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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTTGAAGCTGTGAAGGTTCGTGTTCAGACACAGCCTGGATTTGCTAGGGGGATGTCTGATGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGGAGGgtgagtttttcaataccaataacattatctcccttgttactgctagccttttggtctgatttctgatttttttgcag

Basic information

species Arabidopsis thaliana
transcript AT5G14040.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G14040.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv14s0068g01260.t01 (Vitis vinifera), 5'ss of exon 2
CATTTGAAGCTGTGAAGGTTCGTGTTCAGACACAGCCTGGATTTGCTAGGGGGATGTCTGATGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGGAGGgtgagtttttcaataccaataacattatctccc----ttgttactgc-tagccttttggtctgatttctgatttttttgcag--------
|  | || || |||||||| || ||||| || |||||||| |||||||| ||  |||| |||||||||||||||||| | || ||||||||   |   ||||  |  | ||||           ||  |||||    | |  |||   |||   |  | | | | | |||||| | |   |         
CCATGGAGGCAGTGAAGGTCCGGGTTCAAACTCAGCCTGGTTTTGCTAGAGGTCTGTCAGATGGATTTCCCAAGTTTGTTAAATCCGAAGGTGCCTTGGGgtatgcctatcaaactttgacttctttcctccccaattcgccactttatagtactaagctataactactgattatgtgaaaactttgcag
















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|164094607|gb|ES101038.1|ES101038
EST:     CTGATGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGGAGG                         CTTGTATAAGGGTCTTGCTCCACTCGTGGGGACGTCAGATTCCTT
genomic: CTGATGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGGAGGgtgagttttt ... ttttttgcagCTTGTATAAGGGTCTTGCTCCACTC-TGGGGACGTCAGATTCCTT
EST: gi|47831554|gb|CK121238.1|CK121238
EST:     GGGATGTCTGATGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGGAGG                         CTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTT
genomic: GGGATGTCTGATGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGGAGGgtgagttttt ... ttttttgcagCTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTT
EST: gi|116450593|gb|EG493185.1|EG493185
EST:     GGGATGTCTGATGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGGAGG                         CTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTT
genomic: GGGATGTCTGATGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGGAGGgtgagttttt ... ttttttgcagCTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTT
EST: gi|116407737|gb|EG450329.1|EG450329
EST:     GGGATGTCTGATGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGGAGG                         CTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTT
genomic: GGGATGTCTGATGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGGAGGgtgagttttt ... ttttttgcagCTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTT
EST: gi|124821567|gb|EH906433.1|EH906433
EST:     GGGATGTCTGATGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGGAGG                         CTTGTATAAGGGTCTTGACTCCACTCTGGGGACGTCAGATTCCTTACA
genomic: GGGATGTCTGATGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGGAGGgtgagttttt ... ttttttgcagCTTGTATAAGGGTCTTG-CTCCACTCTGGGGACGTCAGATTCCTTACA
EST: gi|124859158|gb|EH943595.1|EH943595
EST:     TGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGGTAGG                         CTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTT
genomic: TGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGG-AGGgtgagttttt ... ttttttgcagCTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTT
EST: gi|47829559|gb|CK119243.1|CK119243
EST:     GGGATGTCTGATGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGGAGG                         CTTGTATAAGGGTCTTGCTCCCACTCTGGG-ACGTCAGATTCCTT
genomic: GGGATGTCTGATGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGGAGGgtgagttttt ... ttttttgcagCTTGTATAAGGGTCTTGCTCC-ACTCTGGGGACGTCAGATTCCTT
EST: gi|125310039|gb|EL324124.1|EL324124
EST:     GGGATGTCTGATGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGGAGG                         CTTGTATAAGGGT
genomic: GGGATGTCTGATGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGGAGGgtgagttttt ... ttttttgcagCTTGTATAAGGGT
EST: gi|124969172|gb|EL043093.1|EL043093
EST:     TGATGGATTTCCCAAGTTTATCAAGTCCGAAGGTATACGGAGG                         CTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTT
genomic: TGATGGATTTCCCAAGTTTATCAAGTCCGAAGG-ATACGGAGGgtgagttttt ... ttttttgcagCTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTT
EST: gi|47827833|gb|CK117517.1|CK117517
EST:     GGGATGTCTGATGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGGAGG                         CTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTT
genomic: GGGATGTCTGATGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGGAGGgtgagttttt ... ttttttgcagCTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTTGAAGCTGTGAAGGTTCGTGTTCAGACACAGCCTGGATTTGCTAGGGGGATGTCTGATGGATTTCCCAAGTTTATCAAGTCCGAAGGATACGGAGGgtgagtttttcaataccaataacattatctcccttgttactgctagccttttggtctgatttctgatttttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA