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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcctcttccctattcttcaaattttcgatcttttagttcaatttctataaaccctaattttgactgattttggggaaattttgaaaaattagGTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATTGTTCCAAGGCATATTCAATTGGCGGTGAGGAACGATGAAGAATTGAGCA

Basic information

species Arabidopsis thaliana
transcript AT1G51060.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G51060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G151826_T01 (Zea mays), 3'ss of exon 1
-----------gtaattcctcttccctattcttcaaattttcgatcttttagttcaatttctataaaccctaattttgactgattttggggaaattttgaaaaattagGTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATTGTTCCAAGGCATATTCAATTGGCGGTGAGGAACGATGAAGAATTGAGCA
                | | | |   ||| |  | ||    | | |        ||||||| ||    ||||  |||    | ||||     |   || ||     ||||  ||||  | ||||| ||||||||||||||||||||||||||  | || || ||  | || || ||  | || ||| | ||||| || ||  ||| ||
agcattctgtctcggcttcgccttt-tatcccgcgaaaccccaagcgccagaagcaatttc-atctgacctaccttt--tcgtttttattcgatgcttcaa----cagGTCCTGGAGCTTGCTGGGAACGCAGCGAGGGATAACAAGAAGACCCGCATCGTGCCGCGTCACATCCAGCTCGCCGTGCGCAACGACGAGGAGCTGACCA

upper sequence: AT1G51060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ34776 (Selaginella moellendorffii), 3'ss of exon 1
------------------gtaattcctcttccctattcttcaaattttcgatcttttagttcaatttctataaaccctaattttgactgatt---ttggggaaattttgaaaaatt---------------------agGTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATTGTTCCAAGGCATATTCAATTGGCGGTGAGGAACGATGAAGAATTGAGCA
                  ||  ||||   ||||||||       ||||| || | |    |||||  |  | ||         ||  | |||   |||    |||   |   | ||                     ||||  | |||||||| || || || || ||||||||||||||||  |||||||||||| |||| || ||  | || ||||||||||| |||||| |    |
gtgagtgaaatctctcgtgttcttccctctccctatttcattc-ttttccatgtctggaatcaatcgcgctgaaattcttccctgtttcattcttttgaatcaatcgcgctgatttggtcactccatctccatctccagGTGCTCGAATTGGCCGGGAATGCGGCCAGGGATAACAAGAAGAACAGGATTGTTCCACGGCACATCCAGCTCGCCGTGAGGAACGACGAAGAACTCTCGA

upper sequence: AT1G51060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ23553 (Selaginella moellendorffii), 3'ss of exon 1
----------------gtaattcctcttccctattcttcaaattttcgatcttttagttcaatttctataaaccctaattttgactgatt---ttggggaaattttgaaaaat---------------------tagGTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATTGTTCCAAGGCATATTCAATTGGCGGTGAGGAACGATGAAGAATTGAGCA
                ||  |  | | ||||||||       ||||| || | |    |||||  |  | ||         ||  | |||   |||    |||  ||   | |                      ||||  | |||||||| || || || || ||||||||||||||||  |||||||||||| ||||||| ||  | || ||||||||||| |||||| |   ||
gtgagtgaaatctctcgtgttctcccctccctatttcattc-ttttccatgtctcgaatcaatcgcgctgaaattcttccctgtttcattcttttgaatcaatcgtgctgattgggtcactccatctccatctccagGTGCTCGAATTGGCCGGGAATGCGGCCAGGGATAACAAGAAGAACAGGATTGTTCCACGGCATATCCAGCTCGCCGTGAGGAACGACGAAGAACTCTCCA

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|125188096|gb|EL203050.1|EL203050
EST:     CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAATTGGCTGGAAACGCAGCGAGGGAT
genomic: CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATTGGAATTGGCTGGAAACGCAGCGAGGGAT
EST: gi|124915927|gb|EH989801.1|EH989801
EST:     CGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATT
genomic: CGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATT
EST: gi|124732969|gb|EH824371.1|EH824371
EST:     CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAG
genomic: CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAG
EST: gi|125199979|gb|EL214933.1|EL214933
EST:     CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAATTGGCTGGAAACGC
genomic: CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATTGGAATTGGCTGGAAACGC
EST: gi|164080045|gb|ES147290.1|ES147290
EST:     CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGNG                         GTATTGGAATTGGCTGGAAACGCAGCG
genomic: CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATTGGAATTGGCTGGAAACGCAGCG
EST: gi|124833759|gb|EH918198.1|EH918198
EST:     CGGAGCTCCGGTTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATT
genomic: CGGAGCTCCGG-TTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATT
EST: gi|125321830|gb|EL335915.1|EL335915
EST:     CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTAAGGAATTGGCTGGAAACGCAGCGAGGGAT
genomic: CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATT--GGAATTGGCTGGAAACGCAGCGAGGGAT
EST: gi|116452308|gb|EG494900.1|EG494900
EST:     CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATT
genomic: CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATT
EST: gi|125247792|gb|EL261877.1|EL261877
EST:     CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAATTGGCTGGGAACGCAG
genomic: CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATTGGAATTGGCTGGAAACGCAG
EST: gi|124838874|gb|EH923313.1|EH923313
EST:     CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAATTGGCTGGAAACGCA
genomic: CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATTGGAATTGGCTGGAAACGCA
EST: gi|124912079|gb|EH986159.1|EH986159
EST:     CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAATTGGCTGGAAA
genomic: CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATTGGAATTGGCTGGAAA
EST: gi|124934240|gb|EL011327.1|EL011327
EST:     CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAG
genomic: CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAG
EST: gi|164032501|gb|ES169088.1|ES169088
EST:     CTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATT
genomic: CTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATT
EST: gi|125296796|gb|EL310881.1|EL310881
EST:     CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTAGGAATTGGCTGGAAACGCAGCGAGG
genomic: CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATT-GGAATTGGCTGGAAACGCAGCGAGG
EST: gi|125263372|gb|EL277457.1|EL277457
EST:     CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAATTGGCTGGA
genomic: CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATTGGAATTGGCTGGA
EST: gi|164233972|gb|ES056136.1|ES056136
EST:     GAATACCTCGCCGCTGAG                         GTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATT
genomic: GAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATT
EST: gi|116452336|gb|EG494928.1|EG494928
EST:     CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATT
genomic: CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATT
EST: gi|164136802|gb|ES076461.1|ES076461
EST:     CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAATTGGCTG
genomic: CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATTGGAATTGGCTG
EST: gi|124820109|gb|EH904975.1|EH904975
EST:     CTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATT
genomic: CTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATT
EST: gi|124774406|gb|EH864535.1|EH864535
EST:     CCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATT
genomic: CCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATT
EST: gi|164071719|gb|ES023157.1|ES023157
EST:     CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAA
genomic: CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAA
EST: gi|86075126|gb|DR370883.1|DR370883
EST:     CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCTAATACCTC-CCGCCGAG                         GTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATT
genomic: CCGGAGCTCCGGTTTACTTAGCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaattcctc ... gaaaaattagGTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatttctataaaccctaattttgactgattttggggaaattttgaaaaattagGTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATTGTTCCAAGGCATATTCAATTGGCGGTGAGGAACGATGAAGAATTGAGCA
                        gactgat  putative branch site (score: 3)
                                      aaattttgaaaaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattcctcttccctattcttcaaattttcgatcttttagttcaatttctataaaccctaattttgactgattttggggaaattttgaaaaattagGTATTGGAATTGGCTGGAAACGCAGCGAGGGATAACAAGAAGACGAGGATTGTTCCAAGGCATATTCAATTGGCGGTGAGGAACGATGAAGAATTGAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA