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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTATTACGACTATAGAAATCGACGACGAGACATATGAAGAGATTGTTCGGgtatgtaattctcttagctcaataagatttattaatctatgtaggctttagtagtaagataaacgtttttgggttcaaaatatttcagctatcacagtat...

Basic information

species Arabidopsis thaliana
transcript AT1G21190.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G21190.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA16G28300.1 (Glycine max), 5'ss of exon 2
GCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTATTACGACTATAGAAATCGACGACGAGACATATGAAGAGATTGTTCGGgtatgtaattctct-tagctcaataagattta---ttaatctatgtaggctttagtag-taagataaacgtttttgggttc-aaaatatttcagctatcacagtat
|||| |||||||||| | ||||||||||| ||||||||||||||  || |||| ||  | |||||||| || |||||||| ||||| |||||  ||||| ||  |  ||   | || |   | ||  |   ||| ||| | | ||||    ||  |   | ||| ||   |   | |   || |||| |   ||        
GCTTATGATCAGCATCTTAATATGATTCTTGGTGATGTTGAAGAAATTGTTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgtaatcagcaactaagagaaatacatatttattcttttttggctaagctaaatggtagaaatgtgaataattgctggaaaatttgaataattt------

upper sequence: AT1G21190.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA02G09090.1 (Glycine max), 5'ss of exon 2
GCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTATTACGACTATAGAAATCGACGACGAGACATATGAAGAGATTGTTCGGgtatgtaattctct-tagctcaataagattta---ttaatctatg-taggctttagtagtaagataaacgtttttgggttcaaaatatttcagcta-tcacagtat
|||| |||||||||| | ||||||||||| || |||||||||||  | ||||| ||  | |||||||| || |||||||| ||||| |||||  ||||| ||     ||  || || |   | ||  |   ||| | | ||  |    ||| | |||    ||| ||   |   | |   | |||| |  || |   ||   
GCTTATGATCAGCATCTTAATATGATTCTTGGCGATGTTGAAGAAATCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttggaatcagtaactaagagaaatacacatttattttttggcaaagcttaatggtag---aaatgtgaataattgctggaaattttaaataattttag---

upper sequence: AT1G21190.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv18s0072g00710.t01 (Vitis vinifera), 5'ss of exon 2
GCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTATTACGACTATAGAAATCGACGACGAGACATATGAAGAGATTGTTCGGgtatgtaattctcttagctcaataagatt---tattaatctatgtaggctt-tagtagtaagataaacg-------tttttgggttcaaaatatttcagctatcacagtat-------------------------------------------------------------------------------
|| | ||||||||||||||| |||||||| ||||||||||||||  || |||| ||  ||||||||||||| || || |||||||| |||||||| |||||   |   ||    ||  |    ||   | ||||  ||| | |  |  ||| | | | | || |            |||  | || |||  |   | | ||||                                                                                   
GCCTATGATCAGCATTTGAACATGATTCTTGGTGATGTTGAAGAAATTGTTACTACAGTAGAAATCGACGATGAAACTTATGAAGAAATTGTTCGAgtatgctctcaactggcttccttttacttctttcttaaattatctggtttggtagaactgaaacaatccagaagatccactggcataaacataactgcaccaccacaagccccaatcccccaccctgctgagaggaattaaataaataagcataacaagaatgtttctggaatttttttttttttgatag

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|86083319|gb|DR379078.1|DR379078
EST:     TTATTACGACTATAGAAATCGACGACGAGACATATGAAGAGATTGTTCGG                         ACAACGAAGCGAACTGTACCGTTTCTATTCGTGAGAGGAGATGGAGTGATA
genomic: TTATTACGACTATAGAAATCGACGACGAGACATATGAAGAGATTGTTCGGgtatgtaatt ... cttctgtcagACAACGAAGCGAACGGTACCGTTTCTATTCGTGAGAGGAGATGGAGTGATA
EST: gi|19740683|gb|AU226036.1|AU226036
EST:     TTATTACGACTATAGAAATCGACGACGAGACATATGAAGAGATTGTTCGG                         ACAACGAACCGAACGGTACCGTTTCTATTCGTGAGAGGAGATGGAGTGATA
genomic: TTATTACGACTATAGAAATCGACGACGAGACATATGAAGAGATTGTTCGGgtatgtaatt ... cttctgtcagACAACGAAGCGAACGGTACCGTTTCTATTCGTGAGAGGAGATGGAGTGATA
EST: gi|19874534|gb|AU235365.1|AU235365
EST:     TTATTACGACTATAGAAATCGACGACGAGACATATGAAGAGATTGTTCGG                         ACAACGAAGCGAACGGTACCGTTTCTATTCGTGAGAGGAGATGGAGTGATA
genomic: TTATTACGACTATAGAAATCGACGACGAGACATATGAAGAGATTGTTCGGgtatgtaatt ... cttctgtcagACAACGAAGCGAACGGTACCGTTTCTATTCGTGAGAGGAGATGGAGTGATA
EST: gi|164094077|gb|ES052313.1|ES052313
EST:     CGACGACGAGACATATGAAGAGATTGTTCGG                         ACAACGAAGCGAACTGTACCGTTTCTATTCGTGAGAGGAGATGGAGTGATA
genomic: CGACGACGAGACATATGAAGAGATTGTTCGGgtatgtaatt ... cttctgtcagACAACGAAGCGAACGGTACCGTTTCTATTCGTGAGAGGAGATGGAGTGATA

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTATTACGACTATAGAAATCGACGACGAGACATATGAAGAGATTGTTCGGgtatgtaattctcttagctcaataagatttattaatctatgtaggctttagtagtaagataaacgtttttgggttcaaaatatttcagctatcacagtat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctctta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caataaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagataaa