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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCGGTGTTGGTGCCGATGGAGTGATTTTTGCAATGCCAGGAGTCAATGGTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAGgtggggcttttcgatgataatgtctggtgatatgttgttgcgctcgaagtcattggcttttgattttgttcttgtag

Basic information

species Arabidopsis thaliana
transcript AT3G53580.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G53580.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv08s0040g02540.t01 (Vitis vinifera), 5'ss of exon 2
CTTCGGTGTTGGTGCCGATGGAGTGATTTTTGCAATGCCAGGAGTCAATGGTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAGgtgg---ggcttttcgatg---ataatgtctggtga-tatgttgttgcgctcgaagtca--ttggcttttgattttgttcttgtag--------------
||| ||  ||||||| || || ||||| || || ||||| ||  ||||||| ||||||||  ||||| ||||||||||||| ||||| ||||| || |||||         |||| | |   ||  | |||| ||| |   | ||    ||    ||    | | | |   | ||||  ||   |               
CTTTGGGATTGGTGCTGACGGTGTGATCTTCGCCATGCCGGGGATCAATGGCACTGATTATACAATGAGGATTTTCAATTCTGATGGCAGTGAGCCTGAGgtaattaacaatttccacgtacatgttttctgttgagtggatcgtcagtctgtttgttgagtagccctgaaaatttgagctaaaaatgtggaaagtaatt
















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|86065675|gb|DR361432.1|DR361432
EST:     GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAG                         ATGTGTGGCAATGGAGTTCGATGCTTT
genomic: GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAGgtggggcttt ... gttcttgtagATGTGTGGCAATGGAGTTCGATGCTTT
EST: gi|124756133|gb|EH846263.1|EH846263
EST:     TAGTGAACCAGAG                         ATGTGTGGCAATGGAGTTCGATGCTTTGCTAGGTTCATTGCTGAGCTTGAG
genomic: TAGTGAACCAGAGgtggggcttt ... gttcttgtagATGTGTGGCAATGGAGTTCGATGCTTTGCTAGGTTCATTGCTGAGCTTGAG
EST: gi|86065693|gb|DR361450.1|DR361450
EST:     GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAG                         ATGTGTGGCAATGGAGTTCGATGCTTTGCTAGG
genomic: GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAGgtggggcttt ... gttcttgtagATGTGTGGCAATGGAGTTCGATGCTTTGCTAGG
EST: gi|86065698|gb|DR361455.1|DR361455
EST:     GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCANAG                         ATGTGTGGCAATGGAGTTCGATGCTTTGCTAGG
genomic: GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAGgtggggcttt ... gttcttgtagATGTGTGGCAATGGAGTTCGATGCTTTGCTAGG
EST: gi|86065688|gb|DR361445.1|DR361445
EST:     GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAG                         ATGTGTGGCAATGGAGTTCGATGCTTTGCTAGGTTCATTGCTGAGCTTGAG
genomic: GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAGgtggggcttt ... gttcttgtagATGTGTGGCAATGGAGTTCGATGCTTTGCTAGGTTCATTGCTGAGCTTGAG
EST: gi|86065704|gb|DR361461.1|DR361461
EST:     GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAG                         ATGTGTGGCAATGGAGTTCGATGCTTTGCTA
genomic: GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAGgtggggcttt ... gttcttgtagATGTGTGGCAATGGAGTTCGATGCTTTGCTA
EST: gi|86065673|gb|DR361430.1|DR361430
EST:     GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAG                         ATGTGTGGCNNTGGAGTTCGATGCTTTGCTAGGTTCATTGCTGAGCTTGAG
genomic: GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAGgtggggcttt ... gttcttgtagATGTGTGGCAATGGAGTTCGATGCTTTGCTAGGTTCATTGCTGAGCTTGAG
EST: gi|86065690|gb|DR361447.1|DR361447
EST:     GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAG                         ATGTGTGGCAATGGAGTTCGATGCTTTGCTAGGTTCATTGCTGAGCTTGAG
genomic: GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAGgtggggcttt ... gttcttgtagATGTGTGGCAATGGAGTTCGATGCTTTGCTAGGTTCATTGCTGAGCTTGAG
EST: gi|86065706|gb|DR361463.1|DR361463
EST:     GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAG                         ATGTGTGGCAATGGGAGTTCGATGCTTTGCTAGGTTCATTGCTGAGCTTGA
genomic: GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAGgtggggcttt ... gttcttgtagATGTGTGGCAATGG-AGTTCGATGCTTTGCTAGGTTCATTGCTGAGCTTGA
EST: gi|86065696|gb|DR361453.1|DR361453
EST:     GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAG                         ATGTGTGGCAATGGAGTTCGATG
genomic: GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAGgtggggcttt ... gttcttgtagATGTGTGGCAATGGAGTTCGATG
EST: gi|124814688|gb|EH899554.1|EH899554
EST:     TACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAG                         ATGTGTGGCAATGGAGTT
genomic: TACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAGgtggggcttt ... gttcttgtagATGTGTGGCAATGGAGTT
EST: gi|124712660|gb|EH804062.1|EH804062
EST:     CGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAG                         ATGTGTGGCAATGGAGTTCGA
genomic: CGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAGgtggggcttt ... gttcttgtagATGTGTGGCAATGGAGTTCGA
EST: gi|86065685|gb|DR361442.1|DR361442
EST:     GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAG                         ATGTGTGGCAAT
genomic: GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAGgtggggcttt ... gttcttgtagATGTGTGGCAAT
EST: gi|86065692|gb|DR361449.1|DR361449
EST:     GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAG                         ATGTGTGGCAATGGAGTTCGATGGCTTTGCTAGGTTCATTGC
genomic: GTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAGgtggggcttt ... gttcttgtagATGTGTGGCAATGGAGTTCGATG-CTTTGCTAGGTTCATTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCGGTGTTGGTGCCGATGGAGTGATTTTTGCAATGCCAGGAGTCAATGGTACTGATTACGCAATGCGGATTTTCAATTCAGATGGTAGTGAACCAGAGgtggggcttttcgatgataatgtctggtgatatgttgttgcgctcgaagtcattggcttttgattttgttcttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG