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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaattaagcattcctcattaggaagttaggttatatataaggttagctaagatcaaattgttttagaatctgctgactggaacttctctctttgtatagAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC

Basic information

species Arabidopsis thaliana
transcript AT1G27440.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g70190.1 (Oryza sativa), 3'ss of exon 3
---acaattaagcattcctcattaggaagttaggttatatataaggttagctaagatcaaattgttttagaatctgctgactggaacttctctct-ttgtatagAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC
   |  |  ||| |      || |     |  | ||    |||||  | | | |      |||||     ||    ||   || | || || | |    |  ||||||||  | ||| ||||||||||||||||||||||||| ||| | ||||||||||| ||||| |||||  |||| |||||||| ||||||||| |  ||
gtgagcaccaagaacatgcaatcactcgat--gcttcctcataagcattgttgatgaattattgtaacccaaaagtcttgatgaacctgctttatgcaatgcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGACATCTCCACAGACCACCCACCAACCTACTACGAGGACATGCAGCGTTCC

upper sequence: AT1G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 3
acaattaagcattcctcattaggaagttaggttatatataaggttagctaagatcaaattgttttagaatctgctgactggaacttctctct-ttgtat-agAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC
     |||   |||| | |||      |     ||| ||    | | ||  | |||     |  ||| || ||  | |||    |||| | | |  ||| ||||||||  | ||  |||| |||||||| ||||||||||||||  |||||||||||||||| ||||||||  | || ||||||||||| ||||||||| | 
----gtaaattttccgc-tta------tctccaatacatcctatcatct--gctcattggctcgtagcatgtggagtctgatgtttctgtatgtcctatcagAGGTGCCCGCGCGTCGGTTTGGGAGAATTTCAAGAACAACCCGCTGTTTGACATCTCAACCGATCACCCACCCACGTACTACGAAGATATGCAGAGATCT

upper sequence: AT1G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os10g10080.1 (Oryza sativa), 3'ss of exon 3
-acaattaagcattcctcattaggaagttaggttatatata--aggttagctaagatcaaattgttttagaatctgctgactggaacttctctctttgtatagAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC
 | ||||||  |       ||     || |||  |    |   | | | | | | ||    |  |   | ||| |     |  |     |        |  || || ||  | ||| ||||||||||||||||||||||||||||  |||| |||||||| || || |||||   ||| |||||||| ||||||||| | || 
caaaattaaaaaaaaaaagttgctgggtgaggggaagggtggcaaggtggttgaaatt---tcataccaaaatgttgaatcctgcctaacatatgcaatgcagGGGCGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAACCCGATGTTCGACATCTCTACGGACCACCCCCAAACCTACTACGAGGACATGCAGCGTGCA

upper sequence: AT1G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G059825_T01 (Zea mays), 3'ss of exon 3
-------------acaattaagcattcctcattaggaagttaggttatatataaggttagctaagatcaaattgttttagaatctgctgactgg-aacttctctctttgtatagAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC
                  ||         || | || |  | | | || | |     |  | |        | | | ||   |||| ||||||    | |  |   || || ||||||||  | ||| |||| |||||||||||||||||||||||  ||||||||||||| || ||||||||  ||||||||||||||||||||||| |  | 
gtaattcatctatctgtctacaagcaatgcaattggcacctcgctcatttttggtcctc-ccactgcttcctgggtctattctctgatgactgatggcattgcctgttctacagAGGTGCTCGTGCATCGGTCTGGGAGAACTTCAAGAACAACCCGCTGTTTGACATCTCGACCGATCACCCACCAACATACTACGAAGACATGCAGCGCTCG

upper sequence: AT1G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G141094_T02 (Zea mays), 3'ss of exon 2
-acaattaagcat-tcctcattaggaagttaggttatatataa---------ggttagctaagatcaaattgt-tttagaatctgctgactggaacttct-ctctttgtatagAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC
   ||| |   || |  |    ||  |   || ||   |  |           || |   |  |  | ||||| |      |||| |  |||    |||| |   || |||||||||||  | ||| | || |||||||||||||||||||||||  | || |||||||| || ||||||||  |||| |||||||||||||||||| |  | 
gtaaatcatatatctatttgcaagtgatgcagcttccctccactttttccccagtcattcatcacaacattgtgtccttggtctgatctctgatcattctgcatgttctatagAGGTGCTTGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCACCAACTTACTACGAAGACATGCAGCGTTCA

upper sequence: AT1G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G448834_T02 (Zea mays), 3'ss of exon 2
acaattaagcattcctcattaggaagttaggttatatat-aaggttagctaagatcaaattgttttaga-atctgc--tgactggaacttctctctttgtatagAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC
 ||| | |  | ||  |    |    ||   |   ||   || |  |    ||  ||  ||  |||| | || |||  ||  |||    |     |   |  || || ||  | ||  |||||||||||||||||||| |||||||  |||| |||||||| || || |||||| | || |||||||| ||||||||| | |||
gcaagtca--agtcggctccggtccattccatccaatgccaatgccaatatagtacatgtttatttatatatatgccatggttggtggatgatcatgcatgcagGGGCGCTCGCGCGTCGGTGTGGGAGAACTTCAAGGACAACCCGCTGTTCGACATCTCGACGGAGCACCCGTCGACGTACTACGAGGACATGCAGCGCGCC

upper sequence: AT1G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G059845_T01 (Zea mays), 3'ss of exon 3
----------------------------acaattaagcattcctcattagg-aagtta-----ggttatatataaggttagctaagatcaaattgttttagaatctg-----ctgactggaacttctctctttgtatagAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC
                               |  ||| | |||| | | |   | | |       | ||    |||  | |            ||   |    |  |     || |||| |             |  || || ||  | ||  |||||||||||||||||||||||||| |  |||| |||||||| || || |||||| | || |||||||| ||||||||| | |||
gtaccgtagtgctacgagcctgaactacctgacaaaggagtccttagtggatgaatcatcatcactgattagcaagtcttgacgcacctgcgctgcgctgccgtgcgtataactaactgtatacgacgcaacaatgcagGGGCGCCCGTGCGTCGGTGTGGGAGAACTTCAAGAACAACGCGCTGTTCGACATCTCGACGGAGCACCCGCCGACGTACTACGAGGACATGCAGCGCGCC

upper sequence: AT1G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G301552_T01 (Zea mays), 3'ss of exon 10
----acaattaagcattcctca--ttaggaagttaggttatatataa----ggttagctaagatcaaattgt-tttagaatctgctgactggaacttct-ctctttgtatagAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC
    |  ||  | |  ||  ||  | | | || |    |  |  |       || |   |  |  | | ||  |      |||| |  |||    |||| |   || || ||||||||  | ||| | || |||||||||||||||||||||||  | || |||||||| || ||||||||  | || ||||||||||||||||||    | 
gtaaatcatctatctgtctgcaagtgatgcagcttccctccactttttcccagtcattcatcacaacactgcgtccttggtctgatctctgatcattctgcatgttctacagAGGTGCTCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCACCGACTTACTACGAAGACATGCAGCATTCA

upper sequence: AT1G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G000581_T01 (Zea mays), 3'ss of exon 3
-----------------------acaattaagcattcctcattaggaagttaggttatatataaggttagctaagatcaaattgt-tttagaatctgctgactggaacttct-ctctttgtatagAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC
                          ||  ||| | ||||  |       |    | | |     || |   |  |  | | ||  |   |  |||| |  ||     |||| |   || || ||||||||  | ||| | || |||||||||||||||||||||||  | || |||||||| || ||||||||  | || |||||||||||||||||| |  | 
gtaaatcatctatctgtctgcaagtgatgcagcttccctctatgtccgcatcttctttttccccagtcattcatcacaacactgcgtcctgggtctgatctcttatcattctgcatgttctacagAGGTGCTCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCACCGACTTACTACGAAGACATGCAGCGTTCA

upper sequence: AT1G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G023020_T01 (Zea mays), 3'ss of exon 3
acaattaagcattcctcattaggaagttaggttatatataaggttagctaagatcaaattgttttagaatctgctgactggaacttctctctttgtatagAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC
                   ||| || |    ||  |  |         |   |||   |   |||   | || |  | |        | |  |  || ||||||||  ||||  || | |||||||||||||||| ||||||| |||||||||| || ||||| |||||  | || ||||| |||||||||||| | || 
------------------gtagcaactgcttttcaagtttgaacagatttgaatcttgtatgtttgataccttc--attcacttcaatattgtcatacagAGGTGCGCGAGCTTCGCTATGGGAGAACTTCAAGAGCAACCCTCTGTTTGACATTTCCACAGACCACCCTGCCACTTACTATGAAGACATGCAGCGCGCT

upper sequence: AT1G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G152029_T01 (Zea mays), 3'ss of exon 3
----acaattaagcattcctca--ttaggaagtt-----aggttatatataaggttagctaagatcaaattgt-tttagaatctgctgactggaacttct-ctctttgtatagAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC
    |  ||  | |  ||  ||  | | | || |         | | |     || |   |  |  | | ||  |      |||| |  |||    |||| |   || || ||||||||  | ||| | || |||||||||||||||||||||||  | || |||||||| || ||||||||  | || ||||||||||||||| || |  | 
gtaaatcatctatctgtctgcaagtgatgcagcttccctccactttttccccagtcattcatcacaacactgcgtccttggtctgatctctgatcattctgcatgttctacagAGGTGCTCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCATCGACTTACTACGAAGACATGGAGCGTTCA

upper sequence: AT1G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM5G898668_T01 (Zea mays), 3'ss of exon 3
acaattaagcattcctcattaggaagttaggttatatataaggttagctaagatcaaattgttttagaatctgctgactggaacttctctc---tttgtatagAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC
          |||  | | |     ||  |  | | | |  |  |  ||| ||   | |  |            |  ||  ||| || ||    |  |   || || ||| | ||  |||| |||||||||||||||||||||||  | || |||||||| || || |||||| | || |||||||| ||||||||| |  | 
-------gtaattaataaatcaactgtctgtctgtctgtctgtctgtctacgagtgagtgatccggcggcggcttccctcaaacgtcacttacttccgcgcagGGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACGGACCACCCGGCGACGTACTACGAGGACATGCAGCGCTCG

upper sequence: AT1G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G056702_T01 (Zea mays), 3'ss of exon 3
acaattaagcattcctcattaggaagttaggttatatataa-ggttagcta--agatcaaattgttttagaatctgctgactggaacttctctctttgtatagAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC
   |    ||   | |||||           | | |      | | ||| |    ||||||  ||  |   || ||||  ||      |  ||     |  || || ||  | ||| | || |||||||||||||||||||||||  | || ||||||||||| || |||||  | || |||||||| ||||||||| | |||
-gtacgtcgctaccttcattgcacgtcctaataacaagccttgatgagccattgaatcaaagagtcctg--atgtgctacctaccgtata-cttacaatgcagGGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCAACGGACCACCCACCCACGTACTACGAGGACATGCAGCGTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctaagatcaaattgttttagaatctgctgactggaacttctctctttgtatagAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC
                          tgctgac  putative branch site (score: 2)
                                      cttctctctttgtat  putative PPT
          aaattgttttagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaattaagcattcctcattaggaagttaggttatatataaggttagctaagatcaaattgttttagaatctgctgactggaacttctctctttgtatagAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - -gatcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgctga