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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtccagaagagttgcacagcagagaaagataacatgaatgaggagtttgccgtctgcgggttataacgccattttacaattcatcttaacctccagGTTGGAGCTGACATTGTTAAGAAAGCATTGAGCTACCCACTGAAGTTAATCGCCAAGAACGCTGGTGTCAATGGCAGCGTTGTCAGTGAGAAG

Basic information

species Arabidopsis thaliana
transcript AT5G56500.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G56500.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 11
----------------------------------------------------------------------------gttagtccagaagagttgcacagcagagaaagataacatgaatgaggagtttgccgtctgcgggttataacgccattttacaattcatcttaacctcc-agGTTGGAGCTGACATTGTTAAGAAAGCATTGAGCTACCCACTGAAGTTAATCGCCAAGAACGCTGGTGTCAATGGCAGCGTTGTCAGTGAGAAG
                                                                             ||   || |      || | |   |  | | || ||    ||   || ||||  |||         | ||    || ||    |    | ||| |   ||||||||||||| ||||| | || |||  |||||||||| || || || || || ||||| |||||||| ||||| |||||||| |  ||||||
gtttacaaccatgatctactttattcattgtttttgttcgagtgttctataaacctcatctctcaaaagttctgtttttgtgcctgctactatgtatatgggttagaaatgacc---atctcgaatttgttgtcctttctaattgac-ttgttgtatgtattgcttgaactttttagGTTGGAGCTGAAATTGTAAGGAGAGCGCTGAGCTACCCGCTTAAATTGATTGCTAAGAATGCTGGTGTTAATGGAAGCGTTGTTACCGAGAAG

upper sequence: AT5G56500.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G083716_T03 (Zea mays), 3'ss of exon 10
gttagtccagaag----agttgcacagcaga---gaaagataacatgaatga-ggagtttgccgt--ctgcgggttataacgccattttacaattcatcttaacctccagGTTGGAGCTGACATTGTTAAGAAAGCATTGAGCTACCCACTGAAGTTAATCGCCAAGAACGCTGGTGTCAATGGCAGCGTTGTCAGTGAGAAG
|| |   || ||     | |  |  |    |   ||||||  |        |  |||     | |  ||   ||||  |||      | ||| |      | || |  ||||||||||||| || || | ||  ||  ||||||||||||| || || || || || ||||| |||||||||||||| ||||||| |||||||
gtaaaaacaaaatctgcaatcccgtaattcatttgaaagaggatggaggcaacagagcacaaccttgctataggtt-caactatggctgacattctgaactgacatt-agGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATTGCTAAAAACGCCGGTGTCAATGGCAGTGTTGTCACTGAGAAG

upper sequence: AT5G56500.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G095252_T02 (Zea mays), 3'ss of exon 5
gttagtccagaagagttgcacagcagagaaagataacatgaatgaggagtttgccgtctgcgggttataacgccattttacaattcatcttaacctccagGTTGGAGCTGACATTGTTAAGAAAGCATTGAGCTACCCACTGAAGTTAATCGCCAAGAACGCTGGTGTCAATGGCAGCGTTGTCAGTGAGAAG
|| ||  || ||    ||        | ||   ||    || |   |||    |    |   ||||  |     | |       | |  |  |||   ||||||||||||| || || | ||  ||  ||||||||||||| || || || || || || || ||||||||||||||||| |||| |||||||
gtaagaacaaaatctgtgattgattaaaaagagta----gactacagagcagccttgttataggttcgagtataactgacacgctgaagt--accattagGTTGGAGCTGAAATAGTAAGGAGGGCCCTGAGCTACCCACTTAAATTGATTGCTAAAAATGCCGGTGTCAATGGCAGCGTCGTCACTGAGAAG

upper sequence: AT5G56500.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 10
--------------------------------------------gttagtccagaagagttgcaca-gcagagaaagataacatgaatgaggagtttg--ccgtctgcgggttataacgccattttacaattcatcttaac--ctccagGTTGGAGCTGACATTGTTAAGAAAGCATTGAGCTACCCACTGAAGTTAATCGCCAAGAACGCTGGTGTCAATGGCAGCGTTGTCAGTGAGAAG
                                            |||     |     |||      || | ||||     | ||| ||  |  ||     |  || |  |      |   | || | ||||    ||||    | |||||||||||||| ||||| || | |||  | || |||||  |||| ||||| ||||| ||||||||||||||||| || |||||||||||||||
gtgagtcatttatttgatatggagagaatacaagtttcttggatgttgtgatatttttgttttgggtgctgggaaatgcttc-tgactgttgctttcaactcaactcctagcgtggtcatgacttcaaaattgtgtttaattgttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAAAACGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAG

upper sequence: AT5G56500.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 10
-----------------------------------------------gttagtccagaagagttgcacagcagagaaagataacatgaatgaggagtttg---ccgtctgcgggttataacgccattttacaattcatcttaacctc--cagGTTGGAGCTGACATTGTTAAGAAAGCATTGAGCTACCCACTGAAGTTAATCGCCAAGAACGCTGGTGTCAATGGCAGCGTTGTCAGTGAGAAG-------
                                               || |        |  |||       |  || | |  | ||| ||  |  ||      |  || |         |   | || | ||||    ||||  |   |||||||||||||| ||||| || | |||  | || |||||  |||| ||||| |||||||| |||||||||||||| || |||||||||||||||       
gtgagtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgct--cctgactgttgttttcaaattcaactccaaacatggtcatgacttcaaaattgtgtttaatttttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAGAATGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAGGTATCAA

upper sequence: AT5G56500.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G18760.1 (Glycine max), 3'ss of exon 10
-----------------------------------------------gttagtccagaagagttgcacagcagagaaagataacatgaatgaggagtttg---ccgtctgcgggttataacgccattttacaattcatcttaacctc--cagGTTGGAGCTGACATTGTTAAGAAAGCATTGAGCTACCCACTGAAGTTAATCGCCAAGAACGCTGGTGTCAATGGCAGCGTTGTCAGTGAGAAG
                                               || |        |  |||       |  || | |  | ||| ||  |  ||      |  || |         |   | || | ||||    ||||  |   |||||||||||||| ||||| || | |||  | || |||||  |||| ||||| |||||||| |||||||||||||| || |||||||||||||||
gtgagtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgct--cctgactgttgttttcaaattcaactccaaacatggtcatgacttcaaaattgtgtttaatttttgcagGTTGGAGCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAGAATGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAG

upper sequence: AT5G56500.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G18760.3 (Glycine max), 3'ss of exon 10
-------------------------------------------gttagtccagaagagttgcacagcagagaaagataacatgaatgaggagtttg---ccgtctgcgggttataacgccattttacaattcatcttaacctc--cagGTTGGAGCTGACATTGTTAAGAAAGCATTGAGCTACCCACTGAAGTTAATCGCCAAGAACGCTGGTGTCAATGGCAGCGTTGTCAGTGAGAAG
                                           || |        |  |||       |  || | |  | ||| ||  |  ||      |  || |         |   | || | ||||    ||||  |   |||||||||||||| ||||| || | |||  | || |||||  |||| ||||| |||||||| |||||||||||||| || |||||||||||||||
gtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgct--cctgactgttgttttcaaattcaactccaaacatggtcatgacttcaaaattgtgtttaatttttgcaggttggagCTGATATTGTGAAAAGAGCTCTTAGTTACCCTTTGAAATTAATTGCCAAGAATGCTGGTGTCAATGGTAGTGTTGTCAGTGAGAAG

upper sequence: AT5G56500.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 11
----------------------------------------------------gttagtccagaagagttgcacagcagagaaagataacatgaatgaggagtttgccgtctgcgggttataacgc----cattttacaattcatcttaacc---tccagGTTGGAGCTGACATTGTTAAGAAAGCATTGAGCTACCCACTGAAGTTAATCGCCAAGAACGCTGGTGTCAATGGCAGCGTTGTCAGTGAGAAG
                                                    | |  |||  |    ||| |       ||| |    ||  |      | | |   | |  | || ||||  |     | | ||| | |  |  | ||     | |||||||||||||| ||||| |||| ||| ||||| ||||| ||||||||||| ||||| || |||||||| ||||| || || ||||||||||||
gtgatacttgtggctgtgttcaatatgggatttgtccaataccttgagttttggttttcccaatagtttgaatcatgctgaatgtgttcaaaatgtgtcaatatattggc--caggatatagtgtttatcctcttaaagtggacttgaattgattgcagGTTGGAGCTGATATTGTCAAGAGAGCTTTGAGTTACCCTCTGAAGTTAATTGCCAAAAATGCTGGTGTTAATGGAAGTGTGGTCAGTGAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagtttgccgtctgcgggttataacgccattttacaattcatcttaacctccagGTTGGAGCTGACATTGTTAAGAAAGCATTGAGCTACCCACTGAAGTTAATCGCCAAGAACGCTGGTGTCAATGGCAGCGTTGTCAGTGAGAAG
                                          tcttaac  putative branch site (score: 2)
                                      ttcatctt  CT-rich tract
                             attttacaattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtccagaagagttgcacagcagagaaagataacatgaatgaggagtttgccgtctgcgggttataacgccattttacaattcatcttaacctccagGTTGGAGCTGACATTGTTAAGAAAGCATTGAGCTACCCACTGAAGTTAATCGCCAAGAACGCTGGTGTCAATGGCAGCGTTGTCAGTGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC