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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataattagttatcaacaataatgctgtctaagaaaaaatatcatagaaaacagaggatcatgtttatgttttcagcttcattcctctgttttttgctctgctctgttttaacagaggatcaagtttatgtcttaagcctcctctgtttttggctttggtctgtttatactcagATGGTCACAGATTGCGTCAAGGCTTCCGGGTAGAACCGACAACGAGATCAAGAATCTATGGAACTCAAGCATCAAGAAGAAACTGAAACAAAGAGGCATT

Basic information

species Arabidopsis thaliana
transcript AT1G09540.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g18240.1 (Oryza sativa), 3'ss of exon 2
gtaataattagttatcaacaataatgctgtctaagaaaaaatatcatagaaaacagaggatcatgtttatgttttcagcttcattcctctgttttttgctctgctctgttttaacagaggatcaagtttatgtcttaagcctcctctgtttttggctttggtct----gtttatactcagATGGTCACAGATTGCGTCAAGGCTTCCGGGTAGAACCGACAACGAGATCAAGAATCTATGGAACTCAAGCATCAAGAAGAAACTGAAACAAAGAGGCATT
                                                                                | | |      |   |||| |||||    ||||  |    || |  |       |  ||||||||||  || |||| ||  | |     |  ||   ||| ||||| || |||||  || |||| || || ||||| ||||| |||||||||||||| ||||| ||| ||||||||||||| |||   || | |||||||
-------------------------------------------------------------------------------gtaaatttgaactcaattgcactgctagagtttaggatttaattacctcatcaaatcgagcctcctctaattatggccttttttttcacatcaatgagcagGTGGTCTCAAATTGCAACACGGCTGCCTGGAAGAACTGACAATGAGATCAAGAATCTCTGGAATTCATGCATCAAGAAGAAGCTGCGGCAGAAAGGCATT

upper sequence: AT1G09540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g04820.1 (Oryza sativa), 3'ss of exon 3
gtaataattagttatcaacaataatgctgtctaagaaaaaatatcatagaaaacagaggatcatgtttatgttttcagcttcattcctctgttttttgctctgctct-gttttaacagaggatcaagtttatgtcttaagcctcctctgtttttggctttggtctgtttatactcagATGGTCACAGATTGCGTCAAGGCTTCCGGGTAGAACCGACAACGAGATCAAGAATCTATGGAACTCAAGCATCAAGAAGAAACTGAAACAAAGAGGCATT
                                                                   ||   ||  | ||  |||              || |  || ||     ||  | | ||  || ||   | || |   | | |       |||   | | |  ||    || ||||| ||||||||  |   ||| || || || || |||||||||||||||||||| ||||| ||  ||||||||||||| ||    || | |||||||
------------------------------------------------------------------gtaaacttcaatctcaattggcactaccaaaattcaggactagtaactgcaaggcaacactttgatacatcaa-ctaacacagcc-----cttctatttttccatgagaagGTGGTCTCAGATTGCAGCTCAGCTGCCTGGGAGGACTGACAACGAGATCAAGAATCTCTGGAATTCTTGCATCAAGAAGAAGCTCCGGCAGAAAGGCATT

upper sequence: AT1G09540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G017520_T01 (Zea mays), 3'ss of exon 2
gtaataattagttatcaacaataatgctgtctaagaaaaaatatcatagaaaacagaggatcatgtttatgttttcagcttcattcctctgttttttgctctgctctgttttaacagaggatcaagtttatgtcttaagcctcctctgtttttggctttggtctgtttatactcagATGGTCACAGATTGCGTCAAGGCTTCCGGGTAGAACCGACAACGAGATCAAGAATCTATGGAACTCAAGCATCAAGAAGAAACTGAAACAAAGAGGCATT
                                              || ||||   | |  ||   | ||     |||   ||       |  |||||| | |  |  ||    |  ||   |||| || | | |||| |   |  | || ||   |||      |  ||   ||| ||||| ||||||||  ||||| | || || ||||| ||||||||||| |||||||| |||||||| |||||||||||||| ||    || | |||||||
---------------------------------------------gtaaaaaagctaagcccaaaatcat---cacagacaca-------gaattttgcacaggccgattgcttccaag---caagctt-tcttttaaccaggcctttttctttttttttccacatccatggacagGTGGTCTCAGATTGCAACAAGGTTGCCTGGAAGAACTGACAACGAGATTAAGAATCTCTGGAACTCGAGCATCAAGAAGAAGCTCCGGCAGAAAGGCATT

upper sequence: AT1G09540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G171781_T01 (Zea mays), 3'ss of exon 2
gtaataattagttatcaacaataatgctgtctaagaaaaaatatcatagaaaacagaggatcatgtttatgttttcagcttcattcctctgttttttgctctgctctgttttaacagaggatcaagtttatgtcttaagcctcctctgtttttgg--ctttggtctgtttatactcagATGGTCACAGATTGCGTCAAGGCTTCCGGGTAGAACCGACAACGAGATCAAGAATCTATGGAACTCAAGCATCAAGAAGAAACTGAAACAAAGAGGCATT
                                                            | |  || | |  |  ||    | |  || |  || |   ||||    | |   || || | || |||  |   |||        ||| | || |  ||||  | | |  ||    || ||||| || |||||  |   ||| || || || || || || |||||||||||||||||||||||  ||||||||||||| ||||  || | |||||||
-----------------------------------------------------------gtaaatttgaagcctgaagaagtagta-tcagaattctagactgc---atatgtgcaaagcagca-gttggtaatttag-------ctgatattagcactttactttttccatgagaagGTGGTCTCAAATTGCAGCGCAGCTGCCAGGGAGGACTGATAATGAGATCAAGAATCTATGGAACTCGTGCATCAAGAAGAAGCTGAGGCAGAAAGGCATT

upper sequence: AT1G09540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G127490_T01 (Zea mays), 3'ss of exon 2
gtaataattagttatcaacaataatgctgtctaagaaaaaatatcatagaaaacagaggatcatgtttatgttttcagcttcattcctctgttttttgctctgctctgttttaacagaggatcaagtttatgtcttaagcctcctctgtttttggc-tttggtctgtttatactcagATGGTCACAGATTGCGTCAAGGCTTCCGGGTAGAACCGACAACGAGATCAAGAATCTATGGAACTCAAGCATCAAGAAGAAACTGAAACAAAGAGGCATT
                                                              |  |||| |  |      |  |   || |  ||     ||||    |     || || | || |||  |   || |||      || | || ||  ||    | |  ||    || ||||| || |||||  |   ||| || || || || || || |||||||||||||||||||||||  ||||||||||||| || |  || | |||||||
------------------------------------------------------------gtaaatttaagcctgagaaatagta--tcagaattcaagactgc---atacatgcaaagcagca-gttggtaattttagc------tgatattagcacttcacttttccatgagaagGTGGTCTCAAATTGCAGCTCAGCTGCCAGGGAGGACTGATAATGAGATCAAGAATCTATGGAACTCGTGCATCAAGAAGAAGCTCAGGCAGAAAGGCATT

upper sequence: AT1G09540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaataattagttatcaacaataatgctgtctaagaaaaaatatcatagaaaacagaggatcatgtttatgttttcagcttcattcctctgttttttgctctgctctgttttaacagaggatcaagtttatgtcttaagcctcctctgtttttggctttg---gtctgtttatactcagATGGTCACAGATTGCGTCAAGGCTTCCGGGTAGAACCGACAACGAGATCAAGAATCTATGGAACTCAAGCATCAAGAAGAAACTGAAACAAAGAGGCATT
                                                                             | |       |||||       | ||    ||    |||    |  |  ||  | | || |   |  |   ||||    || |    || ||   |   ||| ||||||||||||||  ||   || || ||  | || |||||||||||||||||  | ||||||||| ||||||||||||| ||       |  || || 
-----------------------------------------------------------------------------gatgagagattctgtcaacccttgtgaatggt--cgacatgatacaacattgttatttttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaagtttatgtcttaagcctcctctgtttttggctttggtctgtttatactcagATGGTCACAGATTGCGTCAAGGCTTCCGGGTAGAACCGACAACGAGATCAAGAATCTATGGAACTCAAGCATCAAGAAGAAACTGAAACAAAGAGGCATT
                                        tctgttt  CT-rich tract
                                          tgtttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataattagttatcaacaataatgctgtctaagaaaaaatatcatagaaaacagaggatcatgtttatgttttcagcttcattcctctgttttttgctctgctctgttttaacagaggatcaagtttatgtcttaagcctcctctgtttttggctttggtctgtttatactcagATGGTCACAGATTGCGTCAAGGCTTCCGGGTAGAACCGACAACGAGATCAAGAATCTATGGAACTCAAGCATCAAGAAGAAACTGAAACAAAGAGGCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG