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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatctatctcatgtttatctttatgatgtataaagttgtataaatattctttctggtttcttaaaagagactatgactaaactataaggtttatttcatcaatatttacacagGTATTCACATCAACAAAGGTCTATTAGCTCTTGGAAATGTTATAAGTGCACTTGGAGATGAGAAAAAGAGAAAGGAAGGAGGTCACGTTCCTTACCGTGA

Basic information

species Arabidopsis thaliana
transcript AT5G60930.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G60930.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G10080.1 (Glycine max), 3'ss of exon 5
gttatctatctcatgtttatctttatgatgtataaagttgtataaatattctttctggtttcttaaaagagactatgactaaactataaggtttatttcatcaatatttacacagGTATTCACATCAACAAAGGTCTATTAGCTCTTGGAAATGTTATAAGTGCACTTGGAGATGAGAAAAAGAGAAAGGAAGGAGGTCACGTTCCTTACCGTGA
       |  |   ||| ||   |       ||   | |   | |   |||||| |   |||   ||   | |||| | | ||  || || | |  ||  |||  | |||    || ||||| || ||||| ||| | ||||||||||||||||| ||||||||||| |||||||| |||||| |||| |||||||| || || || || |||||
-----gaaaattgagttaat---tgcatcccattctgctagctgagagttctttataaattc---aagttgtctataatttaataatcagttattgtttttcatgaatta----gGAATTCATATAAACAAGGGTTTGTTAGCTCTTGGAAATGTAATAAGTGCACTGGGAGATGAAAAAAAGCGAAAAGAAGGAGGCCATGTACCATATCGTGA

upper sequence: AT5G60930.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G37800.1 (Glycine max), 3'ss of exon 5
gttatctatctcatgtttatctttatgatgtataaagttgtataaatattctttctggtttcttaaaagagactatgactaaactataa---ggtttatttcatcaatatttacacagGTATTCACATCAACAAAGGTCTATTAGCTCTTGGAAATGTTATAAGTGCACTTGGAGATGAGAAAAAGAGAAAGGAAGGAGGTCACGTTCCTTACCGTGA
                 ||     ||  || | ||  ||  ||     | ||| |||  || |  ||| | | | |   |||  ||| |   | | | |||  |      ||    ||| ||||| ||||| || ||| ||||||||||||| ||||||||||||||||| |||||||| | |||| |||| ||||| || || || || || || ||
----------------ataatagaattttgaa-aatcttacattgccctgcttgctgagttttataaatataatttt-ttaagttattaattgatctgtttgtttttccattgtcaagGCATTCATATCAATAAGGGTTTATTAGCTCTTGGGAATGTTATAAGTGCACTGGGAGATGAAAGAAAGCGAAAAGAAGGTGGCCATGTGCCATATCGCGA

upper sequence: AT5G60930.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G36030.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------gttatc-tatctcatgtttatctttatgatgtataaagttgtataaatatt--ctttctggtttcttaaaagagact-atgacta-aactataaggtttatttcatcaata-------tttacac-----agGTATTCACATCAACAAAGGTCTATTAGCTCTTGGAAATGTTATAAGTGCACTTGGAGATGAGAAAAAGAGAAAGGAAGGAGGTCACGTTCCTTACCGTGA
                                                                      |||| ||| |||| |||   |  || ||| ||| | || |  |||| ||   || ||  |||  ||   |||  | || | || || | |     |||||| || |  |       ||| ||      ||| ||||| ||||| || ||| ||||||||||||| ||||| ||||||||||| |||||||| | |||| |||| ||||| || || || || || || ||
gtattcctgttgataggacatattgataagaaaaggaataaaattaatacaaaaaatattttctctaatatatcatatatcatattttcataaatcatg-atagaattttgaaaatcttacattgctcttttgctagctgagctttataaatataattttttaagttatttaatgatcagtttgtttttccattgtcaagGCATTCATATCAATAAGGGTTTATTAGCTCTTGGGAATGTAATAAGTGCACTGGGAGATGAAAGAAAGCGAAAAGAAGGTGGCCATGTGCCATATCGCGA

upper sequence: AT5G60930.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S74_30V6.1 (Physcomitrella patens), 3'ss of exon 5
gttatctatctcatgtttatctttatgatgtataaagttgtataaatattctttctggtttcttaaaagagactatgactaaactataaggtttatttcatcaatatttacacagGTATTCACATCAACAAAGGTCTATTAGCTCTTGGAAATGTTATAAGTGCACTTGGAGATGAGAAAAAGAGAAAGGAAGGAGGTCACGTTCCTTACCGTGA
    ||||| | |      |  ||  | | | |   | ||   | | |  |    | |    | |  | |  | || || | | ||       ||||      ||||  |  ||||| | ||||| || |||||||| ||||| ||||||||||| || ||||| ||||| ||||| || ||| | ||||||||||| || || || ||||||||
----tctatgttaaaccgcttctttcggt-tgtgttgatggtaagagaggccgcttagcccatcagtatactc-atcacaagaatac------tattctg---atatccatgcagGTGTCCACATAAATAAAGGTCTTTTAGCCCTTGGAAATGTGATCAGTGCCCTTGGTGATGATAAGAAGCGGAAGGAAGGAGGGCATGTCCCGTACCGTGA

upper sequence: AT5G60930.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S80_21V6.1 (Physcomitrella patens), 3'ss of exon 5
gttatctatctcatgtttatctttatgatgtataaagttgtataaatattctttctggtttcttaaaagagactatgactaaactataaggtttatttcatcaata-tttacacagGTATTCACATCAACAAAGGTCTATTAGCTCTTGGAAATGTTATAAGTGCACTTGGAGATGAGAAAAAGAGAAAGGAAGGAGGTCACGTTCCTTACCGTGA
   |    ||| | ||    ||||    |   | | | |        | ||     |  |||   |||| || |||       || | |   |||| |  || |    ||   ||||| | || |||||||| || ||  |||| ||||| || || || |||||  | || ||||| |||||||||||||| |||||||||||||||||| | ||
---aaagttctgacgtgctgcttt-catttcttgatgctacg---gcactcaagtag--ttcgagaaagcgagtat-------ctttgaaagttatgttttcgacggcttttgcagGTGTGCAAATCAACAAGGGACTTCTAGCACTTGGCAACGTAATTAGTGCTTTAGGGGATGACAAAAAGAGAAAGGAGGGAGGTCACGTTCCTTACAGAGA

upper sequence: AT5G60930.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S237_18V6.1 (Physcomitrella patens), 3'ss of exon 5
gttatctatctcatgtttatctttatgatgtataaagttgtataaatattctttctggtttcttaaaagagactatgactaaactataag---gtttatttcatcaatatttacacagGTATTCACATCAACAAAGGTCTATTAGCTCTTGGAAATGTTATAAGTGCACTTGGAGATGAGAAAAAGAGAAAGGAAGGAGGTCACGTTCCTTACCGTGA
                  |        |     | |    |||| ||  |  |||  |   |   | | |         | || ||   |   || | |||  |    |||  | ||||||||||||| |||| ||| || ||||| |||||||| || || |||||||| || ||||||| |||| |||  ||||||||||| ||||||||  | ||
------------------aagcgagccagccccacatgcatatagatcctagttcctgagccaagacaaatttcgctgtttaattaactgtcggtatgtttggtacgaattatctcagGTATTCACATAAACAGAGGCCTTTTAGCACTTGGAAACGTGATCAGTGCACTAGGTGATGAGAGAAAGCGAAGAGAAGGAGGTCATGTTCCTTATAGAGA

upper sequence: AT5G60930.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S36_179V6.1 (Physcomitrella patens), 3'ss of exon 2
gttatctatctcatgtttatctttatgatgtataaagttgtataaatattctttctggt-ttcttaaaagagactatgactaaactataaggtttatttcatcaatatttacacagGTATTCACATCAACAAAGGTCTATTAGCTCTTGGAAATGTTATAAGTGCACTTGGAGATGAGAAAAAGAGAAAGGAAGGAGGTCACGTTCCTTACCGTGA------------------
                             |  |    ||| | |   || | | || || ||  |  | |||| | |||  |  |  ||   | |     | |  | || ||    || | ||||| || | ||| ||| |||| ||||||||||| || |||||||| || ||||| || ||| | || ||||||||||||||||||||||| ||                  
-----------------------------gagtgtttttg-agacgaatgcgtccttgtattaatgcatgagattctgaagatgccgtatattgtgggataaccttgttcac----gtgtgcacataaatagagGCCTACTAGCACTTGGAAATGTGATCAGTGCACTAGGTGATGAAAAGAAGCGTAAAGAAGGAGGTCACGTTCCTTACCGAGACAGCAAGTTAACACGATT

upper sequence: AT5G60930.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ15989 (Selaginella moellendorffii), 3'ss of exon 5
gttatctatctcatgtttatctttatgatgtataaagttgtataaatattctttctggtttcttaaaagagactatgactaaactataag-gtttatttcatcaatatttacacagGTATTCACATCAACAAAGGTCTATTAGCTCTTGGAAATGTTATAAGTGCACTTGGAGATGAGAAAAAGAGAAAGGAAGGAGGTCACGTTCCTTACCGTGA
                                                    | |   || | |    |  |   | |  ||  | | |   |  ||||  | | | ||    ||||| |||| |||||||||||||| ||||||||||| ||||| || || |  |||||||| || || | | | ||||||  | | || || || ||| | ||
---------------------------------------------------gtacgcattgcatggctgccatcgttaagaagttgtcatcatccattt--ttattgttcttgcagGTGTTCATATCAACAAAGGTCTTTTAGCTCTTGGGAATGTAATTAGCGTTCTTGGAGAGGACAAGAGGCGGAAGGAACCAAGACATGTGCCGTACAGGGA

upper sequence: AT5G60930.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ07934 (Selaginella moellendorffii), 3'ss of exon 5
gttatctatctcatgtttatctttatgatgtataaagttgtataaatattctttctggtttcttaaaagagactatgactaaactataag-gtttatttcatcaatatttacacagGTATTCACATCAACAAAGGTCTATTAGCTCTTGGAAATGTTATAAGTGCACTTGGAGATGAGAAAAAGAGAAAGGAAGGAGGTCACGTTCCTTACCGTGA
                                                    | |   || | |    |  |   | |  ||  | | |   |  ||||  |   | ||     |||| |||| |||||||||||||| ||||||||||| ||||| || || |  |||||||| || || ||| ||||||||  | | || || || ||| | ||
---------------------------------------------------gtacgcattgcatggctgccatcgttaagaagttgtcatcatccattttttt--tgttcttgtagGTGTTCATATCAACAAAGGTCTTTTAGCTCTTGGGAATGTAATTAGCGTTCTTGGAGAGGACAAGAAGCGAAAGGAACCAAGACATGTGCCGTACAGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttaaaagagactatgactaaactataaggtttatttcatcaatatttacacagGTATTCACATCAACAAAGGTCTATTAGCTCTTGGAAATGTTATAAGTGCACTTGGAGATGAGAAAAAGAGAAAGGAAGGAGGTCACGTTCCTTACCGTGA
                gactaaa  putative branch site (score: 2)
                               tttatttcatcaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatctatctcatgtttatctttatgatgtataaagttgtataaatattctttctggtttcttaaaagagactatgactaaactataaggtttatttcatcaatatttacacagGTATTCACATCAACAAAGGTCTATTAGCTCTTGGAAATGTTATAAGTGCACTTGGAGATGAGAAAAAGAGAAAGGAAGGAGGTCACGTTCCTTACCGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG