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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactaaacacacttcataaagtctctaatttcttgtcacaacaattgcctactgatgtaggaataattcttgtttttgtctttcagGAAGAGCGGAAAACTCTTGACCGGGAGCTTGCACGTGCAAAGGTTACAGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATA

Basic information

species Arabidopsis thaliana
transcript AT1G24764.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 6
gtaactaaacacact-------tcataaagtctctaatttcttgtcacaacaattgcctactgatgtaggaataattcttgtttttgtct--ttcagGAAGAGCGGAAAACTCTTGACCGGGAGCTTGCACGTGCAAAGGTTACAGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATA
|||||       |||       ||  | | |||  | | |  |||    | ||  |   ||  |||      ||||   |     || |    | |||| ||  | |||| ||||||||| |||||||| || ||||| ||||||||||||||||||||   ||| || ||||||||||||||||||| |||||| |
gtaacatcctttactgttgctttcggataatcttcactgttctgtacgcaaaaaagttgacccatgc-----taatctctaaccatggcacacttagGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACA

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g44340.1 (Oryza sativa), 3'ss of exon 6
gtaactaaacacacttcata---aagtctctaatttcttgtcacaacaattgcctactgatgtaggaataattcttgtttttgtc--tttcagGAAGAGCGGAAAACTCTTGACCGGGAGCTTGCACGTGCAAAGGTTACAGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATA
||||   |  |  |         | ||  || || | |  ||     ||| |  |  | || |      ||||     || ||    | |||||||||  ||||||||||||| || || || || ||||| |||||| | ||||| ||||||||    ||||| |||||||| ||||||||||| |||||||
gtaatgcatgatgccctgagcacacgttcctgatgtttattctacctaatagaatggtaat-tgatgccaatttacacttatgctgatgtcagGAAGAAAGGAAAACTCTTGATCGTGAACTAGCTCGTGCGAAGGTTTCGGCAAATAGAGTTGCAGTAGTGGTGGCAAATGAATGGAAAGATGGCAATGATA

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 3'ss of exon 6
--------------------------gtaactaaacaca-cttcataaagtctctaatttcttgtcacaacaattgcctactgatgtaggaataattcttgtttttgtctttcagGAAGAGCGGAAAACTCTTGACCGGGAGCTTGCACGTGCAAAGGTTACAGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATA
                           ||  | | ||   |||||| |  |||       | |   | |  ||  |   ||| |||      |||   || |  |  | |  |||||  |    || || |||||  | || ||||| |||||||| |||||||||||||| |||||   |||||| || || ||||||||||||  |||||| |
gtaacaacctattctttgactattgcatatgtcatcatgtcttcatgagctcttc--cccccttctataggaacagttcactcatgcttatttaacatttatgatcat-taccagGACCAAAAAAAGACACTTGAATGTGAACTTGCTCGTGCAAAAGTTACAGCAAACAGGGTTGCTGTTGTGGTTGCCAACGAGTGGAAAGATTCTAATGACA

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G008556_T01 (Zea mays), 3'ss of exon 6
gtaactaaaca-cacttcataaa-------gtctctaatttcttgtcaca----acaattgcc-tactgatgtaggaataattcttgtttttgt----ctttcagGAAGAGCGGAAAACTCTTGACCGGGAGCTTGCACGTGCAAAGGTTACAGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATA
||||| ||  | || || || |        | ||  || ||| |||||      ||| ||  |  |   |     || | || ||| |  || |     | | |||||||   || ||| |||||||| || |||||||||||||| ||||||||||||||||||||  |||| || || |||||||||||||||  |||||| |
gtaacaaactatcatttgattacttcatttgccttcaaattcgtgtcattttttacacttttcacatgaacacttgattcatgcttatgcttatgattttattagGAAGAAAAGAGAACACTTGACCGTGAACTTGCACGTGCAAAAGTTACAGCAAACAGAGTTGCTTCTGTTGTTGCTAATGAGTGGAAAGATTCTAATGACA

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G039325_T01 (Zea mays), 3'ss of exon 6
----------gtaactaaacacact--tcataaagtctctaatttcttgtcacaacaattgcctactgatgtaggaata----attcttgtttttgtc--------tttcagGAAGAGCGGAAAACTCTTGACCGGGAGCTTGCACGTGCAAAGGTTACAGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATA
           |   || |     |  |  |   | ||  || | | |||||      || ||   |     | ||| |    |||| || || |||         | | |||||||   || ||| |||||||| || |||||||||||||| |||||||||||||| |||||  |||| || || |||||||||||||||  |||||| |
gtaacaaactatccttagattggttacttcttttgccttcaaatccatgtcaatttttttacccttttcaacatgaacacttgattcatgcttatgtttatgattttattagGAAGAAAAGAGAACACTTGACCGTGAACTTGCACGTGCAAAAGTTACAGCAAACAGGGTTGCTTCTGTTGTGGCCAATGAGTGGAAAGATTCTAATGACA

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 2
---------gtaactaaacacacttcataaagtctctaatttcttgtcacaac-aattgcctactgatgtaggaataattctt-----gtttttgtctttcagGAAGAGCGGAAAACTCTTGACCGGGAGCTTGCACGTGCAAAGGTTACAGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATA
         | | |   |    |||   || |  |      | ||   | | | | |||   ||            || | ||     ||||     | | |||| ||   |||||||||||| || ||||| || |||||||||||| ||||||| || |||||    ||||| ||||||||||||||||||||  ||||||
gtaatacatgaatcctgatgtccttggaaatgcattatgcgttttaggatatctacttgagcaccatgactaatgcaagttttacaacgtttcctattcttagGAGGAAATGAAAACTCTTGATCGTGAGCTAGCTCGTGCAAAGGTTTCAGCAAATAGGGTTGCAGTAGTGGTGGCAAATGAGTGGAAAGATGGCGATGATA

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 6
gtaactaaacacactt-----cataaagtctctaatttcttgtcacaacaattgc-ctactgatg--taggaataattcttgtt------tttgtct--------ttcagGAAGAGCGGAAAACTCTTGACCGGGAGCTTGCACGTGCAAAGGTTACAGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATA
||||     |||||||     | | |    |||||||| ||  | |||  ||| |  |    ||   ||  |  |  | |||||      ||||| |        |  |||||||  | |||||||||||||||||| | || ||||| ||||| |||||||||||||| ||    ||||| |||||||| |||||||||| |||||| |
gtaatgtgtcacacttaccaactttactcttctaatttgtttactcaatcattacattgaccatagctaaaagcatcttttgttgcatgatttgttttgatactatatagGAAGAAAGAAAAACTCTTGACCGGGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 6
-------------gtaactaaacacact-tcataaagtctctaatttcttgtcacaacaatt-gcctactgatgtaggaataatt------cttgtttt--tgtctttcagGAAGAGCGGAAAACTCTTGACCGGGAGCTTGCACGTGCAAAGGTTACAGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATA
              | || ||    ||| |  ||   | | || |   || | |||   ||   ||||      |   |||  ||       |||||||       |  |||||||  | |||||||||||||| ||| | || ||||| ||||| |||||||||||||| ||    ||||| |||||||| |||||||||| |||||| |
gtaatgtgttaaatttaccaactttactcttctagtttgtttactcaattattacactgatccacctaaaagcatcttaattgttgcatgatttgttttgacactatatagGAAGAAAGAAAAACTCTTGACCGAGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 6
-----------------------gtaactaaac--acacttcataaagtctctaatttcttgtcacaa--caattgcctactgatgtaggaataattcttgtttttgtctttcagGAAGAGCGGAAAACTCTTGACCGGGAGCTTGCACGTGCAAAGGTTACAGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATA
                        |    ||||  ||| ||  |  | |||  | | |  || | | |   ||   | || | || |  | |   ||  | ||    |  || |||| ||  | || ||||| ||| ||||| | || ||||| ||||| |||||||||||||| ||   |||||| |||||||| |||||||||| ||||||||
gtaatgtgtgaaaagtcttcagcatgttcaaactcacatttgctttattcttgattgtactgcctctagttaagatcatatttatttttgcacggtttat-ttgacattctttagGAGGAAAGAAAGACTCTAGACAGGGAGTTGGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCTAATGATA

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 6
-----------------------gtaactaaacac--acttcataaagtctctaatttcttgtcacaa--caattgcctactgatgtaggaataattcttgtttttgtctttcagGAAGAGCGGAAAACTCTTGACCGGGAGCTTGCACGTGCAAAGGTTACAGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATA
                        |    |||| |  | ||  |  | |||  | | | ||| | | |   ||   | || | || |  | ||  ||  | ||    |  || |||||||  | |||||||| ||| ||||| | || ||||| ||||| |||||||||||||| ||   |||||| |||||||| ||||||||||  |||||||
gtaacttgttaaaagtcttcagcatgttcaaactcccatttgctttattcttcattatattgactctagttaagatcatatttatttttgcatggtttat-ttgacattctttagGAAGAAAGAAAAACTCTAGACAGGGAGTTGGCCCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTTGTGGTTGCAAATGAATGGAAAGATGCCAATGATA

upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------------gtaactaaacacacttca----taaagtctctaatttc-ttgtcacaa--caattgc-ctactgatgtaggaataattcttgtttttgtct-----ttcagGAAGAGCGGAAAACTCTTGACCGGGAGCTTGCACGTGCAAAGGTTACAGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATA
                                  |    ||  || ||||    || | | |   || |  ||| || |   ||  ||  |||    ||| |   |   | |  ||||  | |     ||||||| ||  | ||||| || ||| ||||||| || ||||||||||| || |||||||| || ||    || ||||||||||| |||||||||| |||||| |
gtaatgtgccatttttaaacaataaatattgaacattgcaagtcatttcaggcttatatttttgcatctagttggcatatgccatgtgttctatcattgttgagttgtctttccttttcttttggaccttcagGAGGAAAGAAAAACCCTCGACAGGGAGCTGGCCCGTGCAAAGGTAACTGCAAACAGGGTGGCAGTAGTTGTAGCAAATGAATGGAAAGATGCTAATGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtcacaacaattgcctactgatgtaggaataattcttgtttttgtctttcagGAAGAGCGGAAAACTCTTGACCGGGAGCTTGCACGTGCAAAGGTTACAGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATA
                  tactgat  putative branch site (score: 2)
                                   ttcttgtttttgtctt  putative PPT
                              aataattcttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactaaacacacttcataaagtctctaatttcttgtcacaacaattgcctactgatgtaggaataattcttgtttttgtctttcagGAAGAGCGGAAAACTCTTGACCGGGAGCTTGCACGTGCAAAGGTTACAGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG