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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccctcattctctaccttcattgaatcatccagataaataaatttgtcgtctctactgcttgaaattttgaaataattataaattgtcagGTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAG

Basic information

species Arabidopsis thaliana
transcript AT1G13320.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 9
-----gtccctcattctctaccttcattgaatcatc---cagataaataa-atttgtcgtctctactgcttgaaattttgaaataattataaattgtcagGTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAG
      ||  | ||| | ||  ||  ||  |          || || |   |||| |   ||    |    ||  |||| || |   | |  | | | ||||   ||||||| | || ||||||||||||||  ||||||| || ||||| ||||||||||| |||||||| |||||||||||| | ||||||
ttgtgttcagtgattatatagtttttttttaatgcagaatggacaagtggtatttataacctgctatttaagatgtttttaactggatctttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG

upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G122135_T04 (Zea mays), 3'ss of exon 9
-----------------------------------------------------gtccctcattctctaccttcattgaatcatccagataaataaatttgtcgtctctactgcttgaaattttgaaataattataaattg----tcagGTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAG
                                                      ||  || ||  |  | |  ||       | || |||    | | ||  || |  |||  | |      | || |||  | || |||    ||||||   ||||||| | || ||||| || |||||  ||||||| ||||| |||||||| ||||| || |||||||||||||||||| ||||||||
gttcgtatcactagacttatgtcaaaacagtaacgctgtggggctactcaagcatctttcctttccatcttgtatcctcgagtgcatataggacattgtgatgtattgactaatggtttagattaactaaccaaaatttggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAG

upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 9
---------------------------------------------gtccctcat-tctctaccttcattgaatcatccagataaataaatttgtcgtctctactgcttgaaatt-----ttgaaataattataaattg----tcagGTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAG
                                             ||| |     ||| || ||| ||    |       |||    | |||||  | |  | ||  | |||||     || || ||| || || |||    ||||||    |||||| | || ||||| || |||||  ||||||| ||||| |||||||||||||| || |||||||||||||||||| | ||||||
gtttgtatcattagggttatgtcaaaacagtatctctttggagctgtctccagcgtctttatctt-atatccttgagtgcatattggactttgtaatgt--attgactaaaattgtcagtttaactaactaaaatttggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAAGAGTTTGGTCCAGAGTGGGCAATGCAGCATATAATCCCTCAG

upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 9
gtccctcattctctaccttcattgaatcatccagataaataa-atttgtcgtctctactgcttgaaattttgaaataatta--taaattgt--cagGTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAG
     |  | ||||||  |   |   |  |   | |  ||          |  | |    | |||   |||    |||  |  | | || |   ||||||| ||||| |||||||| ||||| |||||  |||| || ||||||||||| ||||||||||| ||||| |||||||| ||| ||||||||
---gtttgtgctctacacttccttgctagtgtgggtgcattttgggaactgcatattgcacatgacggtttttgttaaccaccttagttattgtagGTTCATTCAATTCGTGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAGCACATAATTCCTCAG

upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 9
gtccctc-attctctaccttcattgaatcatccagataaataaatttgtcgtctctactgcttgaaattttgaaataattataaattgtcagGTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAG
||   |  | |||  |   |  ||  | |||     ||   ||     |  |||  |   ||       || |  | ||| |   |||| ||||||| || |||||||| || ||||| |||||| ||||||| || |||||||| ||||||||||| ||||| ||||| || ||| |||| |||
gtttgtggactctacatgctagtttgagcatattt-taggaaaccaccttttctacatgactattgtcgttaacctcattgtttgttgt-agGTTCATTCGATCCGTGAGGCAGCTGCTAACAATTTGAAGCGCCTAGCTGAAGAATTTGGTCCTGAGTGGGCTATGCAACACATAATTCCACAG

upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 9
------gtccctca-ttctctaccttcattgaatcatccagataaataaatttgtcgtctctactgcttgaaattttgaaataattataaattgtcagGTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAG
      |  |  || |||  | |     | |   |||   |  || |  || |  |   |  |||| ||    | || | |   |||   ||||| ||||||| ||||| || ||||| ||||| |||||  |||| || ||||||||||| ||||| ||||| ||||| |||||||| ||| ||||||||
gtttgtgctctccacttccttgctagtgtgggtgcattttgggaactgcatattgcacatg-actgtttt---tgttaacaaccttagttattgt-agGTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAG

upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 8
-----------gtccctcattctctaccttcattgaatcatccagataaataaatttgtcgtctctactgcttgaaattttgaaataattataaattgt-cagGTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAG
           | |  ||||  |||    |||| |  |  ||    |   | |  |     | | |   | |  |||     ||||| |   |  |||| |||||| |||| || ||||| |||||||| |||||  | ||||| ||||| ||||| ||||||||||| ||||||||||||||  || |||| |||
tattttaagagggctttcatcatct-ttgtcatcg--ttttctttgtctgtcatctatgtatttatgtagttcaaaagggacaaatattatcatgttgtgcagGTTTACTCCATTCGTGATGCTGCTGCTAACAACTTAAAGCGCCTTGCAGAAGAATTTGGTCCTGACTGGGCAATGCAGCACTTAATTCCACAG

upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S214_34V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------------gtccctcattctctaccttcattgaatcatcca-gataaataaatttgtcgtctctactgcttgaaattt-------tgaaataattata----------aattgtcagGTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAG
                           ||  |  |  | |   |  |     || |||   || |      || || | | | || ||| | |  |       | | ||||||  |           |||   ||||  |||| ||||| || || ||||| |||||||| ||||||||||| ||||||||||||||||| |||||| ||||||| ||  |||| |||
gttcatatattcccatcaagcaatgtttcgatggtggtttgtgtcgagatggtcgtcctcaatcagatctcttttcatatttgcttctttagaactagttcagtaatataatttcattcttttttggattaatagGTGTACTCTATCCGAGAGGCAGCTGCCAACAATCTCAAGCGTCTTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAG

upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S197_114V6.1 (Physcomitrella patens), 3'ss of exon 8
------------------------------------------------------------gtccctcattctctaccttcattgaatcatccagataaataaatttgtcgtctctactgcttgaaattttgaaataattataaattgt-cagGTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAG
                                                             || |  |   | | |      | |  || |   |     |  ||| |    | || | |||  |||  |    |  || |   |||  |||||  |||| ||||| || |||||||| ||||| || ||||||||||| |||||||| ||| | || |||||| |||| || ||  |||| |||
gttcttatattcccatcaagcaatatgtggatgatttctaatcacaagttgctgacttatatcgccaaagttgtcctcgagcttacacacctgtaccttaaggtttatt-catatatttcttttaatcgtttttttttttttttttgaacagGTGTACTCTATCCGAGAGGCTGCTGCGAACAACCTTAAGCGTCTTGCCGAAGAGTTCGGTTCCGAGTGGGCATTGCAACACATCATTCCACAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|116425639|gb|EG468231.1|EG468231
EST:     TCTTTGATGAGAAGCTTGGTGCTCTTTGCATGCAATGGTTACAAGACAAG                         GTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAA
genomic: TCTTTGATGAGAAGCTTGGTGCTCTTTGCATGCAATGGTTACAAGACAAGgtccctcatt ... aaattgtcagGTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAA
EST: gi|86073296|gb|DR369053.1|DR369053
EST:     TCTTTGATGAGAAGCTTGGTGCTCTTTGCATGCAATGGTTACAAGACAAG                         GTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAA
genomic: TCTTTGATGAGAAGCTTGGTGCTCTTTGCATGCAATGGTTACAAGACAAGgtccctcatt ... aaattgtcagGTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaataaatttgtcgtctctactgcttgaaattttgaaataattataaattgtcagGTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAG
                        ttgaaattttgaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccctcattctctaccttcattgaatcatccagataaataaatttgtcgtctctactgcttgaaattttgaaataattataaattgtcagGTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA