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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaagtactctaggttttgggtaatgtttcatgaaagttcttgaaaatgttcttgtgctaatcttctgtttttgtgcagATACTTGGCTCCAGAGTACTTCATGTATGGTAAGGTGAATGATAAGATAGATGTGTATGCATTCGGCGTTGTTCTCCTCGAGTTACTTTCGGGAAGAAAA

Basic information

species Arabidopsis thaliana
transcript AT1G77280.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G77280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os11g08950.1 (Oryza sativa), 3'ss of exon 8
----------gtatgaagtactctaggttttgggtaatgtttcatgaaagttcttgaaaatgttcttgtgctaatct-tctgt-ttttgtgcagATACTTGGCTCCAGAGTACTTCATGTATGGTAAGGTGAATGATAAGATAGATGTGTATGCATTCGGCGTTGTTCTCCTCGAGTTACTTTCGGGAAGAAAA
            ||  | |  |     |||    |  | |||  ||   | |  ||  ||  ||    | | | | | |   | | || |||||||||||||||||||| || |||||| |||| ||||||||||| || || ||||| || || || || || || || || ||  |  |||| || |  |||
gtttgttagctaattgattgtttgctatttcacct--ttttttttgttgggttgtggcaaccttaccttaccagtgtatgcatatcttttgcagATACTTGGCTCCAGAATATTTCATGCATGGCAAGGTGAATGACAAAATTGATGTATACGCTTTTGGTGTCGTCCTTCTTGAACTCATTTCAGGCAAGAAA

upper sequence: AT1G77280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os12g07990.1 (Oryza sativa), 3'ss of exon 6
gtatgaagtactctaggttttgggtaatgtttcatgaaagttcttgaaaatgttcttgtgctaatcttctgtttttgtg-cagATACTTGGCTCCAGAGTACTTCATGTATGGTAAGGTGAATGATAAGATAGATGTGTATGCATTCGGCGTTGTTCTCCTCGAGTTACTTTCGGGAAGAAAA
                               | | ||||     |  |  || ||       || ||    |||   || ||| |||||||||||||||||||||||| | || ||||| |  || ||||| || ||||| || |||||||| || ||||||||| |  | || || || || 
------------------------------gtgaggaaaagaacttgaggtgatc-------aagctcgcatttccatggcagGTACTTGGCTCCAGAGTACTTCATGCACGGCAAGGTCAGCGACAAGATCGACGTGTACGCCTTCGGCGTCGTCCTCCTCGAGCTCGTCTCCGGGAGGAAG

upper sequence: AT1G77280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os12g08050.1 (Oryza sativa), 3'ss of exon 3
----gta--tgaagtactctaggttttgggtaatgtttcatgaaagttctt-----gaaaatgttcttgtgctaatc----ttctgtttttgtg-cagATACTTGGCTCCAGAGTACTTCATGTATGGTAAGGTGAATGATAAGATAGAT-GTGTATGCATTCGGCGTTGTTCTCCTCGAGTTACTTTCGGGAAGAAAA---------------------------------
    |||  || ||     |    ||    |  |  || |||||   |        | ||| |  |||| | | |||    |    | |   || ||| |||||||||||||||||||||||| | || ||||| |  || ||||| ||| ||||| || ||| |||| || ||||||||| |  | || || || ||                                  
gtttgtagctgcagctgcttcttcttcttcttcttcttgatgaagaattcaagtgaggaaaagaacttgaggtgatcaagctggcatctccatggcaggtacttggctccagagtacttcatgcacggcaagGTCAGCGACAAGATCGATCGTGTACGCCTTCAGCGTCGTCCTCCTCGAGCTCGTCTCCGGGAGGAAGCCGGTGAGCTCCGGCGGCGGCAAGGGCAAGGAA

upper sequence: AT1G77280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G032337_T02 (Zea mays), 3'ss of exon 7
---------gtatgaagtactctaggttttgggtaatgtttcatgaaagttcttgaaaatgttcttgtgctaatcttctg-tttttgtgcagATACTTGGCTCCAGAGTACTTCATGTATGGTAAGGTGAATGATAAGATAGATGTGTATGCATTCGGCGTTGTTCTCCTCGAGTTACTTTCGGGAAGAAAA
          ||  || |  | ||   |||   |   || |  || |     ||| |    ||  | | || |  |   | | | |  |||||||||||||||| || ||||||||| |||| ||||||    | || || ||||||||||| ||||| ||||| || || ||| |  | || || || |||
gtttgtttcttaacaattgttttattgttt---ttccgtctgttgtag--cattggagcaattgctttactgacatagagatatcttggcagATACTTGGCTCCTGAATACTTCATGCATGGCAAGGTGGGCAACAAAATCGATGTGTATGCTTTCGGTGTTGTACTTCTGGAGCTCATCTCTGGCAGGAAA

upper sequence: AT1G77280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA06G12410.1 (Glycine max), 3'ss of exon 8
-------------------gtatgaa-gtac--tctaggttttgggta-atgtttc--atgaaagttc-ttgaaaatgttcttgtgcta-atcttctgtt--tttgtgcagATACTTGGCTCCAGAGTACTTCATGTATGGTAAGGTGAATGATAAGATAGATGTGTATGCATTCGGCGTTGTTCTCCTCGAGTTACTTTCGGGAAGAAAA
                   | || |   |||  ||    || |  ||| ||| | |  |   | || | ||  ||||| || |    ||  | ||    |  ||| ||||| ||||||||||| || ||||||||||| || || || ||||||||||| ||||| ||||||||||| || || ||||| ||| | ||||| || ||||| 
gtttgtacttttaaaccctgcataactataccatcccctttataagtacatgctgccgagagaggtgcatttgaaatggtcctaaattatgtattacactcatttatgcagTTACTTGGCTCCTGAATACTTCATGTACGGCAAAGTAAATGATAAGATTGATGTCTATGCATTCGGTGTCGTGCTCCTTGAGCTTCTTTCAGGGAGAAAG

upper sequence: AT1G77280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA04G42390.1 (Glycine max), 3'ss of exon 8
-------------------gtatgaa-gtac--tctaggttttgggta-atgtttcat---gaaagttc--------ttgaaaatgttcttgtgcta-atcttctgtt--tttgtgcagATACTTGGCTCCAGAGTACTTCATGTATGGTAAGGTGAATGATAAGATAGATGTGTATGCATTCGGCGTTGTTCTCCTCGAGTTACTTTCGGGAAGAAAA
                   | || |   |||  |||   || || ||| ||| | ||    ||||||          ||  ||||| || |    ||  | ||   ||  ||| ||||| ||||||||||| || ||||||||||| || || || ||||||||||| ||||| ||||||||||| || || ||||| ||| | ||||| || ||||| 
gtttgtacttttaaaccctgcataattataccatctcccttatgcgtacatgctgcactgagaaagtgtattagaatttagaaatggtcctaaattatgtattacattcatttatgcagTTACTTGGCTCCTGAATACTTCATGTACGGCAAAGTAAATGATAAGATCGATGTCTATGCATTCGGTGTCGTGCTCCTTGAGCTTCTTTCAGGGAGAAAG

upper sequence: AT1G77280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA14G24660.1 (Glycine max), 3'ss of exon 9
---------------gtatgaagtactctaggttt-tgggtaatgtttcatgaaagttc--ttgaaaatgttcttgtgctaatcttctgtttttgtgcagATACTTGGCTCCAGAGTACTTCATGTATGGTAAGGTGAATGATAAGATAGATGTGTATGCATTCGGCGTTGTTCTCCTCGAGTTACTTTCGGGAAGAAAA
                     | ||||  |  ||  |   |  ||  |   |||| | |  || ||   | |||  |    | |     | ||| ||||| ||| ||||||| || ||||||||||| ||||| || ||||| ||||| ||||| |||||||| || || || || || ||| | ||||| |||||||| 
gtttgtactttcaattctcatattactgaacattcatacatgctgcgtacagaaattgcatttaaagtagctctaatttctaacacacttatttttgcagTTACATGGCTCCTGAATACTTCATGTACGGTAAAGTAAATGACAAGATTGATGTCTATGCATTTGGTGTAGTGCTTCTTGAGCTTCTTTCTGGAAGAAAG

upper sequence: AT1G77280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G09620.1 (Glycine max), 3'ss of exon 9
--------------gtatgaagtactctaggttttgggta-atgtttcatgaaa-gttcttgaaaatgttcttgtg-ctaatcttctgtttttgtgcagATACTTGGCTCCAGAGTACTTCATGTATGGTAAGGTGAATGATAAGATAGATGTGTATGCATTCGGCGTTGTTCTCCTCGAGTTACTTTCGGGAAGAAAA
               | | |  ||    |   ||     |      | | |||  |   || |||  |||||  |  ||||    ||  |||| ||||| ||| ||||||| || |||||||||||||| || || ||||| ||||| ||||| |||||||| || || || || || ||| | ||||| || ||||| 
gtttgtacttacaattctcacataactgatcattcatacatgcagctgaggaattgcattttaaatagttctaatttctaacacactaatttt-tgcagTTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGACAAGATTGATGTCTATGCATTTGGTGTAGTGCTTCTTGAGCTTCTTTCAGGGAGAAAG

upper sequence: AT1G77280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv18s0001g01680.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------------------------------------------------------------gtatgaagtactctaggttttgggtaatgtttcatgaa---agttcttgaaaatgttcttgtgctaatcttctgtttt-tgtgcagATACTTGGCTCCAGAGTACTTCATGTATGGTAAGGTGAATGATAAGATAGATGTGTATGCATTCGGCGTTGTTCTCCTCGAGTTACTTTCGGGAAGAAAA
                                                                              |||   | | | | | |||    |  ||  | |  ||   | | ||||  | ||     || |  | | | | |||| | ||||| ||| ||||||| || |||||||||||||| || || ||||| ||||||||||| || ||||| || ||||| ||||| ||| | |||||||||||||||
gtttgtgcttcttctctagtagctataacttctatgtcccacattcttgtcatttttcagaagatcaataaaccccactattttgaattatggctttaaaatcttgagtaaaaaagttattacttgtcattgagaaagttcagaacatttattttctctgcagTTACATGGCTCCTGAATACTTCATGTATGGCAAAGTAAATGAGAAGATAGATGTCTACGCATTTGGTGTTGTCCTCCTTGAGCTTCTTTCGGGAAGAAAA

upper sequence: AT1G77280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S242_29V6.1 (Physcomitrella patens), 3'ss of exon 8
--gtatgaagt---actctag-gtttt-----gggtaatgtttcatgaaagt---------tcttgaaaatgttcttgtgctaatcttctgtttttgtgcagATACTTGGCTCCAGAGTACTTCATGTATGGTAAGGTGAATGATAAGATAGATGTGTATGCATTCGGCGTTGTTCTCCTCGAGTTACTTTCGGGAAGAAAA
  || ||   |   ||| | | | |||      |  | ||| ||||  | ||         || |  | |  |   ||  ||    || | | | |   ||| |||||||| || || |||||||||||||| | |||||| || ||||| |||||||| |||||||| || || ||  | ||| |  |  |||| || |||
gggtgtgggattaaactgtggcgctttcctgcagccactgtatcatcgacgtagcagtcgatcgttgatacataactg-actggcgttatatctctac-cagGTACTTGGCCCCGGAATACTTCATGTATGGGAGGGTGAACGACAAGATCGATGTGTACGCATTCGGTGTAGTGCTTTTAGAGCTTATCACGGGTAGGAAA

upper sequence: AT1G77280.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S226_111V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------------------------------------------------------------------------------------------------gtatgaagtactctaggttttgggtaatgtttcatgaaagttcttgaaaatgttcttgtgctaatcttctgtttttgtgcagATACTTGGCTCCAGAGTACTTCATGTATGGTAAGGTGAATGATAAGATAGATGTGTATGCATTCGGCGTTGTTCTCCTCGAGTTACTTTCGGGAAGAAAA
                                                                                                             ||| || | |    |    |  | |  ||| ||  | |   |     || |    ||| |||| |    ||||| ||||||| || |||||||| ||||||||||||||||| |  ||||| || || |  || || ||  | || || || || || |||||| | ||| | ||  |  | 
gtaacatctcgtgacacttcgtatttgcacgtaatgaaatttagatagttattgagtatttttttacgctgaacaaactgtgttgcaataatggtgacggatggaggttgtaagaggaagctca---ctatgctcttgtctctcgca---ttagagaattagatttgagcta-tgaattgtttgtgtgcagCTATTTGGCTCCCGAGTACTTCATGTATGGAAGAGTGAACGAGAAAACCGACGTATACTCCTTTGGTGTGGTCCTTCTCGAGCTCCTTACTGGTCGGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttcatgaaagttcttgaaaatgttcttgtgctaatcttctgtttttgtgcagATACTTGGCTCCAGAGTACTTCATGTATGGTAAGGTGAATGATAAGATAGATGTGTATGCATTCGGCGTTGTTCTCCTCGAGTTACTTTCGGGAAGAAAA
                               tgctaat  putative branch site (score: 2)
                                     tcttctgtttttgt  CT-rich tract
                ttgaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaagtactctaggttttgggtaatgtttcatgaaagttcttgaaaatgttcttgtgctaatcttctgtttttgtgcagATACTTGGCTCCAGAGTACTTCATGTATGGTAAGGTGAATGATAAGATAGATGTGTATGCATTCGGCGTTGTTCTCCTCGAGTTACTTTCGGGAAGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA