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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttggatgtctcattttgtatcttctttgttacattgtttccacatggcttcattgtatgaagcttttttcttttacttttagcttattttatctggattgtttctttcttgcagGTTCCATTCTGTCCAATGGTTGGATCTGAGGTTTACTCATCAGAGGTTAAGAAAACAGAGGTTCTCATGGAGAATTTTAGACGTGCCATTGGTCTACGTA

Basic information

species Arabidopsis thaliana
transcript AT5G22330.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 2
gtaattttggatgtctcat-tttgtatcttctttgttacattgtttccacatggcttcattgtatgaagcttttttcttttacttttagcttattttatctggattgtttctttcttgcagGTTCCATTCTGTCCAATGGTTGGATCTGAGGTTTACTCATCAGAGGTTAAGAAAACAGAGGTTCTCATGGAGAATTTTAGACGTGCCATTGGTCTACGTA
       |  |||||| |  | ||  || | |||| || |    ||||| |||  |   |  | |  |       | | |||         | | ||||||  ||| |||   | |  ||||| || |||||||| ||||| ||||| || || || || |||||||| |||||||| ||||| || |||||||||||  |  | || || ||| | ||||
-------tcaatgtcttacatctgcttcatttttggtaaa--acttcca-atgtttcattcatgttgatggagaatatctta---------tgtgttatctt-attattttactat-acagGTCCCTTTCTGTCCTATGGTAGGATCAGAAGTGTATTCCTCAGAGGTCAAGAAAACTGAGGTGCTAATGGAGAATTTCCGTAGAGCTATAGGTTTGCGTA

upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G032267_T02 (Zea mays), 3'ss of exon 2
gtaattttggatgtctcattttgtatcttctttgttacattgtttccacatggcttcattgtatgaagcttttttcttttacttttagcttattttatctggattgtttctttcttgcagGTTCCATTCTGTCCAATGGTTGGATCTGAGGTTTACTCATCAGAGGTTAAGAAAACAGAGGTTCTCATGGAGAATTTTAGACGTGCCATTGGTCTACGTA
          ||||  |    ||    |  |  | |    || || |   ||| |||| ||||  |   ||| | || | |  ||  | |  ||   ||     |||  ||    ||||||| ||||||||||| ||||| ||||| || || ||||| |||||||| |||||||| ||||| || ||||| |||||  |  | || || ||| | ||||
--------aaatgttac----tgatgttgataagctgtgatgcttgc---tggattcactgtagca---tttatgctataatcttctgatgtttccttccc--ctgtcactgcaatgcagGTCCCATTCTGTCCTATGGTAGGATCAGAAGTGTACTCCTCAGAGGTCAAGAAAACTGAGGTGCTGATGGAAAATTTCCGTAGAGCTATAGGTTTGCGTA

upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 2
gtaattttggatgtctcattttgtatcttctttgttacattgtttccacatggcttcattgtatgaagcttttttcttttacttttagcttattttatctggattgtttctttcttgcagGTTCCATTCTGTCCAATGGTTGGATCTGAGGTTTACTCATCAGAGGTTAAGAAAACAGAGGTTCTCATGGAGAATTTTAGACGTGCCATTGGTCTACGTA
           | || |  |    |   || || |     |||||         |||  ||| |   | || |  |  || |||   ||| ||  ||    | || |  |  ||| ||||||||| ||||| ||||||||||| ||||| |||||||| ||||| || ||||| || |||||||||||||| ||||||||||| ||||||||||| ||||
----------gtttccctctcaagactctcattctcgtggtgttttttt----tttctctgtgttttgattgtgaccctt-cttgctgctgataataat--gtttatgccactct-gcagGTTCCTTTCTGCCCAATGGTTGGTTCTGAAGTTTACTCCTCAGAAGTAAAGAAGACCGAGGTTCTCATGGAAAATTTTAGACGGGCCATTGGTCTGCGTA

upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 2
gtaattttggatgtctcattttgtatcttctttgttacattgtttccacatggcttcattgtatgaagcttttttcttttacttttagcttattttatctggattgtttctttcttgcagGTTCCATTCTGTCCAATGGTTGGATCTGAGGTTTACTCATCAGAGGTTAAGAAAACAGAGGTTCTCATGGAGAATTTTAGACGTGCCATTGGTCTACGTA
                                 ||| | || |    ||     ||| |||| |   | || || |   | |||   ||||||   |  |   ||  |||     ||||||| || ||||| || |||||||| || || |||||||| || || || ||||| || |||||||||||||| |||||| |||| ||||||||||| ||||
---------------------------------gtttctttctcaagactctcattctttgtgttgtgattgttaccccttcttgctgcttat---aattaagtttattccactctgcagGTACCGTTCTGCCCTATGGTTGGCTCCGAAGTTTACTCCTCGGAAGTAAAGAAGACTGAGGTTCTCATGGAAAATTTTCGACGGGCCATTGGTCTGCGTA

upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------gtaattttggatgtctcattt-tgtatcttctttgttacattgtttccacatggctt-cattgta----tgaagcttt---tttcttttacttttagcttattttatctggattgt--ttctttcttgcagGTTCCATTCTGTCCAATGGTTGGATCTGAGGTTTACTCATCAGAGGTTAAGAAAACAGAGGTTCTCATGGAGAATTTTAGACGTGCCATTGGTCTACGTA
                                               |||| |   | ||  |  | |  || |   || |    || | ||||  ||  || || | ||    ||     ||   |  |||   |||   |  | |   |||||  || |  ||||   || |||||||| ||||| |||||||| ||||| ||||| |||||||||||||| |||||||| ||| || | ||||| |||||  |||| || |||||||||||||
gtacaacttaaatgtactcttaccattttttgttcagtagtgtcttgaattctctttatcagagctgtagatttagattctggggttctctccagttgattttcagtctagctctgggatgttgaatgccttactcttcaggggtgtgagatctgctttttacttctgatttacagGTTCCTTTCTGCCCAATGGTGGGATCAGAGGTATACTCATCAGAGGTAAAGAAAACTGAGATTTTAATGGAAAATTTCCGACGGGCTATTGGTCTACGTA

upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S40_79V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaattttggatgtctcattttgtatcttctttgttacattgtttccacatggcttcattgtatgaagcttttttcttttacttttagcttattttatctggattgtttctttcttgcagGTTCCATTCTGTCCAATGGTTGGATCTGAGGTTTACTCATCAGAGGTTAAGAAAACAGAGGTTCTCATGGAGAATTTTAGACGTGCCATTGGTCTACGTA
  |||     |      |||    |||||| |  |   |   |      || | | | |||      |    |||| |  | |  |||||||||                  |||| ||| |||  |||||||| ||||| || || || ||||||||||| || |||||||| || ||||| ||||||||||||||     |                 
--aatgcattacaagcgattccaaatcttcgtcttctgagcat-----gattgttacgttggtgtccgaccgtttcataaagtcgtagcttattcc-------------tcatcttacagATTCTGTTCTGTCCGATGGTAGGGTCCGAAGTTTACTCATCCGAAGTTAAGAAGACGGAGGTGCTCATGGAGAATTTCCACTGC----------------

upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaattttggatgtctcattttgtatcttctttgttacattgtttccacatggcttcattgtatgaagcttttttcttttacttttagcttattttatctggattgtttctttcttgcagGTTCCATTCTGTCCAATGGTTGGATCTGAGGTTTACTCATCAGAGGTTAAGAAAACAGAGGTTCTCATGGAGAATTTTAGACGTGCCATTGGTCTACGTA
     |||| | || |   ||      | |||||  | | || ||  | |  || || || | ||    ||  |  | || | |  |||          ||| |||| |     || |||||||||||||| |||||||| || || || |||||||||||||| |||||||| || || ||||| |||||||||||  | ||||| ||||| || ||||
-----tttgaaagtattgattgaa---tgctttg--aaaatgatttgaaa--gcctccttctctgggcattcctattgtttcatcgagcca--------tggtttgtattcccttttcagGTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAGAAGACGGAAGTTCTTATGGAGAATTTCCGCCGTGCAATTGGGCTTCGTA

upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ33466 (Selaginella moellendorffii), 3'ss of exon 2
gtaattttggatgtctcattttgtatcttctttgttacattgtttccacatggcttcattgtatgaagcttttttcttttacttttagcttattttatctggattgtttctttcttgcagGTTCCATTCTGTCCAATGGTTGGATCTGAGGTTTACTCATCAGAGGTTAAGAAAACAGAGGTTCTCATGGAGAATTTTAGACGTGCCATTGGTCTACGTA
                                                          |||| | |||||  |||||| |  ||    | ||   |       |||||   |  || ||||||||||| ||||||||||| ||||| ||||||| ||| || || |||||||| || || ||||||||||| || ||| | ||  | || || || ||||
--------------------------------------------------------gtttgtttcaagctcatttcttctctttccttcatacaatgggaattttgttctgtggttccagGTTCCATTTTGTCCAATGGTGGGATCGGAGGTTTTCTCTTCCGAAGTTAAGAAGACCGAAGTTCTCATGGAAAACTTTCGTCGCTCGATCGGCCTGCGTA

upper sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ27201 (Selaginella moellendorffii), 3'ss of exon 2
gtaattttggatgtctcattttgtatcttctttgttacattgtttccacatggcttcattgtatgaagcttttttcttttacttttagcttattttatctggattgtttctttcttgcagGTTCCATTCTGTCCAATGGTTGGATCTGAGGTTTACTCATCAGAGGTTAAGAAAACAGAGGTTCTCATGGAGAATTTTAGACGTGCCATTGGTCTACGTA
                                                          |||| | |||||  |||||| |  ||    | ||   |       |||||   |  || ||||||||||| ||||||||||| ||||| ||||||| ||| || || |||||||| || || ||||||||||| || ||| | ||  | || || || ||||
--------------------------------------------------------gtttgtttcaagctcatttcttctctttccttcatacaatgggatttttgttctgtggttccagGTTCCATTTTGTCCAATGGTGGGATCGGAGGTTTTCTCTTCCGAAGTTAAGAAGACCGAAGTTCTCATGGAAAACTTTCGTCGCTCGATCGGCCTGCGTA

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|116443983|gb|EG486575.1|EG486575
EST:     CTGGGAAAACAGCTTTGGCTCTTGGAATCTCTCAAGAGCTGGGAAGCAAG                         GTTCCATTCTGTCCAATGGTTGGATCTGAGGTTTACTCATCAGAGGTTAAG
genomic: CTGGGAAAACAGCTTTGGCTCTTGGAATCTCTCAAGAGCTGGGAAGCAAGgtaattttgg ... tttcttgcagGTTCCATTCTGTCCAATGGTTGGATCTGAGGTTTACTCATCAGAGGTTAAG
EST: gi|125054012|gb|EL124897.1|EL124897
EST:     CTGGGAAAACAGCTTTGGCTCTTGGAATCTCTCAAGAGCTGGGAAGCAAG                         GTTCCATTCTGTCCAATGGTTG
genomic: CTGGGAAAACAGCTTTGGCTCTTGGAATCTCTCAAGAGCTGGGAAGCAAGgtaattttgg ... tttcttgcagGTTCCATTCTGTCCAATGGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcttttttcttttacttttagcttattttatctggattgtttctttcttgcagGTTCCATTCTGTCCAATGGTTGGATCTGAGGTTTACTCATCAGAGGTTAAGAAAACAGAGGTTCTCATGGAGAATTTTAGACGTGCCATTGGTCTACGTA
                                      ttgtttctttcttgc  CT-rich tract
     tttttcttttactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattttggatgtctcattttgtatcttctttgttacattgtttccacatggcttcattgtatgaagcttttttcttttacttttagcttattttatctggattgtttctttcttgcagGTTCCATTCTGTCCAATGGTTGGATCTGAGGTTTACTCATCAGAGGTTAAGAAAACAGAGGTTCTCATGGAGAATTTTAGACGTGCCATTGGTCTACGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA