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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTTGGGATACTTTTAGATTTCGTTTGGTATGAGCCGCTTACTAGAAGTAAAGCAGATAATCTTGCAGCTCAAAGAGCAAGAGACTTCCATATCGGATGgtaaatgttaaaactttttaacaaataaaaactcatattttaccatcaagtcttggtgagcttatagaatatcttttgttttcgggtcatgcttgaag

Basic information

species Arabidopsis thaliana
transcript AT3G18080.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G18080.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA09G30910.1 (Glycine max), 5'ss of exon 7
GGGTTGGGATACTTTTAGATTTCGTTTGGTATGAGCCGCTTACTAGAAGTAAAGCAGATAATCTTGCAGCTCAAAGAGCAAGAGACTTCCATATCGGATGgtaaatgttaaaactttttaacaaataaaaa-ctcatattttaccatcaagtctt--ggtgagcttatagaatatcttttgttttcgggt---catgcttgaag--------------------------
|| ||||||| || || ||||| |||||||||||||| ||||| |||   || || || ||| |||||||||||||||| |||||||| ||||| ||||||||||  |    |   |||   || | |  | |  |||||  |    ||||||||  | |  |  | |  | | ||   ||        |   || ||||||                            
GGATTGGGATCCTCTTGGATTTTGTTTGGTATGAGCCTCTTACAAGATCAAAGGCTGACAATTTTGCAGCTCAAAGAGCCAGAGACTTTCATATTGGATGgtaaaaatctttagcatttgttaactgaggatcctatattgcaagtacaagtctttagttatgaatgtgaattttcccctgcaaagactttcacacgcttgataacaataataatgcttaaattcaccag

upper sequence: AT3G18080.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA07G11310.1 (Glycine max), 5'ss of exon 7
GGGTTGGGATACTTTTAGATTTCGTTTGGTATGAGCCGCTTACTAGAAGTAAAGCAGATAATCTTGCAGCTCAAAGAGCAAGAGACTTCCATATCGGATGgtaaatgttaaaactttttaacaaataaaaactcatattttaccatcaagtct-tggtgagcttatagaatatcttttgttttcgggtcatgcttgaag---
|| ||||||| || || ||||| |||||||||||||| ||||| |||   || || || ||| | |||||||||||||| |||||||| ||| | ||||||||||  |    |   |||       | ||| |  ||| |   ||   | | |     |   || || | | ||      |  |   |||   |  | |   
GGATTGGGATCCTCTTGGATTTTGTTTGGTATGAGCCTCTTACAAGATCAAAGGCCGACAATTTAGCAGCTCAAAGAGCCAGAGACTTTCATGTTGGATGgtaaacatctttaacatttgtttttaagaaaatagtatatg--cactgactgtacacaggatttttacactttcaaccaatcacaaatcacaatatatgata
















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|125011729|gb|EL083998.1|EL083998
EST:     GAGACTTCCATATCGGATG                         GTTTATTCACCCATTAGTATATGGAGAGTATCCAAAGACAATGCAGAACAT
genomic: GAGACTTCCATATCGGATGgtaaatgtta ... atgcttgaagGTTTATTCACCCATTAGTATATGGAGAGTATCCAAAGACAATGCAGAACAT
EST: gi|164130186|gb|ES092108.1|ES092108
EST:     CTTGCAGCTCAAAGAGCAAGAGACTTCCATATCGGATG                         GTTTATTCACCCATTGGTATA
genomic: CTTGCAGCTCAAAGAGCAAGAGACTTCCATATCGGATGgtaaatgtta ... atgcttgaagGTTTATTCACCCATTAGTATA
EST: gi|125270906|gb|EL284991.1|EL284991
EST:     AAAGCAGATAATCTTGCAGCTCAAAGAGCAAGAGACTTCCATATCGGATG                         GTTTATTCACCCATTA
genomic: AAAGCAGATAATCTTGCAGCTCAAAGAGCAAGAGACTTCCATATCGGATGgtaaatgtta ... atgcttgaagGTTTATTCACCCATTA
EST: gi|124740168|gb|EH831330.1|EH831330
EST:     AAAGCAGATAATCTTGCAGCTCAAAGAGCAAGAGACTTCCATATCGGATG                         GTTTATTACACCCATTAGTATATGGAGAGTATCCAAA
genomic: AAAGCAGATAATCTTGCAGCTCAAAGAGCAAGAGACTTCCATATCGGATGgtaaatgtta ... atgcttgaagGTTTATT-CACCCATTAGTATATGGAGAGTATCCAAA
EST: gi|125006488|gb|EL078757.1|EL078757
EST:     AAAGCAGATAATCTTGCAGCTCAAAGAGCAAGAGACTTCCATATCGGATG                         GTTTATTCACCCAT
genomic: AAAGCAGATAATCTTGCAGCTCAAAGAGCAAGAGACTTCCATATCGGATGgtaaatgtta ... atgcttgaagGTTTATTCACCCAT
EST: gi|116477432|gb|EG520024.1|EG520024
EST:     AAAGCAGATAATCTTGCAGCTCAAAGAGCAAGAGACTTCCATATCGGATG                         GTTTATTCACCCATTAGTATATGGAGAGTATCCAAAGACAATGCAGAACAT
genomic: AAAGCAGATAATCTTGCAGCTCAAAGAGCAAGAGACTTCCATATCGGATGgtaaatgtta ... atgcttgaagGTTTATTCACCCATTAGTATATGGAGAGTATCCAAAGACAATGCAGAACAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGTTGGGATACTTTTAGATTTCGTTTGGTATGAGCCGCTTACTAGAAGTAAAGCAGATAATCTTGCAGCTCAAAGAGCAAGAGACTTCCATATCGGATGgtaaatgttaaaactttttaacaaataaaaactcatattttaccatcaagtcttggtgagcttatagaatatcttttgttttcgggtcatgcttgaag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA