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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctacttctgcttcgttcgattttgattttgttgtatatcgtgtgtatacatctgtttgatttttggtgttttgatttcatggaatcagGAGCTTGCTGAGATGAAGAGGAGATTAAAGGAGATGGAGGAAGAAGCTGCTGCGCTACGAGAGATGCAAGCAAAAGTCGAAAAAGAAATGGGAGCTACTC

Basic information

species Arabidopsis thaliana
transcript AT5G10350.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G10350.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S422_18V6.1 (Physcomitrella patens), 3'ss of exon 1
------gtctacttctgcttcgttcgattttgattttgttgt----atatcgtgtgtatacatctgtttgatttttggtgttttgatttcatggaatcagGAGCTTGCTGAGATGAAGAGGAGATTAAAGGAGATGGAGGAAGAAGCTGCTGCGCTACGAGAGATGCAAGCAAAAGTCGAAAAAGAAATGGGAGCTACTC
       | |  | | | |  | |  | |   |   ||  |     | || |     ||   |   |||||||    || ||||  | |         |||| || |  |||||||||| | | || || ||||||||||| |||||||| ||  |||| || |||||||| || ||||||||||||||| | |||  ||
gtttttatgtcttccaggtctgatgaaatgctagcgtgacgctggaaaattgacaacatgtttacttttgattggaagtctttttctgtgcgtttgctagGAACTAGAGGAGATGAAGAAGCGTTTGAAAGAGATGGAGGAGGAAGCTGCCGCATTACGTGACATGCAAGCCAAGGTCGAAAAAGAAATGAGCGCTGTTC

upper sequence: AT5G10350.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S3_616V6.1 (Physcomitrella patens), 3'ss of exon 1
--gtctacttctgcttcgttcgattttgattttgttgtatatcg-tgtgtatacatctgtttga------tttttggtgttttgatttcatggaatca-gGAGCTTGCTGAGATGAAGAGGAGATTAAAGGAGATGGAGGAAGAAGCTGCTGCGCTACGAGAGATGCAAGCAAAAGTCGAAAAAGAAATGGGAGCTACTC
   |  |     || ||   | |   | || |       |||   ||||| |  ||   | |||      |||||| ||||   |||   ||   | | |||||| |  ||||||||||   | || ||||||||||||||||| || ||||| ||||| || |||||||| ||||| || ||||| ||||| | || ||
gattacagactagcatctcaccaccattatgtaaacacctataactgtgttttgatggttctgacccgtgtttttgttgttcacattatgtgcttttaagGAGCTGGAGGAGATGAAGAAACGTTTGAAGGAGATGGAGGAAGAGGCCGCTGCTCTACGTGATATGCAAGCTAAAGTTGAGAAAGAGATGGGTGGTAGTC

upper sequence: AT5G10350.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S85_168V6.2 (Physcomitrella patens), 3'ss of exon 1
------gtctacttctgcttcgttcgattttgattttgttgtatatcgtgtg-tatacatctgtttgatttttggt-gttttgatttcatgg--aatcagGAGCTTGCTGAGATGAAGAGGAGATTAAAGGAGATGGAGGAAGAAGCTGCTGCGCTACGAGAGATGCAAGCAAAAGTCGAAAAAGAAATGGGAGCTACTC
      ||   | | ||         ||  | |  || ||   |  | | || | |    |||||   ||     | || |  |||   ||   | ||||||||| |  ||||||||||   | || ||||||||||| |||||||||||||| || || || ||||| || |||||||| || || ||||| | || ||
ccataggtgggcgtttgtcagtaatcatgctaacattcttagctgccatttgatgttttcctgttcatttccccattgtctccattatgtgcccattcagGAGCTAGAGGAGATGAAGAAACGCTTGAAGGAGATGGAAGAAGAAGCTGCTGCTCTGCGCGACATGCAGGCTAAAGTCGAGAAGGAGATGGGCGGTAGTC

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|19875827|gb|AU236658.1|AU236658
EST:     TTCCCGATCCGGATATCGATATGTCTGCAGCCGATGAGGACGCCGTTACG                         GAGCTTGCTGAGATGAAGAGGAGATTAAAGGAGATGGAGGAAGAAGCTGCT
genomic: TTCCCGATCCGGATATCGATATGTCTGCAGCCGATGAGGACGCCGTTACGgtctacttct ... atggaatcagGAGCTTGCTGAGATGAAGAGGAGATTAAAGGAGATGGAGGAAGAAGCTGCT
EST: gi|47828577|gb|CK118261.1|CK118261
EST:     TTCCCGATCCGGATATCGATATGTCTGCAGCCGATGAGGACGCCGTTACG                         GAGCTTGCTGAGATGAAGAGGAGATTAAAGGAGATGGAGGAAGAAGCTGCT
genomic: TTCCCGATCCGGATATCGATATGTCTGCAGCCGATGAGGACGCCGTTACGgtctacttct ... atggaatcagGAGCTTGCTGAGATGAAGAGGAGATTAAAGGAGATGGAGGAAGAAGCTGCT
EST: gi|125238333|gb|EL252418.1|EL252418
EST:     CCGGATATCGATATGTCTGCAGCCGATGAGGACGCCGTTACG                         GAGCTTGCTGAGATGAAGAGGAGAATTAAAGGAGATGGAGGAAGAAGCTGC
genomic: CCGGATATCGATATGTCTGCAGCCGATGAGGACGCCGTTACGgtctacttct ... atggaatcagGAGCTTGCTGAGATGAAGAGGAGA-TTAAAGGAGATGGAGGAAGAAGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatcgtgtgtatacatctgtttgatttttggtgttttgatttcatggaatcagGAGCTTGCTGAGATGAAGAGGAGATTAAAGGAGATGGAGGAAGAAGCTGCTGCGCTACGAGAGATGCAAGCAAAAGTCGAAAAAGAAATGGGAGCTACTC
                                   ttttgat  putative branch site (score: 4)
                     tttgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctacttctgcttcgttcgattttgattttgttgtatatcgtgtgtatacatctgtttgatttttggtgttttgatttcatggaatcagGAGCTTGCTGAGATGAAGAGGAGATTAAAGGAGATGGAGGAAGAAGCTGCTGCGCTACGAGAGATGCAAGCAAAAGTCGAAAAAGAAATGGGAGCTACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT