274.1|AM111274
EST:     TCGTTGAGACTCCCAAGACGGATTTTGATTTCTGGAAAACTCTTTTTCCG                         GTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCA
genomic: TCGTTGAGACTCCCAAGACGGATTTTGATTTCTGGAAAACTCTTTTTCCGgtaagtgagt ... ttgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCA
EST: gi|164133052|gb|EL981459.1|EL981459
EST:     GACGGATTTTGATTTCTGG-AAACTCTTTTTCCG                         GTTGCTGTGGCACACACAATTGGTCATGTGGCTGC
genomic: GACGGATTTTGATTTCTGGAAAACTCTTTTTCCGgtaagtgagt ... ttgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaactttttgatattttgttgtactgaaagtggtttatgttgaattgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT
      ttttgat  putative branch site (score: 4)
     tttttgatattttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgtcattatatagcttctagtatttcattctagtttaaagtattgaactttttgatattttgttgtactgaaagtggtttatgttgaattgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtttat