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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagcctatccactctgtagacttattttgtgtttgtctcccgtctttgtatgtttttttagttcatgctatattttgtttctatgtatgatttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTATTTAATGGGAGAAGGAATGACGGAGGGCAGGCTGAGTATACCTGCCCAT

Basic information

species Arabidopsis thaliana
transcript AT1G79000.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 7
gtaaaagcctatccactctgtagacttattttgtgtttgtctcccgtctttgtatgtttttttagttcatgctatattttgtttctatgtatgatttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTATTTAATGGGAGAAGGAATGACGGAGGGCAGGCTGAGTATACCTGCCCAT
||||   ||| |    | | | |   | || ||| | | ||  |    ||||  | | ||  |  |  ||  || || || |||  ||| |||  || |||||||||| || ||||| || |||||    |||||||| |||||||||||| |||||||||| ||||||||||| |||||||| || ||||| ||||||||| 
gtaagttcctttttcatttttggtgattttgtgtctgtatcatcaaaatttgggtatcttccttttgtatattaaatctt-tttaaatg-atgtattctgcagTGGGTTCAGTGTGACAAGTGTGAATGCTGGCAGCACCAGATATGTGCTCTATTTAATGGTAGAAGGAATGATGGAGGGCAAGCAGAGTACACCTGCCCAA

upper sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 6
gtaaaagcc-tatccactctgtagacttattttgtgtttgtctcccgtctttgtatgtttttttagttcatgctatattttgtttctatgtatgatttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTATTTAATGGGAGAAGGAATGACGGAGGGCAGGCTGAGTATACCTGCCCAT
||||   |   |    |  ||     |  |||  |    |         ||   || ||||| |  ||  ||||| |  ||  ||| |   |    || |||||||||| |||||||| ||||||||    ||||| ||||| || ||||||||||||||||| |||||||| || ||||| || ||||| ||||| |||||  
gtaagtactgcagttccattgatatgtggtttcataaaagctcaagagtttctgatatttttct--tttgtgctaaacatt--ttcaaaccacacattctgcagTGGGTTCAATGTGACAAATGTGAATGTTGGCAACATCAAATTTGTGCTTTATTTAATGGAAGAAGGAACGATGGAGGACAAGCTGAATATACTTGCCCCA

upper sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 7
gtaaaagcctatccactctgtagacttattttgtgtttgtctcccgtctttgtatgtttttttagttcatgctatattttgtttctatgtatgatttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTATTTAATGGGAGAAGGAATGACGGAGGGCAGGCTGAGTATACCTGCCCAT
      |  | |  | | ||    | ||| |    ||||  |   ||     || ||||||||  || ||     || |  | ||| |||         ||||||||| ||||||||||||||||| || ||||| ||||| || ||||||||||||||||| ||||| ||||| || || || ||||| ||||| |||||  
------gtatgttaagtgtgc---catatgtgtcatttggtt---gttcagctaagtttttttgttttattaaccatctattctctgtgt---------gcagTGGGTTCAATGTGATAAATGTGAAGCATGGCAACATCAAATTTGTGCTTTATTTAATGGCAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA

upper sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 7
gtaaaagcctatccactctgtagacttattttgtgtttgtctcccgtctttgtatgtttttttagttcatgctatattttgtttctatgtatgatttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTATTTAATGGGAGAAGGAATGACGGAGGGCAGGCTGAGTATACCTGCCCAT
           | |      | | ||||||||||  || |     | |  | ||  || ||||| |  |   | || ||| | |  |||           |||||||| |||||||||||||||||||| ||||| ||||| || ||||| |||||||||||  |||| ||||| || || || ||||| || || |||||  
----------gtgcgtatcat-gtcttattttgt--ttattgattggcagtttactttgttttaata-accatctactttatctgcatg-----------cagTGGGTTCAATGTGATAAATGTGAGGCATGGCAACATCAAATTTGTGCCTTATTTAATGGTCGAAGAAATGATGGTGGACAAGCTGATTACACTTGCCCTA

upper sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 9
gtaaaagcctatccactctgtagacttattttgtgtttgtctcccgtctttgtatgtttttttagttcatgctatattttgtttctatgtatgatttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTATTTAATGGGAGAAGGAATGACGGAGGGCAGGCTGAGTATACCTGCCCAT
                   |||   | | | ||    ||| ||   |  ||||    ||    ||||  |    | | ||     | | |    | | |||||||||| ||||||||||| ||||| || ||||| ||||| || ||||| ||||||||||| ||||| ||||| || || || ||||| ||||| |||||  
-------------------gtatgttaagtgtgc-catgtgtcattttgttgttcagttaacaagtttttttgttttattaaccatctattctttgtgtgcagTGGGTTCAATGTGATAAGTGTGAAGCATGGCAACATCAAATTTGTGCCTTATTTAATGGTAGAAGAAATGATGGTGGACAAGCTGAATATACTTGCCCTA

upper sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 6
gtaaaagcctatccactctgtagacttatttt-gtgtttgtctcccgtctttgtatgtttttttagt--tcatgctatattttgtttctatgtatgatttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTATTTAATGGGAGAAGGAATGACGGAGGGCAGGCTGAGTATACCTGCCCAT
           |    | | |  | || |||| || | ||||     | || |  | || | | ||   ||   ||    ||||    | ||  |   ||||||||||||| |||||||| |||||||| || ||||| ||||| || ||||| || || |||||  | |||||||| || ||||||||||| ||||| |||||  
----------gtatgttttattcatttcttttagtatctgtcatt-atgttggattattgtctgagcaatcgctcttatgtttgaacatttgcttctattttgcagTGGGTTCAATGTGACAAATGTGAAGCTTGGCAACATCAAATTTGTGCCTTGTTCAATGGTCGGAGGAATGATGGTGGGCAGGCTGAATATACTTGCCCTA

upper sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ09423 (Selaginella moellendorffii), 3'ss of exon 2
gtaaaagcctatccactctgtagacttattttgtgtttgtctcccgtctttgtatgtttttttagttcatgctatattttgtttctatgtatgatttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTATTTAATGGGAGAAGGAATGACGGAGGGCAGGCTGAGTATACCTGCCCAT
                                  || |||     |  | | ||| |||| |   | | ||  |  | |   ||    ||||| ||| |||||||||| |||||||| || ||  | |  ||||||||||| || ||||| ||||||||||| ||||| ||||| || ||  |  | || | ||  ||||| |
----------------------------------gtatgt-----gcttctatattttttctctttccttgaaacgtctgactt----gtatggtttatgcagTGGGTTCAATGTGACAAGTGCAATGTATGGCAGCATCAAATCTGTGCCTTATTTAATGGTAGAAGAAATGAAGGTGGTGACACGGAATTTATTTGCCCCT

upper sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ34595 (Selaginella moellendorffii), 3'ss of exon 5
gtaaaagcctatccactctgtagacttattttgtgtttgtctcccgtctttgtatgtttttttagttcatgctatattttgtttctatgtatgatttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTATTTAATGGGAGAAGGAATGACGGAGGGCAGGCTGAGTATACCTGCCCAT
                          ||| |  | ||| | |      | | ||| |||| |   | | ||  |  |     ||    ||||| ||| |||||||||| |||||||| || ||  | |  ||||||||||| || ||||| ||||||||||| ||||| ||||| || ||  |  | || | ||  ||||| |
-------------------------gtatgtgtttttttttttttacttctatattttttctctttccttgaaacgtccgactt----gtatggtttatgcagTGGGTTCAATGTGACAAGTGCAATGTATGGCAGCATCAAATCTGTGCCTTATTTAATGGTAGAAGAAATGAAGGTGGTGACACGGAATTTATTTGCCCCT

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|116465026|gb|EG507618.1|EG507618
EST:     CTAAGGCAAGACTCGAGAAAAAGAAAAATGATGAAGAGACTGAAGAATGG                         TGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTA
genomic: CTAAGGCAAGACTCGAGAAAAAGAAAAATGATGAAGAGACTGAAGAATGGgtaaaagcct ... atttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTA
EST: gi|116428303|gb|EG470895.1|EG470895
EST:     CTAAGGCAAGACTCGAGAAAAAG-AAAATGATGAAGAGACTGAAGAATGG                         TGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTA
genomic: CTAAGGCAAGACTCGAGAAAAAGAAAAATGATGAAGAGACTGAAGAATGGgtaaaagcct ... atttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTA
EST: gi|116462330|gb|EG504922.1|EG504922
EST:     CTAAGGCAAGACTCGAGAAAAAGAAAAATGATGAAGAGACTGAAGAATGG                         TGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTA
genomic: CTAAGGCAAGACTCGAGAAAAAGAAAAATGATGAAGAGACTGAAGAATGGgtaaaagcct ... atttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTA
EST: gi|116447334|gb|EG489926.1|EG489926
EST:     CTAAGGCAAGACTCGAGAAAAAGAAAAATGATGAAGAGACTGAAGAATGG                         TGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTA
genomic: CTAAGGCAAGACTCGAGAAAAAGAAAAATGATGAAGAGACTGAAGAATGGgtaaaagcct ... atttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTA
EST: gi|116414729|gb|EG457321.1|EG457321
EST:     CTAAGGCAAGACTCGAGAAAAAGAAAAATGATGAAGAGACTGAAGAATGG                         TGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTA
genomic: CTAAGGCAAGACTCGAGAAAAAGAAAAATGATGAAGAGACTGAAGAATGGgtaaaagcct ... atttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTA
EST: gi|116455249|gb|EG497841.1|EG497841
EST:     CTAAGGCAAGACTCGAGAAAAAGAAAAATGATGAAGAGACTGAAGAATGG                         TGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTA
genomic: CTAAGGCAAGACTCGAGAAAAAGAAAAATGATGAAGAGACTGAAGAATGGgtaaaagcct ... atttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTA
EST: gi|116418401|gb|EG460993.1|EG460993
EST:     CTAAGGCAAGACTCGAGAAAAAGAAAAATGATGAAGAGACTGAAGAATGG                         TGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTA
genomic: CTAAGGCAAGACTCGAGAAAAAGAAAAATGATGAAGAGACTGAAGAATGGgtaaaagcct ... atttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTA
EST: gi|116447332|gb|EG489924.1|EG489924
EST:     CTAAGGCAAGACTCGAGAAAAAGAAAAATGATGAAGAGACTGAAGAATGG                         TGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTA
genomic: CTAAGGCAAGACTCGAGAAAAAGAAAAATGATGAAGAGACTGAAGAATGGgtaaaagcct ... atttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtatgtttttttagttcatgctatattttgtttctatgtatgatttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTATTTAATGGGAGAAGGAATGACGGAGGGCAGGCTGAGTATACCTGCCCAT
                                              tttttgc  CT-rich tract
                        tatattttgtttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaagcctatccactctgtagacttattttgtgtttgtctcccgtctttgtatgtttttttagttcatgctatattttgtttctatgtatgatttttgcagTGGGTCCAATGTGATAAATGTGAGGCGTGGCAGCATCAGATATGTGCTTTATTTAATGGGAGAAGGAATGACGGAGGGCAGGCTGAGTATACCTGCCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA