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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatcaatctacctattgtgtcattttcgagaaaactatgaaaccaaactaacagcatttttggggtatataagtaacagagaggttgttgtgcagGTCGGTTTATATCGTGTACACAATGCTAGGGGATGTTAGCATCTTCCTTGTTGGCAAAGACGAGTATGATGAACTTGCTT

Basic information

species Arabidopsis thaliana
transcript AT1G15370.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G15370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G03510.1 (Glycine max), 3'ss of exon 2
gtacatcaatctacctattgtgtcattttcgagaaaactatgaaaccaaactaacagcatttttg--gggtatataagtaacagagaggttgttgtgc---agGTCGGTTTATATCGTGTACACAATGCTAGGGGATGTTAGCATCTTCCTTGTTGGCAAAGACGAGTATGATGAACTTGCTT
    | | | |||| ||||||    |  |        || |  ||     ||     |||| ||    | |     ||||       | ||  |||||   ||||| |||||||| || |||||  |||| || ||||| |||||||   |||| ||||| ||||| |||||||||||||| |
--ctaactacctac-tattgttcattcatattccttgctgtagaaagttgcttgtctcattcttatatgatgctatagtactcattcgttttctgtgcatcagGTCAGTTTATATTGTATACACGGTGCTTGGCGATGTCAGCATCTATGTTGTGGGCAAGGACGAATATGATGAACTTGCCT

upper sequence: AT1G15370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0002g06730.t01 (Vitis vinifera), 3'ss of exon 2
--gtacatcaatctacctattgtgtcattttcgagaaa-actatgaaaccaaactaacagcatttttggggtatataagtaacagagaggttgttgtg-cagGTCGGTTTATATCGTGTACACAATGCTAGGGGATGTTAGCATCTTCCTTGTTGGCAAAGACGAGTATGATGAACTTGCTT
       | |      | |      ||  ||  ||||  | ||  ||||  |        || |  |  |   |   | |||      | |   |||  ||| || || |||||||| |||||  |||| || ||||| |||||||   |||| ||||| || |||||||||||||||||||
cctagtgttagaaaggcca--aaaacaccttgtagaatcagtaccaaacgtactcttagtcactaatttgtacttggattaatccgatgttccctgtatcagATCAGTGTATATCGTTTACACGGTGCTCGGAGATGTCAGCATCTATGTTGTGGGCAAGGATGAGTATGATGAACTTGCTT
















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|86081993|gb|DR377752.1|DR377752
EST:     GATAATCTCAAAGGCGTTAAAAATGAGGAGCTTCTCGTTGCTTGCCACAA                         GTCGGTTTATATCGTGTACACAATGCTAGGGGATGTTAGCATCTTCCTTGT
genomic: GATAATCTCAAAGGCGTTAAAAATGAGGAGCTTCTCGTTGCTTGCCACAAgtacatcaat ... tgttgtgcagGTCGGTTTATATCGTGTACACAATGCTAGGGGATGTTAGCATCTTCCTTGT
EST: gi|152035004|gb|BP841901.2|BP841901
EST:     GATAATCTCAAAGGCGTTAAAAATGAGGAGCTTCTCGTTGCTTGCCACAA                         GTCGGTTTATATCGTGTACACAATGCTAGGGGATGTTAGCATCTTCCGTGT
genomic: GATAATCTCAAAGGCGTTAAAAATGAGGAGCTTCTCGTTGCTTGCCACAAgtacatcaat ... tgttgtgcagGTCGGTTTATATCGTGTACACAATGCTAGGGGATGTTAGCATCTTCCTTGT
EST: gi|164019194|gb|ES195872.1|ES195872
EST:     CTCGTTGCTTGCCACAA                         GTCGGTTTATATCGTGTACACAATGCTAGGGGATGTTAGCATCTTCCTTGT
genomic: CTCGTTGCTTGCCACAAgtacatcaat ... tgttgtgcagGTCGGTTTATATCGTGTACACAATGCTAGGGGATGTTAGCATCTTCCTTGT
EST: gi|152035520|gb|BP856874.2|BP856874
EST:     GATAATCTCAAAGGCGTTAAAAATGAGGAGCTTCTCGTTGCTTGCCACAA                         GTCGGTTTATATCGTGTACACAATGCTAGGGGATGTTAGCATCTTCCTTGT
genomic: GATAATCTCAAAGGCGTTAAAAATGAGGAGCTTCTCGTTGCTTGCCACAAgtacatcaat ... tgttgtgcagGTCGGTTTATATCGTGTACACAATGCTAGGGGATGTTAGCATCTTCCTTGT
EST: gi|86076188|gb|DR371945.1|DR371945
EST:     ATCTCAAAGGCGTTAAAAATGAGGAGCTTCTCGTTGCTTGCCACAA                         GTCGGTTTATATCGTGTACACAATGCTAGGGGATGTTAGCATCTTCCTTGT
genomic: ATCTCAAAGGCGTTAAAAATGAGGAGCTTCTCGTTGCTTGCCACAAgtacatcaat ... tgttgtgcagGTCGGTTTATATCGTGTACACAATGCTAGGGGATGTTAGCATCTTCCTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccaaactaacagcatttttggggtatataagtaacagagaggttgttgtgcagGTCGGTTTATATCGTGTACACAATGCTAGGGGATGTTAGCATCTTCCTTGTTGGCAAAGACGAGTATGATGAACTTGCTT
                         tatataagtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatcaatctacctattgtgtcattttcgagaaaactatgaaaccaaactaacagcatttttggggtatataagtaacagagaggttgttgtgcagGTCGGTTTATATCGTGTACACAATGCTAGGGGATGTTAGCATCTTCCTTGTTGGCAAAGACGAGTATGATGAACTTGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG