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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaagctccttgtatcaacttcttagtaccatttcgttgttttgatctttgtggtaatcctttggttttgattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG

Basic information

species Arabidopsis thaliana
transcript AT1G67430.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G67430.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G10910.2 (Glycine max), 3'ss of exon 2
------------------------------------------gtaagtaaagctccttgtatcaac----ttcttagtaccatttcgttgttttgatctttgtggtaatcctttggttttgattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
                                           ||  |     ||  |  | | ||    ||  | ||  | ||   |         |    |  |  || | | |||||   |||||||||||||||||||||||  |||| ||||||||||| || |||
gtaggttttattcacacttttcttttttactttttgatatcgatacttgttattcgctaaaacgacggcgtttgtggtctctttcaatctgagccccccacttttttttcttatcgtttttcatttgcagCTTGCAAGGCTAGAGGCGCCGACCTTAGGGTTCATTTTAAG

upper sequence: AT1G67430.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G27940.1 (Glycine max), 3'ss of exon 2
---------------------------------gtaagtaaagctccttgtatcaacttcttagtaccatttcgttgttttgatctttgtggtaatcctttggttttgattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
                                 |||       | | |  | || |              |    | | |  ||||  |   |  |    | || ||   | |||||||||||||||||||||  |||| ||||||||||| || |||
gtaggtttcattagtaatcacttttttgtgtttgtagaatcgacacttattctctaaacgacgacgtttataatctctctcaatctgagcatttttttaatcgtctttcatatgcagCTTGCAAGGCTAGAGGCGCCGACCTTAGGGTTCATTTTAAG

upper sequence: AT1G67430.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ26852 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtaaagctccttgtatcaacttcttagtaccatttcgttgttttgatctttgtggtaatcctttggttttgattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
               ||  | || |||  |   |  | ||||||   | | ||| |                |||||   |||||||||||||| ||||| ||||||||  |||| |||||||||
--------------gtgagtgaaattcgcaa-gcgctctcgttgacctcagcttgga---------------ttgatc--gcagCTTGCAAGGCGAGAGGCTCCGATCTCCGGGTCCACTTCAAG

upper sequence: AT1G67430.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ21308 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtaaagctccttgtatcaacttcttagtaccatttcgttgttttgatctttgtggtaatcctttggttttgattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
               ||  | || |||  |   |  | ||||||     | || ||          |||| ||     | |||||||||||||| ||||| ||||||||  |||| |||||||||
--------------gtgagtgaaattcgcaa-gcgctctcgttg-----acctctgc---------ttggattga---tcgcagCTTGCAAGGCGAGAGGCTCCGATCTCCGGGTCCACTTCAAG

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|116454165|gb|EG496757.1|EG496757
EST:     GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT                         CTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
genomic: GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTgtaagtaaag ... gattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
EST: gi|152035881|gb|BP863620.2|BP863620
EST:     GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT                         CTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
genomic: GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTgtaagtaaag ... gattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
EST: gi|116451520|gb|EG494112.1|EG494112
EST:     GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT                         CTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
genomic: GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTgtaagtaaag ... gattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
EST: gi|116454163|gb|EG496755.1|EG496755
EST:     GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT                         CTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
genomic: GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTgtaagtaaag ... gattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
EST: gi|125021887|gb|EL094156.1|EL094156
EST:     GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT                         CTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAGAATAC
genomic: GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTgtaagtaaag ... gattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAGAATAC
EST: gi|116451521|gb|EG494113.1|EG494113
EST:     GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGT                         CTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
genomic: GTGAAGTACTCGCAAGAACCCGACAATCAGACCAAGTgtaagtaaag ... gattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtaccatttcgttgttttgatctttgtggtaatcctttggttttgattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG
                                         ttttgat  putative branch site (score: 4)
                                         ttttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaaagctccttgtatcaacttcttagtaccatttcgttgttttgatctttgtggtaatcctttggttttgattttgcagCTTGCAAGGCTAGAGGATCCGATCTTAGGGTTCACTTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT