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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagctttgttaaaaaagcattccttttcacaactctttttactaacaaaagttttcaatttcatagctacttattatgtttctcattgtttggtttgcctttgtttcagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G61780.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G61780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g32350.2 (Oryza sativa), 3'ss of exon 2
gtcagctttgttaaaaaagcattccttttcacaactctttttactaacaaaagttttcaatttcatagctacttattatgtttctcattgtttggtttgcctttgtttcagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAG
      ||| |     |         ||    |  | || ||| |  | |   ||| |   | | |   | |||  ||||| |   |        ||||   | | |  |||||||| | || ||  | ||||| || ||||| |||||||||||||||||||||||||| || ||||| ||||||
------tttctcgtgtagttcaaaacttatgaatttattcttattctccagtctttcc--ctccctttttgctt--tatgtattgaaactaaaactttgtgct-gctcaagGCTCGCCGTGGTGGAGTGGATGAACCATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG

upper sequence: AT5G61780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: AC207890.3_FGT002 (Zea mays), 3'ss of exon 1
gtcagctttgttaaaaaagcattccttttcacaactctttttactaacaaaagttttcaatttcatagctacttattatgtttctcattgtttggtttgcctttgtttcagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAG
    ||  | | ||  | | | ||  |||||  | | |   | ||    |   |  ||| ||   |||      ||| | ||| |   |  ||  ||     | |||  |||||||| | || ||  | || ||||| ||||||||||||||||| |||||||||||||||||||| || || |||
--ttgcactttgaactatgtactcagtttca--attgtagcttcttgatattttactcatttctctag------attttattttttgcttgtttattcatggt-gttctagGCTCGCCGTGGTGGAGTTGACGAGCCCTTTGCATGGGAAAGCAGAGAGTTTCTAAGGAAGCTTTGTATAGGGAAG

upper sequence: AT5G61780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
gtcagctttgttaaaaaagcattccttttcacaactctttttactaacaaaagttttcaatttcatagctacttattatgtttctcattgtttggtttgcctttgtttcagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAG
    |   | || |   || ||   || |  |     | || || |   | | | |||   ||  |  ||| || | || |||| | ||||||   ||     || |  |||||||  | || ||  | |||||||| ||||||||||||||||| |||||||| |||||||| ||||| || |||
--tggaactatttactgagtatcaattgtagc----ttcttgacaattgacattcttctcatttct--ctagttttcatttttcgc-ttgttta--ttcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG

upper sequence: AT5G61780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G00910.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------------gtcagctttg---ttaaaaaagcattccttttcacaactctttttactaacaaaagttttcaatttcatagct-acttattatgtttctcattgtttggtttgcctttgtttcagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAG
                                                                         |   ||||   || |  | |  |||| | |   || |  |   | |   ||| | ||||  |   |  ||| |  | ||    ||    || |||| ||     || |   |||| || ||||| ||| |||||||||| ||||| |||||||| || ||||||||| |||||||||||||||| |||
gtaattttacttggttcatggaattgaaattgctgtgactgtgaattgaaattcttttgaaattctgttgtaccgattttgtggtttatgatgttttccgtattctaatt--tcaaaattgaaaatgctttctgtgctactgctgaggtgtttacattaaagttctttgtttaaaaattttgatagGCGCGTAGAGGTGGTGTAGATGAGCCGTTTGCGTGGGAAAGTAGAGAGTTTCTACGGAAGCTTTGCATTGGGAAG

upper sequence: AT5G61780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G33320.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------------gtcagctttg--ttaaaaaagcattccttttcacaactctttttactaacaaaagtttt-----caatttcatagctacttattatgt-ttctcattgtttggtttgcctttgtttcagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAG
                                                                     ||   ||||  |||| || |  |||| | |   || | |    | | | ||  | |||     | | |||   | |  |||   |   ||     | |||| ||      | |   |||| || ||||| ||| |||||||||| |||||||||||||| || ||||||||| ||||||| |||||||| |||
gtaattttacttgattcatggatattttgttgtaactatgaactgaaattgttttgaaatgcttctgtatcgattttgtgttaataatgttttccgtgttctaatt-tcgaaattgaaaattgctttttgtgctacttctggggtgtttacattacgttaaagctctttgtttaaaaaatttgctagGCGCGTAGAGGTGGTGTAGATGAGCCGTTTGCATGGGAAAGTAGAGAGTTTCTACGGAAGCTCTGCATTGGGAAG

upper sequence: AT5G61780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G38010.1 (Glycine max), 3'ss of exon 2
gtcagctttgttaaaaaagcattccttttcacaactctttttactaacaaaagttttcaatttcatagctacttatt---atgtttctcattgtttggtttgcctttgtttcagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAG
   |  |||  | |     | ||  ||      | |  ||   | |  |||   ||| |   ||   | || ||  |    ||||  |  || |||  ||     || ||  |||| || ||||| ||| | || ||||||||||||||||||||||| |||||||| |||||||| ||||| || |||
-gtacttttagttatttgactttttttcattggattaattaatcaattaaataatttaaggctctgtgttaattgctttagtgttgttttttttttttttgcgaattattgtagGCGCGTAGAGGTGGTGTGGACGAGCCTTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG

upper sequence: AT5G61780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G17050.4 (Glycine max), 3'ss of exon 2
gtcagctttgttaaaaaagcattccttttcacaactctttttactaacaaaagttttcaatttcatagctacttatt---atgtttctcattgtttggtttgcct-ttgtttcagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAG
   || |||  | |     | ||  ||      | |  ||   | |  |||   ||| ||  |    | || ||  |    ||||| |  || |||  |||||   ||||   |||| || ||||| ||| | || ||||| ||||||||||||||||| |||||||| |||||||| ||||| || |||
-gtagttttagttatttgactttttttcattggattaattaatcaattaaataatttaaagctttgtgttaattgctttagtgttttttttttttttttttgcgaattgtggtagGCGCGTAGAGGTGGTGTGGACGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG

upper sequence: AT5G61780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0283g00020.t01 (Vitis vinifera), 3'ss of exon 2
gtcagctttgttaaaaaagcattccttttcacaactctttttactaacaaaagttttcaatttcatagctacttattatgtttctcattgtttggtttgcctttgtttcagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAG
      |||||||| ||    ||  |||   || ||     |  ||| ||| | | |  |||      ||  | | |  |  |||| || | |  | |  | ||  |  |||| || || || ||  | |||||||| ||||||||||| ||||| |||| | |||||||||| ||||||||||||
--ggattttgttaagaacattttgttttgttcagct----gtgataataaatggtattgatta---gacttatgactgggagtctctttttctcctctctcattcct--agGCCCGTAGGGGTGGAGTTGATGAGCCGTTTGCATGGGACAGCAGAGAGTATTTAAGGAAGCTCTGCATTGGAAAG

upper sequence: AT5G61780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ35031 (Selaginella moellendorffii), 3'ss of exon 1
gtcagctttgttaaaaaagcattccttttcacaactctttttactaacaaaagttttcaatttcatagctacttattatgtttctcattgtttggtttgcctttgtttcagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAG
                                             |    || || |   |||   ||  | | ||   || ||      ||||   || ||| |   ||||| || || |     |  ||||||||||| |||||||| ||| |||||||||| |||||    ||||| || |||
------------------------------------------gtgagtgcaaattct-ggttttgcaggcagtgatccggtctcatgccttttg--ctggcttgg---cagGCCCGAAGGGACACCAGCGATGAGCCTTTCGCATGGGACAGCCGGGAGTTTCTCAGGAACAAATGCATCGGGAAG

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|86069265|gb|DR365022.1|DR365022
EST:     CACCTCCGGAAAAGACCATCACTCTTTCTTCTCTTATGGCTCCTAAGATG                         GCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTT
genomic: CACCTCCGGAAAAGACCATCACTCTTTCTTCTCTTATGGCTCCTAAGATGgtcagctttg ... tttgtttcagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTT
EST: gi|86069266|gb|DR365023.1|DR365023
EST:     CACCTCCGGAAAAGACCATCACTCTTTCTTCTCTTATGGCTCCTAANATG                         GCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTT
genomic: CACCTCCGGAAAAGACCATCACTCTTTCTTCTCTTATGGCTCCTAAGATGgtcagctttg ... tttgtttcagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatttcatagctacttattatgtttctcattgtttggtttgcctttgtttcagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAG
                                       tttgcctttgtttc  CT-rich tract
             tacttattatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagctttgttaaaaaagcattccttttcacaactctttttactaacaaaagttttcaatttcatagctacttattatgtttctcattgtttggtttgcctttgtttcagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA