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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctataacatgatatccaccctatcttttgttccaaattatgtaaaggtcaatctcattgttaattaagttagtatttgggataatcttgttgattttgaaggttagatttcccagcaacccatacttgggtctgcttttcgctaattttacttatggaacaatgtgggattgataatcttaattctgacagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGAC

Basic information

species Arabidopsis thaliana
transcript AT3G09810.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 6
gtaagctataaca-tgatatccac-cctatcttttgttccaaatta-tgtaaaggtcaatctcattgttaattaagttagtatttgggataatcttgttgattttgaaggttagatttcccagcaacccatacttgggtctgcttttcgctaattttacttatggaacaatgtgggattgataatcttaattc-tgacagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGAC
||| | | |     ||||| | |  ||| |  ||||||     ||| |||  | | || |||      |  |    | |    |  |    | ||     ||    |   |   ||||     | | |||    |    |||   |   |  | || | | |||  |||   | |  |||  ||  ||    | |  ||||||||||| || || |  |||||||||||  |||||||||||||||| ||||| |||||||| || ||| | |||||||| ||  |||| ||  | ||  
gtatgttgttctgctgataccaaaacctgtgctttgtttggtgttaatgttgaag-cattcttcacactggtctgatgatctct--gatcgacctgagaaatgcaaattatcctatttgtattctagccacttctattgctgtcctggac--agttaattaatg--acaccattgatttgtgaacattgtccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTATGGTGATATTATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCT

upper sequence: AT3G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G404855_T01 (Zea mays), 3'ss of exon 5
gtaagctataacatgatatccaccctatcttttgttccaaattatgtaaaggtcaatctcattgttaattaagttagtatttgggataatcttgttgattttgaaggttagatttcccagcaacccatacttgggtctgcttttcgctaattttacttatggaacaatgtgggattgataatcttaatt-ctgacagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGAC
                              | |||||       || ||   |  || |   ||| ||||    | ||  |     | ||   |      |  |   | ||      |    | | ||  ||     | || ||    |  | | || |||      |     |||   ||    | || |   ||||||||||| || || |  ||||||||||| || ||||||||||| |||||||| || || || |||||| | ||||||||  |  |||||||  | || |
-----------------------------gtatgttctctcagctgaaagtattcatttttctgtcaattgttgttgtgctcttagtgatg--gcctgcctgaagcatcaggcagtgctaatatcaattatttttcttactatt-ataagctgtgctgatgctgatgtaactcattctgaactgcatttgcctccagCTTGTGAAGAATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTATGGTGACATCATTAGCGATCTATGTGCTGGTTTGATTGGGGGCTTGGGCC

upper sequence: AT3G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 5
gtaagctataacatgatatccaccctatcttttgttccaaattatgtaaaggtcaatctcattgttaattaagttagtatttgggataatcttgttgattttgaaggttagatttcccagcaacccatacttgggtctgcttttcgctaattttacttatggaacaatgtgggattgataatcttaattctgacagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGAC
                                                               ||   ||  || |||   ||  |  |||   ||   | | ||   | |||   |     |    || ||   |||   | |    |  ||| || ||       | |  ||     | |||   |||    |||||||||| || || |  |||||||| || || |||||||||||||||||||| || ||||| || ||| | ||||||||  |  | |||||  | || |
---------------------------------------------------------------gtatgttctgtcagt---tgaaagtatccgtttctctgtcaattgttgataggctcttgatagttatttt--tcttaatattatcagcttttctgatactgttgtttatgaactgca-tctgccttc----agCTTGTGAAGAATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTATGGTGACATTATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCC

upper sequence: AT3G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0040g01700.t01 (Vitis vinifera), 3'ss of exon 4
gtaagctataacatgatatccaccctatcttttgttccaaattatgtaaaggtcaatctcattgttaattaagttagtatttgggataatcttgttgattttgaaggttagatttcccagcaacccatacttgggtctgcttttcgctaattttacttatggaacaatgtgggattgataatcttaattctgacagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGAC
                                                                                   | | ||| |    ||      || | |   |||   |||    ||||   |   |||  |  | |||   ||     ||||| |       ||     |||| | |   |||||||||||| || || || ||||||||||| ||||||||||| || |||||||| || ||||| || ||| | ||||||||  |  |||||||||||||  
-----------------------------------------------------------------------------------gcaaaatatgtaagaaaaacgagatca---ttctaggcatatgatac--agaaatgcactaggataaaacta-----ggaaccactctaactt--ctctcttgaata-aacagCTTGTGAAGAATCCTGCGCTTTTTGATGTGTTGGTGATGCCTAACCTCTATGGTGACATTATTAGTGATCTCTGTGCTGGCTTGATTGGGGGACTAGGCT

upper sequence: AT3G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S83_44V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaagctataacatgatatccaccctatcttttgttccaaattatgtaaaggtcaatctcattgttaattaagttagtatttgggataatcttgttgattttgaaggttagatttcccagcaacccatacttgggtctgcttttcgctaattttacttatggaacaatgtgggattgataatcttaattctgacagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGAC
                                                                                |||||||     |  |||| | ||||   | |   | ||   ||  |||  |   | |   | |   ||  | ||  |||  | | || ||          | ||  || || ||| | || || ||||| ||| | |||||||| ||||| ||||| ||||| || || ||||| |||||||||||||| ||||| ||  |||| || ||||| |
--------------------------------------------------------------------------------ttgggat-----tagtgatat-gaagagaataacacacactcacatatatatatatatatatata--tatatatatatataaatccatttg-------ccgtgttccttgtg-cagTTGGTAAAGAACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTACGGTGATATCATCAGCGATTTGTGCGCTGGTCTAATTGGCGGTCTAGGGC

upper sequence: AT3G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S199_33V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaagctataacatgatatccaccctatcttttgttccaaattatgtaaaggtcaatctcattgttaattaagttagtatttgggataatcttgttgattttgaaggttagatttcccagcaacccatacttgggtctgcttttcgctaattttacttatggaacaatgtgggattgataatcttaattctgacagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGAC
                                                                                          |   ||   || ||  |||     |    | |    |||     ||   | |  || | |  | |  ||    | | |     |  | |    |  | |   |||| | ||||| |||||| || | |||||||| ||||||||||| ||||| ||||| ||||| ||||||||||| |||||||||||| |||| ||  ||||| 
------------------------------------------------------------------------------------------ccatttcccttcgactgtttttagtgtgtgta-tgaatatgatcgttatcctgacgatgacgtaatcta----atatttcttaaacg-tgccttgcacttgtacagTTGGTGAAGAACCCATCATTGTTTGATGTGTTGGTGATGCCTAATCTTTATGGTGATATCATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGAT

upper sequence: AT3G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S78_143V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaagctataacatgatatccaccctatcttttgttccaaattatgtaaaggtcaatctcattgttaattaagttagtatttgggataatcttgttgattttgaaggtt---agatttcccagcaacccatacttgggtctgcttttcgctaattttacttatggaacaatgtgggattgataatcttaattctgacagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGAC
        | |  ||  |  ||| | ||||    || ||  | |||| | |    | ||    |||   |||   | | |  ||    |       |||   |||  ||   |||||  || | ||    | |  |  |    |   ||| ||  || | | |    |  |   ||| |  | ||  | ||     ||| | || ||||| || | ||| || ||||||||||||||||| ||| | |||||||| |||||||| ||| | |||||||| ||  |||| ||  | ||  
-------gtta-gtgtcaagcactcaatctggcatttca--tgatgtcaggccacagcttgccgtt---taatgcaatgtgcggctgcaatccacagatgaggaaccttgaaagattctcctgtaa----tgccagatttccttaagcgcaaacgtttcat-tcttcctgtcatggactcgtgattgtgat----gcagTTGGTAAAAAATCCGGGACTCTTCGATGTCTTGGTGATGCCTAATTTATATGGAGACATTATCAGTGATCTCTGTGCTGGTCTGATTGGAGGGTTGGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgctaattttacttatggaacaatgtgggattgataatcttaattctgacagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGAC
                                        tcttaat  putative branch site (score: 3)
                                attgataatcttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctataacatgatatccaccctatcttttgttccaaattatgtaaaggtcaatctcattgttaattaagttagtatttgggataatcttgttgattttgaaggttagatttcccagcaacccatacttgggtctgcttttcgctaattttacttatggaacaatgtgggattgataatcttaattctgacagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA