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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattattgatatgtaactgtgttcatttacctttcatcctttgttattttcttgtggttactaacatcgttttccttttaacagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA

Basic information

species Arabidopsis thaliana
transcript AT5G65930.3
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 18
------------gtattattgatatgtaactgtgttcatttacctttcatcctttgttattttcttgtggttactaacatcgttttccttttaacagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA
             ||  | |  | | ||||  |     |   | ||  ||  ||||  |||    |     |  | |    |  ||   |    |||||| | || || ||||| || ||||| ||||| ||||| || ||||| ||||| ||||||||||||||||||||||| || || |||||   ||| | ||
gtgaccttttttttaacacttctttttaac-atacatgtgctcattagattatttgcaattggactccatgtgtttatcatgaattttgtgatgcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA

upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 17
----------------gtattattgatat--gtaactgtgttcatttacctttcatcctttg--ttattttcttgtggttactaacatcgttttcctttta------acagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA
                 |||  ||  | |   |  |     | || ||  ||| ||   | |   | ||  ||   |||| |  |    || ||   ||||       |||||  ||||||| || ||||| ||||| |||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| |||||    || | ||
gtgaatatttcaaatgctatcttttgtgttgatgccatcagtaatataaattttatttctaggactgttcactgagggtttcatatgatgtgttgaatttatgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA

upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
-------------------------------------------------gtattattgatatg-taactgtgttcatttacctttcatcctttgttattttcttgtggttactaacatc-gttttcctttta----acagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA
                                                  | |||||  || | |   ||  ||||| |    |      ||| |  |  | ||| | ||  ||  ||| |||    || |      |||||| ||||||| || ||||| ||||| ||||| || || || ||||| ||||| ||||||||||||||||| ||||||||||| |||||    || | ||
gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA

upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 19
--------gtat-tattgatatgtaactgtgttcatttacctttcatcctttgttat-----tttcttgtggttactaacatcgttttcc----ttttaa--cagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA
        | ||  |  |  | || | |      |||||  | |  |   | |  |      |  |||    | | || ||   | |       ||  ||  ||||||||||| ||||| ||||||||||| ||||| |||||||| ||||| |||||||||||||| |||||||| || || || || |||||   ||| | ||
gtatttgaggatacaaaggcaagtcatttatcatatttatttcttgtttatgggaacatatataacttacactcattatcaatttctcgtggatttgcaatgcagTATTTGGTGCAGTCTGCTGTAGATGGTTATAATGTTTGCATATTTGCCTATGGTCAAACTGGCTCTGGAAAGACATTTACAATCTATGGATCTGACAACA

upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 22
gtattattgatatgtaactgtgttcatttacctttcat-----cctttgttattttcttgtggttactaacatcgttttccttttaa---cagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA
     | | |||   || ||| || ||||     | ||     | | | | | || |   |  |||| ||  ||   |   |||  |   ||||||||||| || || ||||||||||| ||||| |||||||| ||||| |||||||||||||| |||||||| || || || || |||||    || | ||
--gcaagtcata---aattgtatttatttcttgcttatggaaacatatataacttacac-tcattaccaatttctcgtgtatttgcaatgcagTATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGATCTGGAAAGACATTTACAATCTATGGATCGGACATCA

upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 19
--------------------gtattattgatatgtaactgtgtt--catttacctttcatcctttgttat-tttcttgtggttactaacatcgttttccttttaa------------cagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA-------
                      || || | | | |   |  | |  ||| ||| ||  |     | | || ||| || |  | | || ||  ||||| |||||              ||||| || || || || ||||| ||||| ||||| |||||||| ||||| ||||||||||||||||||||||| ||||| || || |||||   ||| | ||       
gtcttagtataacaaattatagatcatagttttttgctttagatagcatatacattgaaatggatttaatattttttatactcattaccaatgtttttcttttggaaatttgcaatgcagtacttagTGCAATCTGCTGTGGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGTTCTGGAAAGACTTTTACAATCTATGGAGTTGAAAACAATCCTGG

upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 19
--------------------------gtattattgatatgtaactgtgttcatttacctttcatc--ctttgttattttcttgtggttactaacatcgttttccttttaa------------cagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA
                           |  || |  | ||     |     || ||| ||  |     |||  ||||||  | |  | | ||  |  ||||| |||||              ||||| || || || || ||||||||||| ||||| |||||||| ||||| || ||||||||||||||||| || ||||| || || |||||   ||| | ||
gcaagtcttagtataacaaattaaagatcctagttttttgctttagataatatgtacattgaaatagatttaatatttttctatactcattactaatgtttttcttttggacatttgcaatgcagTACTTAGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTACGGTCAAACTGGTTCTGGGAAGACTTTTACAATCTATGGAGCTGAAAACA

upper sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
--------gtattattgatatgtaactgtgttcatttacctttcatcctttgttattttcttgtggttactaacatc-gttttccttttaacagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA
          || ||  || | |    |       ||   || |||   ||  || ||     ||  |  ||   ||  | ||  |  |  ||||||||||| || |||||||||||||| ||||| || ||||| |||||||||||||| |||||||||||||| || ||||| || |||||   |||  | |
gcaagtcaacatcatgaatgtttgttagcaacttgtttgattacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttcatcctttgttattttcttgtggttactaacatcgttttccttttaacagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA
                             tactaac  putative branch site (score: 0)
                                   catcgttttcctttt  CT-rich tract
          tttgttattttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattattgatatgtaactgtgttcatttacctttcatcctttgttattttcttgtggttactaacatcgttttccttttaacagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA