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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagatagtttgttgtatcagtgctcttgtttatatccatggctgaagtctttggatattatcaacttttttctatgtttgtttgcagATTCCTGGTGTGCCCATCATGTATGTGACTAATCGCAAGTACTCAATAGAGAAGTTGCCTGAAGCTACACTTGGTGGAG

Basic information

species Arabidopsis thaliana
transcript AT2G46230.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G46230.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G41500.1 (Glycine max), 3'ss of exon 6
---------------------------------------------------------------------gta-aagatagtttgttgtatcagtgctcttgtttatatccatggctgaagtctttggatattatcaacttttttctatgtttgt---ttgcagATTCCTGGTGTGCCCATCATGTATGTGACTAATCGCAAGTACTCAATAGAGAAGTTGCCTGAAGCTACACTTGGTGGAG
                                                                     | |  |  | | ||  ||| |    | |      | |  | ||     |  ||    ||   ||  ||   |   ||  |||| |   |||||||||||||||||||| || |||||  | || || |||||||||||||| |||   ||||||||||| ||| |||||||||
gtaaagttattaatcatttatttgtctttcatggttttaatattggaccatattaccatgacctacgaagcatgaactgggtttctgtgttgcagATTCCTGGTGTGCCAATTATGTACATCACCAGAC-CTACGAAGCATGAACTGGGTTTCTGTGTTGCAGATTCCTGGTGTGCCAATTATGTACATCACCAAACGCAAGTACTCAATTGAGCGATTGCCTGAAGCAACAATTGGTGGAG
















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|86084884|gb|DR380643.1|DR380643
EST:     GCTTCATAGTGGCTACATGTGATAGAGACTTAAAGCGAAGGATTCGAAAG                         ATTCCTGGTGTGCCCATCATGTATGTGACTAATCGCAAGTACTCAATAGAG
genomic: GCTTCATAGTGGCTACATGTGATAGAGACTTAAAGCGAAGGATTCGAAAGgtaaagatag ... ttgtttgcagATTCCTGGTGTGCCCATCATGTATGTGACTAATCGCAAGTACTCAATAGAG
EST: gi|164010362|gb|ES142274.1|ES142274
EST:     GAGACTTAAAGCGAAGGATTCGAAAG                         ATTCCTGGTGTGCCCATCATGTATGTGACTAATCGCAAGTACTC
genomic: GAGACTTAAAGCGAAGGATTCGAAAGgtaaagatag ... ttgtttgcagATTCCTGGTGTGCCCATCATGTATGTGACTAATCGCAAGTACTC
EST: gi|164129558|gb|ES129019.1|ES129019
EST:     AGACTTAAAGCGAAGGATTCGAAAG                         ATTCCTGGTGTGCCCATCATGTATGTGACTAATCGCAAGTACTC
genomic: AGACTTAAAGCGAAGGATTCGAAAGgtaaagatag ... ttgtttgcagATTCCTGGTGTGCCCATCATGTATGTGACTAATCGCAAGTACTC
EST: gi|164190436|gb|ES103627.1|ES103627
EST:     AGACTTAAAGCGAAGGATTCGAAAG                         ATTCCTGGTGTGCCCATCATGTATGTGACTAAATCGCAAGTACTC
genomic: AGACTTAAAGCGAAGGATTCGAAAGgtaaagatag ... ttgtttgcagATTCCTGGTGTGCCCATCATGTATGTGACTAA-TCGCAAGTACTC
EST: gi|47829180|gb|CK118864.1|CK118864
EST:     GCTTCATAGTGGCTACATGTGATAGAGACTTAAAGCGAAGGATTCGAAAG                         ATTCCTGGTGTGCCCATCATGTATGTGACTAATCGCAAGTACTCAATAGAG
genomic: GCTTCATAGTGGCTACATGTGATAGAGACTTAAAGCGAAGGATTCGAAAGgtaaagatag ... ttgtttgcagATTCCTGGTGTGCCCATCATGTATGTGACTAATCGCAAGTACTCAATAGAG
EST: gi|164186213|gb|ES047993.1|ES047993
EST:     ACATGTGATAGAGACTTAAAGCGAAGGATTCGAAAG                         ATTCCTGGTGTGCCCATCATGTATGTGACTAATCGCAAGTACTCAATAGAG
genomic: ACATGTGATAGAGACTTAAAGCGAAGGATTCGAAAGgtaaagatag ... ttgtttgcagATTCCTGGTGTGCCCATCATGTATGTGACTAATCGCAAGTACTCAATAGAG
EST: gi|163975383|gb|ES020473.1|ES020473
EST:     ACATGTGATAGAGACTTAAAGCGAAGGATTCGAAAG                         ATTCCTGGTGTGCCCATTCATGTATGTGACTAATCGCAAGTACTCAATAGA
genomic: ACATGTGATAGAGACTTAAAGCGAAGGATTCGAAAGgtaaagatag ... ttgtttgcagATTCCTGGTGTGCCCAT-CATGTATGTGACTAATCGCAAGTACTCAATAGA
EST: gi|86080730|gb|DR376487.1|DR376487
EST:     GCTTCATAGTGGCTACATGTGATAGAGACTTAAAGCGAAGGATTCGAAAG                         ATTCCTGGTGTGCCCATCATGTATGTGACTAATCGCAAGTACTCAATAGAG
genomic: GCTTCATAGTGGCTACATGTGATAGAGACTTAAAGCGAAGGATTCGAAAGgtaaagatag ... ttgtttgcagATTCCTGGTGTGCCCATCATGTATGTGACTAATCGCAAGTACTCAATAGAG
EST: gi|47828370|gb|CK118054.1|CK118054
EST:     GCTTCATAGTGGCTACATGTGATAGAGACTTAAAGCGAAGGATTCGAAAG                         ATTCCTGGTGTGCCCATCATGTATGTGACTAATCGCAAGTACTCAATAGAG
genomic: GCTTCATAGTGGCTACATGTGATAGAGACTTAAAGCGAAGGATTCGAAAGgtaaagatag ... ttgtttgcagATTCCTGGTGTGCCCATCATGTATGTGACTAATCGCAAGTACTCAATAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatccatggctgaagtctttggatattatcaacttttttctatgtttgtttgcagATTCCTGGTGTGCCCATCATGTATGTGACTAATCGCAAGTACTCAATAGAGAAGTTGCCTGAAGCTACACTTGGTGGAG
                                cttttttctatgttt  CT-rich tract
                      atattatcaacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagatagtttgttgtatcagtgctcttgtttatatccatggctgaagtctttggatattatcaacttttttctatgtttgtttgcagATTCCTGGTGTGCCCATCATGTATGTGACTAATCGCAAGTACTCAATAGAGAAGTTGCCTGAAGCTACACTTGGTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG