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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgatttactctgttttcttcttactcagctatttggctataccttttatctgtcttttcatgctctatccttgtttaccagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA

Basic information

species Arabidopsis thaliana
transcript AT1G51690.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
-------------gtatt-tgatttactct-gttttcttcttactc-agctatttggctat---accttttatctgtcttttcatgctctatccttgtttaccagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA
              |||| || | | |||| ||||| ||||| ||  |  || |||  |||   | ||   |||| | ||||  || |  |   ||     | |||||||||||||||| |||||||| ||||||||||| || ||||| || || ||||| || ||||| |||    | || |  || || || || |||||||
atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaaactcacatctatgtttttttgatgaactgtt-----ctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 3
gtatttgatttactctgttttcttcttactcagctatttggctataccttttatctgtcttttcatgctctatccttgtttaccagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA
   | |  | |||     |  || |||| | |  ||  ||   ||  || || | |  ||  |  ||   | || |     |  |||||||||| || ||||| ||||| || || ||||| |||||||| || |  ||||| |||||||||||||||||  | ||||| || || || |||||||
--gtatattgtacaagactaactgcttagtgaagtacctg-taatttctgttgtttaactaatt-tgtcttgtcatg--cgattagTTTGATTATCTGAAGAGCTTGGAAATTGAAGAGAAGATTAACAAGATAAAGTGGTGCCAAACAGCAAATGGAGCATTGTTTCTTCTGTCCACAAATGATA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 3
gtatttgatttactctgttttcttcttactcagctatttggctataccttttatctgtcttttcatgctctatccttgttt----accagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA
||||   |||  | |     |  |          |||||| || |     |||  ||   ||| ||    |    |||||     | ||||||||||| || ||||| ||||| || || ||||| |||||| |||| | |||||||||| |||||||||| ||  | | ||| || || || ||||| |
gtat---attctcacaaacattgttaagtggtattatttgtct-tctgaattacttgaaatttgataaagtgatgttgttatggaatcagTTTGATTATCTTAAGAGCTTGGAAATTGAAGAGAAGATTAACCAAATAAAATGGTGTCAAGCAGCAAATGGTGCATTGTATCTTCTATCCACAAATGACA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 3
gtatttgatttactctgttttcttcttactcagctatttggctataccttttatctgtcttttcat---gctctatccttgtttaccagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA
||||   |||  | |     |  | |        |||||| || ||    |||  ||   ||| |    |   | |  || || |  ||||||||||||||||||| ||||| || || ||||| |||||| |||| |  ||||||||| || ||||| | ||  | ||||| || || || ||||| |
gtat---attctcgcaagcattgtttagtggtattatttgtct-tatgaattacttgaaatttgacaaagtgatgttattattgaatagTTTGATTACCTCAAGAGCTTGGAAATTGAAGAGAAGATTAACCAAATAAAGTGGTGTCAAGCAACAAATTGTGCATTGTTTCTTCTATCCACAAATGACA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 3
gtatttgatttactctgttttcttcttactcagctatttggctataccttttatctgtcttttcatgctctatccttgtt-taccagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA
||| ||      | ||| ||  | ||  || |  |  |||  |  | |    || |     || |||   | |  ||||| |  |||||||| || || ||||||||||| ||||| ||||||||||||||||| | |||||| |||||||| ||||| ||| | || || || || || |||||||
gtaattttcagtcactggttaatgctgcctgaaatgcttg--tggagcagaaatgttaacatttatgacatgtgattgttgtttcagTTTGACTATCTTAAGAGTTTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCCAATGGTGCTTTGTTCCTTCTATCCACAAATGATA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 3
gtatt--tgatttactctgttttctt-cttactcagctatttggctataccttttatctgtcttttcatgctctatccttgtttaccagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA
||| |  | ||||  || ||  | || |     || |   | ||  | |    | |  | | | |  |||    ||| ||||||  |||||||| || || |||||||||||||| || |||||||| |||||||| |||||||| |||||||| ||||| || || || || || || || |||||||
gtaatcatcatttggtcagtaatgttgcaccaacatcctatgggtcagaagagtcaa-tatttataaatgtatgatcattgttt--cagTTTGACTATCTTAAGAGTTTGGAGATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAACAGCTAATGGTGCCCTGTTCCTTCTTTCTACAAATGATA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 3
gtatttgatttactctgttttcttcttactcagctatttggctataccttttatctgtcttttcatgctctatccttgtt-taccagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA
||| ||      | ||| ||  | ||  |  |  |  |||  |  | |    ||||     || |||   | |  ||||| |  |||||||| || || |||||| |||| ||||| ||||||||||||||||| | |||||| |||||||| ||||| ||| | || || || || || |||||||
gtaattttcagtcactggttaatgctgcccgaaatgcttg--tggagcagaaatcttaacatttatgacttgtgattgttgtttcagTTTGACTATCTTAAGAGTCTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCTAATGGTGCTTTGTTCCTTCTATCCACAAATGATA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 3
gtatt--tgatttactctgttttctt-cttactcagctatttggctataccttttatctgtcttttcatgctctatccttgtttaccagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA
||| |  | ||||  || ||  | || |     || |   | ||  | |    | |      || | |||    ||| ||||||  |||||||| || || ||||||||||| || || |||||||| |||||||| |||||||| |||| ||| ||||| || || || || || || || |||||||
gtaatcatcatttggtcagtaatgttgcaccaacatcctatgggtcagaagagtcaata--tttataatgtatgatcattgttt--cagTTTGACTATCTTAAGAGTTTGGAAATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAATAGCTAATGGTGCCCTCTTCCTTCTTTCTACAAATGATA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------gtatttgatttactctgttttcttcttactcagctatttggctataccttttatctgtcttttcatgctctatccttgtttaccagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA
                            | | ||  ||| | |     | | || |||  ||| |      | |  |||||  ||      |||    ||| ||   |   |||||||| || || ||||| ||||| |||||||||||||| || || || |||||||| || ||||||||||| || || ||||| || || || |||||||
gtatttctttcatcagttactcctgcctgaagtttgtttgcaccaccctttgctcactaggctctg-----aaatgttttaattgatgccacattgcttattctctgtgctcagTTTGACTATCTGAAGAGCTTGGAAATAGAGGAGAAAATCAATAAGATCAGATGGTGCCAGACAGCAAATGGTGCCCTGTTTCTTCTATCTACGAATGATA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 3
------------gtatttgattta-ctctgttttcttcttactcagctatttggctataccttttatctgtct-tttcatgctctatccttgtttac-cagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA
              ||    | |  |  || |||  |   |||  | | |   | | || |||     || ||  ||  |    |||  ||| |||  |||||||||||  | ||||||||||| ||||||||||| || || |||||||| ||||| || || || ||||  ||||  || || || || || ||||| |
gggattgttctgagatacagtatggcgttgattttgttgcacttcgtt-tccagttctatcttactgatgcctgcttttttgaatatgtttggttatgcagTTTGATTATTTGAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGGTGGTGCCAGACTGCTAATGCTGCTCAGTTCCTACTTTCTACAAATGACA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------------------------------------gtatttgatttactctgttttcttcttactcagctatttggctataccttttat-----ctgtctt---ttcatgct-ctatccttgtttac-cagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA
                                                                                            ||| | |  | |||| |||  |  ||||| || |     | |||   | | ||     | || ||   || | | | || |  || |||   |||||||||||| | ||||||||||| ||||||||||| || || ||||||||||||||||| || || || |  ||||  ||  |  | || || ||||| |
gtaatgttagcaacgctaaggtgagtcgtggtaatttttcaagattgcgcccacatagttttctagaatattgatagtttccttaaaatcattatatcaacttctctttttcatatttactaagtttgcaagttatctttatcatattgaccgtgttcggtttacgatactgtatttctttctgcagTTTGATTACTTGAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGTCAGACTGCCAACGCCGCTCAGTTCTTAATTTCTACGAATGACA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 3
------------gtatttgatt-tactctgttttcttcttactcagctatttggctatacctttt--atctgtcttttcatgctctatccttgtttaccagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA
             | |||||   || ||   || | |   |||  | |  |      ||  ||    |   ||  |||  ||        |||||   ||||| |||||||| ||||||||||| ||||||||||| || |||||||| |||||||| || ||  | ||||  || |  ||||| || || || ||||| |
tgtgtagggatactgtttgacggtaatccagttgcattacactt-gttggtcaatcctattttacgaacacgtgcttttctgaatgtattttgttatgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatttgatttactctgttttcttctta--------ctcagctatttggctataccttttatctgtc-ttttcatgctc---tatccttgtttac--cagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA
 |||||| | |  | | ||   || ||            |   ||||   | |    || |    || ||||||   ||   ||| ||| ||     |||||||||||| | ||||||||||| ||||||||||| || || |||||||||||||| || || || ||||  ||||  ||||| || || ||||||||||
ttatttgttgtgttgttttgattttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttcactttcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ09063 (Selaginella moellendorffii), 3'ss of exon 3
gtatttgatttactctgttttcttcttactcagctatttggctataccttttatctgtcttttcatgctctatccttgtttaccagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA
                    |   ||| |||     ||      |     |  |   |   ||  || | |  |    ||  ||||||||| |||||||||||  ||||||||||||| || || |||||||| ||||||||||| || || || || |||| |||| |  | || || ||||| |
-------------------gtgcgcttgctctatcgttgaagcgtgttgatgctacattacttt-tgttttggc----ttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 3
gtatttgatttactctgttttcttcttactcagctatttggctataccttttatctgtcttttcatgctctatccttgtttaccagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA
                    |   ||| |||     ||      |    || ||    | || | |  | | |     ||  ||||||||| |||||||||||  ||||||||||||| || || |||||||| ||||||||||| || || || || |||| |||| |  | || || ||||| |
-------------------gtgcgcttgctctatcgttgaagcgtg---ttgatgctacattactttttttttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctatttggctataccttttatctgtcttttcatgctctatccttgtttaccagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA
                                    ctctatccttgttt  CT-rich tract
                 ttttatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgatttactctgttttcttcttactcagctatttggctataccttttatctgtcttttcatgctctatccttgtttaccagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC