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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcctagattatcattattgtagtctgcactctcaaccttaacctcctctcctattctggttagttcgcaagaagctcaatttgatgatagtatctctgatctagGTCATTGACAAGTCCTTTGGATTTGATACTGCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTG

Basic information

species Arabidopsis thaliana
transcript AT4G32840.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 3'ss of exon 6
gtaagtcctagattatcattattgtagtctgcactctcaaccttaacctcctctcctattctggttagttcgcaagaagctcaatttgatgatagtatctctgatctagGTCATTGACAAGTCCTTTGGATTTGATACTGCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTG
                       ||| | |   || || | |  | | |    |   ||| |  | |    || |   ||| |  |||||| |    | | ||  | |||| || |||||||||||||| ||||| |||||||| |||||||||||  | || || ||||| || |||||||| ||    ||||  || || |||||||
-----------------------gtactttcttctttccagcaca-cttgagtttggattttcttca---tgctaatcgctaagattgatgttgaattgtttgcac-agGTGATCGACAAGTCCTTTGGTTTTGACACTGCGGTGGAGGAGGCTCAGAGGGCCATCAATGCTGCTCATGTTGAGGCTGAGAGTGCAGAGAATGGCATTG

upper sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 8
gtaagtcctagattatca----ttattgtagtctgcactctcaaccttaacctcctctcctattctggttagttcgc------aagaagctcaatttgatgatagtatctctgatctagGTCATTGACAAGTCCTTTGGATTTGATACTGCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTG
|||| |  | |||||  |    ||||| | | |||||     || | | ||  |   |   || |||   | ||         ||||||  |   ||  |  |      |   |   |||| || |||||||||||||| ||||||| ||| || || ||||| || ||||| ||| ||||||| |||||||| ||  | ||||  || || || || |
gtaatttat-gattacaagcgtttatttttgcctgcaaag--aagcattacaactcttttgatactgcacaatttttctattaaagaagtactgattttttctgtacattaaaactcagGTTATAGACAAGTCCTTTGGTTTTGATAGTGCTGTAGAAGAGGCCCAGCGTGCCATTGATGCAGCTCATGTTGAGGCTTCAAGTGCTGAGAATGGAATAG

upper sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
gtaagtcctagattatcattattgtagtctgcactctcaaccttaacctcctctcctattctggttagttcgcaagaagctcaatttgatga------tagtatctctgatctagGTCATTGACAAGTCCTTTGGATTTGATACTGCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTG
||||    |   |   |||| | ||  | |        ||    ||       |   ||| ||    | || || ||| ||    |  | ||      |  || |  || |  |||| ||||||||||| ||||| || || || || |||||||||||||||||||| || ||||| || ||||| |||||    ||||  || || || || |
gtaatatgtttctccacattttagtgatattttggtggaaaa--aatggaagatgacatt-tgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG

upper sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 1
gtaagtcctagattatcattattgtagtctgcactctcaaccttaacctcctctcctattctggttagttcgcaagaagctcaatttgatgatagtatctctgatctagGTCATTGACAAGTCCTTTGGATTTGATACTGCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTG------------------------------
                                                                       | |  | ||| |  ||  |  || ||| | || | ||||| || |||||||| ||||| ||||||||||| || || || || || ||||| ||||||||||| ||||| |||||  | ||||  ||||| || || |                              
-------------------------------------------------------------gcagagacctgtactatgctga--ttatttgta-tatatatggt-taggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG

upper sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 8
----------gtaagtcctagattatcattattgtagtctgcactctcaaccttaac-ctcctctcctattctggttagtt----cgcaagaagct-caatttgatgatagtatctctg-----atctagGTCATTGACAAGTCCTTTGGATTTGATACTGCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTG
          |  | | |||  || |  |  ||  ||  ||||         ||    |    ||| |  | |||     |     |||   | ||  | | || ||||  | | | |         ||||| || |||||||| ||||| ||||||||||| || || || || || ||||| ||||||||||| ||||| |||||  | ||||  ||||| || || |
gtaatttttggccacttctac-ttgttctcttttcagcttgcatagatgcttttgctgcatacctcttgatttggaagactgtagtgcagagacctgtactatgctgattatttgtatatatatggttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG

upper sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G080375_T04 (Zea mays), 3'ss of exon 6
gtaagtcctagattatcattattgtagtctgcactctcaaccttaacctcctctcctattctggttagttcgcaagaagctcaatttgatgatagtatctctgatctagGTCATTGACAAGTCCTTTGGATTTGATACTGCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTG
             ||  ||         ||||    |  |    ||  |       |||| |   |   |      |   |||   |||       |   || ||  |||| ||||||||||| ||||||||||| ||||| || |||||||| ||  | || || ||||| || ||||| || ||    |||| ||| |||||||| |
------------gtacgatctgctcctcctgcgtatttgaaaaaaaaatagctaattattgtccattcctgattgtagcttcatcctga-------actgcttatgcagGTGATTGACAAGTCGTTTGGATTTGACACTGCTGTGGAGGAGGCCCAGAGGGCCATCAATGCTGCTCATGTCGAGGCTGAAAGTGCGGAGAACGGCATCG

upper sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G443985_T03 (Zea mays), 3'ss of exon 8
gtaagtcctagattatcattattgtagt-ctgcactctcaaccttaacctcctctcctattctggtta-gttcgcaagaagctcaatttg-atga------tagtatctctgatctagGTCATTGACAAGTCCTTTGGATTTGATACTGCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTG
||||    |   |   |||| | ||     |    | | ||  |  |      |   |    || | |  |   |||  | | | || ||  |||         || |  || |  |||| ||||||||||| ||||| || || || || || ||||||||||||||||| || ||||| || ||||| || ||    ||||  || || || || |
gtaatatgtttctccacattttagtgacatttttgtgtaaaaatggaagatgccatttgacatgatcacatgaacaacgaaccccatatgcgtgaattcaccgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTCGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAGGCTGTAAGTGCTGAGAATGGTATAG

upper sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 7
------------gtaagtcctagattatcattattgt---agtctgcactctcaaccttaacctcc-tctcctattctggttagttcgcaagaagctcaatttgatgatag--tatctctgatctagGTCATTGACAAGTCCTTTGGATTTGATACTGCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTG
              ||   |    || |  ||  |        ||  | ||| | | ||||  | | | |    |  ||||||  |   ||||| ||  || |   ||| |  |   | |  | ||||| |||||||| || ||||| |||||||||||||||||||||||||||||||| ||||||||||| |||||||||||    ||| | || || |||||||
gtatgcttgttcacaatgtcatattttttgttcctccctggaactctaatcttatcattaaaatacatttgaagtgttggttatctatgaagaaacttcatgttcggattgccttctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG

upper sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 8
gtaagtc---ctagattatcattattgtagtctgcactctcaaccttaacctcctctcc----tat-tctg----gttagttcgc----aagaagctcaatttgat---gatagtatc--tctgatctagGTCATTGACAAGTCCTTTGGATTTGATACTGCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTG
||| |       | | | |||| ||| | || |   |    |||  ||| ||  ||       ||| ||||    |||||||| |    | ||| ||  ||    |   ||| || |   | |  | ||||| |||||||| || ||||| |||||||||||||||||||||||||||||||| ||||||||||| |||||||||||    ||| | || || || ||||
gtatgcttgttcacaatgtcat-atttttgtttctccctggaactctaatcttatcattaaaatatatctgaagtgttagttctctatgaggaaacttcatcatgttcggattgtcttctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGTATTG

upper sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 8
gtaagtcctagattatcattattgtagt--ctgcactctcaaccttaacctcctctcctattctgg--ttagttcgcaagaag-ctcaatttgatgatagtatctct-gatctagGTCATTGACAAGTCCTTTGGATTTGATACTGCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTG
|||  | || |  |||      || | |   |    |||   |   | | |  ||    |  || |  ||||   | ||   | ||  |  | |   |    ||||| |||  |||| |||||||| || ||||| ||||||||||| ||||| || || || ||||| |||||||| || ||||||||| |    ||| | || || || ||||
gtac-ttcttgcctattgcacctgaattaattttgttcttttctccatctttttcaataaaccttgcattagcctgtaatgtgtcttcaccttagactgccttctcttgattcagGTTATTGACAAATCGTTTGGTTTTGATACTGCTGTTGAAGAAGCACAGCGTGCCATTAATGCGGCACATGTTGAATCTGAAAGTATTGAGAATGGTATTG

upper sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S327_30V6.1 (Physcomitrella patens), 3'ss of exon 8
---------gtaagtcctagattatcattattgtagtctgcactctcaaccttaacctcctctcctattctggttagttcgcaagaagctcaatttgat-------gatagtatctctgatc--tagGTCATTGACAAGTCCTTTGGATTTGATACTGCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTG
          | |  ||||    |   | |      | | |||       ||||    |   |  |       ||  ||||   |       | ||| |       |  | |   |   ||    || | ||||| ||||||||||||||||| ||||| || || || || ||||| || || |||||||| ||||| |||||    |||    | || ||  |||
gtactatacatcatccctactacacagtgacgcgctttttcacatgtgtgcttatttccacatgttgcctgaattcattcgtgtgcgttctgacttgttctcttttgggatttgtttcaatgaacagATAATTGATAAGTCCTTTGGATTTGACACTGCTGTGGAAGAAGCACAACGAGCAATCAATGCAGCTCATGTGGAAGCAGAAAGTACTCATAATGGTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctattctggttagttcgcaagaagctcaatttgatgatagtatctctgatctagGTCATTGACAAGTCCTTTGGATTTGATACTGCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTG
                                            ctctgat  putative branch site (score: 4)
                                         tatctct  CT-rich tract
                            aatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcctagattatcattattgtagtctgcactctcaaccttaacctcctctcctattctggttagttcgcaagaagctcaatttgatgatagtatctctgatctagGTCATTGACAAGTCCTTTGGATTTGATACTGCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC