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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcaaaacttcatcccaatttttctgattcataaacaaaaaagtttggctgagatttttggattattcagGTTGGTATGGAATTCTGGGCAAGATGGGCTCATAGAGCTCTGTGGCACGCTTCTCTATGGAATATGCATGAG

Basic information

species Arabidopsis thaliana
transcript AT4G25700.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G25700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G37560.2 (Glycine max), 3'ss of exon 2
gtaagtttcaaaacttcatcccaattt-ttctga---ttcataaacaaaaaagttt---ggctgagattt--ttggat--------tattcagGTTGGTATGGAATTCTGGGCAAGATGGGCTCATAGAGCTCTGTGGCACGCTTCTCTATGGAATATGCATGAG
||||||   | |     ||  | |||| || |||   |   || | ||   | ||    | ||   |||   |||| |        | ||||||| | ||||||||| |||||||||||||||||||||||||| ||||| |||||  | ||| | ||||| |||
gtaagtcctatactcctatatctatttattatgaaattgggtatataattcaattctgcgtcttgaattcaattgggtatgtctaattttcagGTGGCTATGGAATTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGCTTCCTTGTGGCACATGCACGAG

upper sequence: AT4G25700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G29790.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------gtaagtttcaaaacttcatcc-caattt-----ttctgattcataaacaaaaaagtttggctgagatttttggattattcagGTTGGTATGGAATTCTGGGCAAGATGGGCTCATAGAGCTCTGTGGCACGCTTCTCTATGGAATATGCATGAG
                                                   |    |||| || |   |      |||     || ||| |  || |   ||   ||   ||| |  | |  |||| ||||||| ||||||||||| ||||| |||||||||||||| ||||| ||||| ||||| || ||| | |||||||||
gtgagttatcctttaaactaattatgattccaattgggttttgaatggtttttgagttcagaattgggtgagttgtttgtgaattttgagtgttagattcaagtattcaactgggtatgtctgatt-ttcagGTGGGTATGGAATTTTGGGCTAGATGGGCTCATAGGGCTCTCTGGCATGCTTCGCTGTGGCACATGCATGAG

upper sequence: AT4G25700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G30230.2 (Glycine max), 3'ss of exon 2
gtaagtttcaaaacttcatccc--aatt---tttctgattca---taaacaaaaaagtttggctgagatttttggattattcagGTTGGTATGGAATTCTGGGCAAGATGGGCTCATAGAGCTCTGTGGCACGCTTCTCTATGGAATATGCATGAG
||||||   | | ||| ||     ||||   ||| | |||||             | ||    || |  | |   ||| ||||||| | ||||||| | |||||||||||||||||||||||||| ||||| |||||  | ||| | ||||| |||
gtaagtcctatatctttattatgaaattgggtttattattcaattctgggtgttgaattcaattgggcatgtctaatt-ttcagGTGGCTATGGAACTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGCTTCCTTGTGGCACATGCACGAG

upper sequence: AT4G25700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G24530.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------gtaagtttcaaaacttcatcccaatttttctgattcataaacaaaaaagtttggctgagatttttggattattcagGTTGGTATGGAATTCTGGGCAAGATGGGCTCATAGAGCTCTGTGGCACGCTTCTCTATGGAATATGCATGAG
                                                      |    |||| || |   |     | ||| ||| |  |       | | ||    || |  | |  |||| ||||||| |||||||| || ||||| ||||||||||| || ||||| ||||| ||||| || ||| | |||||||||
gtgagtaatcatccttttaattgattatgattccaattcagttttgaattgctttttaattcagaattgggtga-gttctttgtgaattttgggtggtaga-ttcaattgggtatgtctgatt-ttcagGTGGGTATGGAGTTTTGGGCTAGATGGGCTCACAGGGCTCTATGGCATGCTTCCCTGTGGCACATGCATGAG

upper sequence: AT4G25700.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------gtaagtttcaaaacttcatcccaattttt----ctgattcataaacaaaaaagtttggctgagat-----ttttggattattcagGTTGGTATGGAATTCTGGGCAAGATGGGCTCATAGAGCTCTGTGGCACGCTTCTCTATGGAATATGCATGAG
                            |  ||||| |      |  |   |||      |||  |   |  | |    |||     || ||     ||||  |||  |||||| || ||||| |||||||| ||||||||||| | |||||| |||||||| ||  ||||| | ||||| |||
gtaagtgcctttttcccttcattttccttcggtttctagttccaaatcatgtttgcgaagctgggtttgaggcgattgcgttgaatcgaaataggtattttttatt-ctcagGTAGGCATGGAGTTCTGGGCGAGATGGGCTCACAAAGCTCTCTGGCACGCCTCCTTATGGCACATGCACGAG

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|47830830|gb|CK120514.1|CK120514
EST:     TCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTTGGTGCTGCT                         GTTGGTATGGAATTCTGGGCAAGATGGGCTCATAGAGCTCTGTGGCACGCT
genomic: TCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTTGGTGCTGCTgtaagtttca ... gattattcagGTTGGTATGGAATTCTGGGCAAGATGGGCTCATAGAGCTCTGTGGCACGCT
EST: gi|86061532|gb|DR357289.1|DR357289
EST:     TCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTTGGTGCTGCT                         GTTGGTATGGAATTCTGGGCAAGATGGGCTCATAGAGCTCTGTGGCACGCT
genomic: TCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTTGGTGCTGCTgtaagtttca ... gattattcagGTTGGTATGGAATTCTGGGCAAGATGGGCTCATAGAGCTCTGTGGCACGCT
EST: gi|86061534|gb|DR357291.1|DR357291
EST:     TCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTTGGTGCTGCT                         GTTGGTATGGAATTCTGGGCAAGATGGGCTCATAGAGCTCTGTGGCACGCT
genomic: TCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTTGGTGCTGCTgtaagtttca ... gattattcagGTTGGTATGGAATTCTGGGCAAGATGGGCTCATAGAGCTCTGTGGCACGCT
EST: gi|125193659|gb|EL208613.1|EL208613
EST:     TCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTTGGTGCTGCT                         GTTGGTATGGAATTCTGGG
genomic: TCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTTGGTGCTGCTgtaagtttca ... gattattcagGTTGGTATGGAATTCTGGG
EST: gi|125022756|gb|EL095025.1|EL095025
EST:     TCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTTGGTGCTGCT                         GTTGGTATGGAATTCTGGGCAAGATGGG
genomic: TCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTTGGTGCTGCTgtaagtttca ... gattattcagGTTGGTATGGAATTCTGGGCAAGATGGG
EST: gi|47830828|gb|CK120512.1|CK120512
EST:     TCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTTGGTGCTGCT                         GTTGGTATGGAATTCTGGGCAAGATGGGCTCATAGAGCTCTGTGGCACGCT
genomic: TCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTTGGTGCTGCTgtaagtttca ... gattattcagGTTGGTATGGAATTCTGGGCAAGATGGGCTCATAGAGCTCTGTGGCACGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatttttctgattcataaacaaaaaagtttggctgagatttttggattattcagGTTGGTATGGAATTCTGGGCAAGATGGGCTCATAGAGCTCTGTGGCACGCTTCTCTATGGAATATGCATGAG
      ttctgat  putative branch site (score: 3)
           attcataaacaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttcaaaacttcatcccaatttttctgattcataaacaaaaaagtttggctgagatttttggattattcagGTTGGTATGGAATTCTGGGCAAGATGGGCTCATAGAGCTCTGTGGCACGCTTCTCTATGGAATATGCATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT