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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtttgcctacataaaaactgttttacagtgttgtatgatggcagatatttagcattttacttgattgtgcataacttcagccttttttatgtcgttagGTACACTATGGAAAGACCAAGGTTCAGTGACCATCTAGAGGCAATCAAGTTTATCTGCAAAGACTTCTGGTCTGAGGTCTTCAAGAAGCAGATTGATAAT

Basic information

species Arabidopsis thaliana
transcript AT3G05000.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G05000.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os09g06970.3 (Oryza sativa), 3'ss of exon 1
gtgtttgcctacataaaaactgttttacagtgttgtatgatggcagatatttagcattttacttgattgtgcataacttcagccttttttatgtc----gttagGTACACTATGGAAAGACCAAGGTTCAGTGACCATCTAGAGGCAATCAAGTTTATCTGCAAAGACTTCTGGTCTGAGGTCTTCAAGAAGCAGATTGATAAT
       |  |  |||   |||| | |      | | || |    | |  ||| |      | |  | ||||     || | | |  ||| |||      | || || || |||||  | ||  | || ||||| ||||| || |||||||| ||||||||||||||||| ||||| ||| | ||||||||||||||||| |||
---agcacaaatgtaactgctgtctgaattgcatatgtg-tattgggttcttacctccactccttgtagtgctgcgattaaccataatttctgttcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAAT

upper sequence: AT3G05000.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os07g19060.2 (Oryza sativa), 3'ss of exon 1
--gtgtttgcctacataaaaactgttttacagtgttgtatgatggcagatatttagcattttacttgattgtgcataacttcagccttttttatgtcgttagGTACACTATGGAAAGACCAAGGTTCAGTGACCATCTAGAGGCAATCAAGTTTATCTGCAAAGACTTCTGGTCTGAGGTCTTCAAGAAGCAGATTGATAAT
     | |  ||||  |   |    ||| || | || |||  |||    |      ||    | |          ||||   ||  | | ||      | || || ||||||||  | ||  | || ||||| ||||| || |||||||| ||||||||||||||||| ||||| ||| | ||||||||||| ||||| |||
acaaatataactactcactgaaatatttgcattctt-tatattggttccttacctccaggccagtgctgcaaagttaaccaaagtttctgtt-caaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGTTATTCAAGAAGCAAATTGACAAT

upper sequence: AT3G05000.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM5G886989_T03 (Zea mays), 3'ss of exon 2
-gtgtttgcctacataaaaactgttttacagtgttgtatgatggcagatatttagcattttacttgattgtgcata---acttcagccttttttatgtcgttagGTACACTATGGAAAGACCAAGGTTCAGTGACCATCTAGAGGCAATCAAGTTTATCTGCAAAGACTTCTGGTCTGAGGTCTTCAAGAAGCAGATTGATAAT
    | || |    |     |||| | |   | || | || |    |  |     || |  |  |   | |||| |   |    |   | || |   |  | || || || |||||  | ||  | || ||||| ||||| || ||||||||||||||||||||||| || ||||| ||| | ||||||||||||||||| |||
cagatctgtcagtttt----ctgtgtgattattttttttggtcagtgcaacactccaatgcatgtacatctgcagactcaaccaaatttattgttcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAAT

upper sequence: AT3G05000.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G123807_T02 (Zea mays), 3'ss of exon 2
-gtgtttgcctacataaaaactgttttacagtgttgtatgatggcagatatttagcattttacttgattgtgcataacttcagccttttttat--gtcgttagGTACACTATGGAAAGACCAAGGTTCAGTGACCATCTAGAGGCAATCAAGTTTATCTGCAAAGACTTCTGGTCTGAGGTCTTCAAGAAGCAGATTGATAAT
    | || ||   |     |||| | |     || | |  |    |  ||    || |  |  |  || ||||  |||  | | |||||| |   |  | || || || |||||  | ||| | || ||||| ||||| || |||||||| ||||||||||||||||||||||| ||| | |||||||| |||||||| |||
caaatctgtctcagtttt--ctgtgtgattaatttttttagtcagtgcaatgctccaatgcatgtacttctgca-gactcaaccattttttgttcatattcagATATACCATGGAGCGTCCACGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTCTGGTCAGAGCTGTTCAAGAAACAGATTGACAAT

upper sequence: AT3G05000.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G42850.1 (Glycine max), 3'ss of exon 1
gtgtttgcctacataaaaactgttttacagtgttgtatgatggc-------agatatttagcattttacttgattgtgcataacttcagccttttttatgtcgttagGTACACTATGGAAAGACCAAGGTTCAGTGACCATCTAGAGGCAATCAAGTTTATCTGCAAAGACTTCTGGTCTGAGGTCTTCAAGAAGCAGATTGATAAT
    ||  ||   |||  | |||  |  |||  |  |||||| |       ||  | ||| |||   | |||||||    ||   | |   | |  | ||| |||||||| || |||||  | ||  ||||||  || ||||| ||||| |||||||| |||||||| || || ||||||||| ||||||||||||||||||| || 
---gttaactttgtaatga-tgtaatgtagttctacatgatgactctctaaagggaattatcatgaaatttgattgaat-tag--taaaattgtggtttgttgttagGTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTTCATCTGCAAGGATTTTTGGTCTGAGCTCTTCAAGAAGCAGATTGACAAC

upper sequence: AT3G05000.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv14s0030g00700.t01 (Vitis vinifera), 3'ss of exon 1
-gtgtttgcctacataaaaactgttttacagtgttgtatgatggcagatatttagcattttacttgattgtgcataacttcagccttttttatgtcgttagGTACACTATGGAAAGACCAAGGTTCAGTGACCATCTAGAGGCAATCAAGTTTATCTGCAAAGACTTCTGGTCTGAGGTCTTCAAGAAGCAGATTGATAAT
 | |  ||   | ||| | |      || |   ||  |          | |||    ||||   |  |  |    |     ||   ||||| | |  |||| || |||||||| || ||  |||| ||||| ||||||||||||||||||||||||||||| ||||||||||||||| ||||||||||||| || || || 
agggagtgatcatatatatagccccata-atccttagacttccttttttctttttttttttgtgtagtcataataataaaaaggtatttttttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAAC

upper sequence: AT3G05000.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ32385 (Selaginella moellendorffii), 3'ss of exon 1
------------------------------------------------------------------------------------------gtgtttgcctacataaaaactgttttacagt--gttgtatga-tggcagatatttagcattttacttgattgtgcataacttcagccttttttatgtcgttagGTACACTATGGAAAGACCAAGGTTCAGTGACCATCTAGAGGCAATCAAGTTTATCTGCAAAGACTTCTGGTCTGAGGTCTTCAAGAAGCAGATTGATAAT
                                                                                           || |||| | | | ||   |  |||    |   |  | | | |  || || | ||    |  |   | | ||   |   |  | | |||||  | |    || ||||| |  ||  | ||  | ||||  |||||  | || |  |||||||| || ||||| || |||||| | ||||| ||||||||||||||||| |||
gtaaaattttcttacattgccgtggagctcaaatgcttgcgaggaatgtggcttgcattccttgatctgcttagattggttccagtggatctgcttgcttgcgtgaattttccttttggattgatcttgtaagttccaaatgtataaatctcaagaaggtggttttttcttcgatcttttttcctctttccagATACACAAGAGATCGTCCGCGATTCACAGACCACTTGGAAGTCATCAAGTTCATATGCAAGGATTTCTGGGCGGAGGTTTTCAAGAAGCAGATTGACAAT

upper sequence: AT3G05000.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ20859 (Selaginella moellendorffii), 3'ss of exon 1
-------------------------------------------------------------------gtgtttgcctacataaaaactgttttacagt--gttgtatga-tggcagatatttagcattttacttgattgtgcataacttcagccttttttatgtcgttagGTACACTATGGAAAGACCAAGGTTCAGTGACCATCTAGAGGCAATCAAGTTTATCTGCAAAGACTTCTGGTCTGAGGTCTTCAAGAAGCAGATTGATAAT
                                                                    || |||| | | | ||   |  |||    |   |  | | | |  || || | ||    |  |   | | ||   |   |  | | |||||  | |    || ||||| |  ||  | ||  | ||||  || ||  | || |  |||||||| || ||||| || |||||| | ||||| ||||||||||||||||| |||
gtaaaattttctgctcaaatgcttgcgaggaatgtggcttgatctgcttagattggttccagtggatctgcttgcttgcgtgaattttccttttggattgatcttgtaagttccaaatgtataaatctcaagaaggtggttttttcttctatcttttttcctctttccagATACACAAGAGATCGTCCGCGATTCACAGATCACTTGGAAGTCATCAAGTTCATATGCAAGGATTTCTGGGCGGAGGTTTTCAAGAAGCAGATTGACAAT

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|124963258|gb|EL037606.1|EL037606
EST:     CGGCCACCAGCTCTCCGAGAG                         GTACACTATGGAAAGACCAAGGTTCAGTGACCATCTAGAGGCAATCAAGTT
genomic: CGGCCACCAGCTCTCCGAGAGgtttgtttta ... atgtcgttagGTACACTATGGAAAGACCAAGGTTCAGTGACCATCTAGAGGCAATCAAGTT
EST: gi|86086179|gb|DR381938.1|DR381938
EST:     CGGAGGATCGAGGCCATTGGTTATCAGGTCGGCCACCAGCTCTCCGAGAG                         GTACACTATGGAAAGACCAAGGTTCAGTGACCATCTAGAGGCAATCAAGTT
genomic: CGGAGGATCGAGGCCATTGGTTATCAGGTCGGCCACCAGCTCTCCGAGAGgtttgtttta ... atgtcgttagGTACACTATGGAAAGACCAAGGTTCAGTGACCATCTAGAGGCAATCAAGTT
EST: gi|125249410|gb|EL263495.1|EL263495
EST:     CGGAGGATCGAGGCCATTGGTTATCAGGTCGGCCACCAGCTCNCCGAGAG                         GTACACTATGGAAAG
genomic: CGGAGGATCGAGGCCATTGGTTATCAGGTCGGCCACCAGCTCTCCGAGAGgtttgtttta ... atgtcgttagGTACACTATGGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatatttagcattttacttgattgtgcataacttcagccttttttatgtcgttagGTACACTATGGAAAGACCAAGGTTCAGTGACCATCTAGAGGCAATCAAGTTTATCTGCAAAGACTTCTGGTCTGAGGTCTTCAAGAAGCAGATTGATAAT
                         gcataac  putative branch site (score: 3)
                                     ccttttttat  putative PPT
                                       ttttttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtttgcctacataaaaactgttttacagtgttgtatgatggcagatatttagcattttacttgattgtgcataacttcagccttttttatgtcgttagGTACACTATGGAAAGACCAAGGTTCAGTGACCATCTAGAGGCAATCAAGTTTATCTGCAAAGACTTCTGGTCTGAGGTCTTCAAGAAGCAGATTGATAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - -taaaaac