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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcatatgattcttatattttctgaaattgcttagggcgaagtttggttcttagaaaatgagttctgtaatttttttgttgtttccccttttatttgcagCTCTTGGAGAGTAAGATACAAGAGGCAAAAGCAAAGAAAGATACGCTCCTTGCACGTGCTCGCACTGCTAA

Basic information

species Arabidopsis thaliana
transcript AT1G65260.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G65260.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G47890.1 (Glycine max), 3'ss of exon 6
-agcatatgattcttatatt-ttctgaaattgcttagggcgaagtttggttcttagaaaatgagttct-gtaatttttttgttgtttccccttttatttgcagCTCTTGGAGAGTAAGATACAAGAGGCAAAAGCAAAGAAAGATACGCTCCTTGCACGTGCTCGCACTGCTAA
     |   |||  |  ||| || | ||||   |||      ||    |||  | | ||    |||   |||||   | |     ||    |||| |   ||||| |||||||| |||||||| ||||||||  ||||||||||||| |||   ||| | ||||   |||| | 
tgtgttgctattgctgaattcttttaaaatcagttattaattagcactgtt--tgggaatcatgttggagtaatgcatgtaactatttttgttttctcaacaGCTTTTGGAGAGCAAGATACAGGAGGCAAAGTCAAAGAAAGATACCCTCAAAGCAAGAGCTCAGTCTGCAA-
















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|125113556|gb|EL164331.1|EL164331
EST:     AACTAGATCAGCAAAAAGGTGTTGTCGACAATCTTGTTTCAAATACAAGG                         CTCTTGGAGAGTAAGATACAAGAGG
genomic: AACTAGATCAGCAAAAAGGTGTTGTCGACAATCTTGTTTCAAATACAAGGgttagttttc ... ttatttgcagCTCTTGGAGAGTAAGATACAAGAGG
EST: gi|125206346|gb|EL221300.1|EL221300
EST:     CAAAAAGGTGTTGTCGACAATCTTGTTTCAAATACAAGG                         CTCTTGGAGAGTAAGATACAAGAGGCAAAAGCAAAGAAAGATACGCTCCTT
genomic: CAAAAAGGTGTTGTCGACAATCTTGTTTCAAATACAAGGgttagttttc ... ttatttgcagCTCTTGGAGAGTAAGATACAAGAGGCAAAAGCAAAGAAAGATACGCTCCTT
EST: gi|116484854|gb|EG527446.1|EG527446
EST:     AACTAGATCAGCAAAAAGGTGTTGTCGACAATCTTGTTTCAAATACAAGG                         CTCTTGGAGAGTAAGATACAAGAGGCAAAAGCAAAGAAAGATACGCTCCTT
genomic: AACTAGATCAGCAAAAAGGTGTTGTCGACAATCTTGTTTCAAATACAAGGgttagttttc ... ttatttgcagCTCTTGGAGAGTAAGATACAAGAGGCAAAAGCAAAGAAAGATACGCTCCTT
EST: gi|124741134|gb|EH832296.1|EH832296
EST:     AACTAGATCAGCAAAAAGGTGTTGTCGACAATCTTGTTTCAAATACAAGG                         CTCTTGGAGAGTAAGATACAAG
genomic: AACTAGATCAGCAAAAAGGTGTTGTCGACAATCTTGTTTCAAATACAAGGgttagttttc ... ttatttgcagCTCTTGGAGAGTAAGATACAAG
EST: gi|125203812|gb|EL218766.1|EL218766
EST:     CAAAAAGGTGTTGTCGACAATCTTGTTTCAAATACAAGG                         CTCTTGGAGAGTAAGATACAAGAGGCAAAAGCAAAGAAAGATACGCTCCTT
genomic: CAAAAAGGTGTTGTCGACAATCTTGTTTCAAATACAAGGgttagttttc ... ttatttgcagCTCTTGGAGAGTAAGATACAAGAGGCAAAAGCAAAGAAAGATACGCTCCTT
EST: gi|124954318|gb|EL029422.1|EL029422
EST:     AACTAGATCAGCAAAAAGGTGTTGTCGACAATCTTGTTTCAAATACAAGG                         CTCTTGGAGAGTAAGATACAAGAGGCAAAAGCAAAGAAAGATACGCTCCT
genomic: AACTAGATCAGCAAAAAGGTGTTGTCGACAATCTTGTTTCAAATACAAGGgttagttttc ... ttatttgcagCTCTTGGAGAGTAAGATACAAGAGGCAAAAGCAAAGAAAGATACGCTCCT
EST: gi|124838800|gb|EH923239.1|EH923239
EST:     CAATCTTGTTTCAAATACAAGG                         CTCTTGGAGAGTAAGATACAAGAGGCAAAAGCAAAGAAAGATACGCTCCTT
genomic: CAATCTTGTTTCAAATACAAGGgttagttttc ... ttatttgcagCTCTTGGAGAGTAAGATACAAGAGGCAAAAGCAAAGAAAGATACGCTCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttcttagaaaatgagttctgtaatttttttgttgtttccccttttatttgcagCTCTTGGAGAGTAAGATACAAGAGGCAAAAGCAAAGAAAGATACGCTCCTTGCACGTGCTCGCACTGCTAA
                         tttttttgttgtttcc  CT-rich tract
                      taatttttttgttgtt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcatatgattcttatattttctgaaattgcttagggcgaagtttggttcttagaaaatgagttctgtaatttttttgttgtttccccttttatttgcagCTCTTGGAGAGTAAGATACAAGAGGCAAAAGCAAAGAAAGATACGCTCCTTGCACGTGCTCGCACTGCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - -ctgaaat
- - - - - - - - - - - - - - - - - - - - agtttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - agaaaat