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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttatctttggtttgttattcagttattgttacctttttaattattatacatatgaagttgagttgatgccatgtaaatgattgtgattgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGATTGGAGGAAGCTCAAGATATCTTGCCTCTAAATTTGGAGCTGAATGCAT

Basic information

species Arabidopsis thaliana
transcript AT1G64970.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G64970.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv16s0039g01410.t01 (Vitis vinifera), 3'ss of exon 1
------ttttttatctttggtttgttattcagttattgttacctttttaattattatacatatgaagt-tgagttg-atgccatg-taaatgattgtgattgaaaaaagAT-GAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGATTGGAGGAAGCTCAAGATATCTTGCCTCTAAATTTGGAGCTGAATGCAT---
       |  || | |||  |||| |||    || ||  ||  | | ||    |||      ||  |  ||||| |   |  | | |   ||  |||| |||          || ||||  ||||| | |  ||||| ||| |||||||| ||||||||||||||||| |||||||| ||  | ||    || | ||| ||    |||     
gttcgcctgctttttttttttttgctatgtgtttctt--tatttctctaccgtttaaggtggtggcgcgtgagtggcgcgtgacggtgggtgtctgtgtttgtgttgttgcagAGGAGGGAGAGAAGAGGCCAAAGAGAGTGGTGGATGTGGGGTGTGGGATTGGAGGGAGCTCAAGGTACTTGGCTAAGAAGTATGGGGCCAGTTGCCAAGG
















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|86030499|gb|DR326252.1|DR326252
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCSGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
EST: gi|86030501|gb|DR326254.1|DR326254
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
EST: gi|86030496|gb|DR326249.1|DR326249
EST:     AGCTCAGATCNGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
EST: gi|86030505|gb|DR326258.1|DR326258
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
EST: gi|86030506|gb|DR326259.1|DR326259
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
EST: gi|86030474|gb|DR326227.1|DR326227
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
EST: gi|86030482|gb|DR326235.1|DR326235
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
EST: gi|86030497|gb|DR326250.1|DR326250
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCSGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGA
EST: gi|86030493|gb|DR326246.1|DR326246
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
EST: gi|86030502|gb|DR326255.1|DR326255
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCSGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGG
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGG
EST: gi|86030479|gb|DR326232.1|DR326232
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
EST: gi|86030484|gb|DR326237.1|DR326237
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
EST: gi|86030478|gb|DR326231.1|DR326231
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
EST: gi|86030504|gb|DR326257.1|DR326257
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTT
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTT
EST: gi|86030490|gb|DR326243.1|DR326243
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
EST: gi|86030492|gb|DR326245.1|DR326245
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
EST: gi|86030486|gb|DR326239.1|DR326239
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTG
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTG
EST: gi|86030476|gb|DR326229.1|DR326229
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGGTGTGGG
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGG-TGTGGG
EST: gi|86030485|gb|DR326238.1|DR326238
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
EST: gi|86030500|gb|DR326253.1|DR326253
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
EST: gi|86030491|gb|DR326244.1|DR326244
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCNCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
EST: gi|86030494|gb|DR326247.1|DR326247
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGG
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGG
EST: gi|86030471|gb|DR326224.1|DR326224
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
EST: gi|86030483|gb|DR326236.1|DR326236
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAA-GATAAAGAAAGTAGTG
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTG
EST: gi|86030477|gb|DR326230.1|DR326230
EST:     GCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGNCGGTKKKKACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGG
genomic: GCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTT-ACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGG
EST: gi|86030488|gb|DR326241.1|DR326241
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
EST: gi|86030472|gb|DR326225.1|DR326225
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
EST: gi|86030498|gb|DR326251.1|DR326251
EST:     AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTCGCCGGTGTTACTG                         ATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA
genomic: AGCTCAGATCCGTATGATTGAAGAGTCTCTCCGTTTTGCCGGTGTTACTGgttagcttcc ... ttgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattatacatatgaagttgagttgatgccatgtaaatgattgtgattgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGATTGGAGGAAGCTCAAGATATCTTGCCTCTAAATTTGGAGCTGAATGCAT
                   agttgat  putative branch site (score: 5)
                                            attgaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttttatctttggtttgttattcagttattgttacctttttaattattatacatatgaagttgagttgatgccatgtaaatgattgtgattgaaaaaagATGAAGAGGAGGAGAAAAAGATAAAGAAAGTAGTGGATGTTGGGTGTGGGATTGGAGGAAGCTCAAGATATCTTGCCTCTAAATTTGGAGCTGAATGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - ggtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgta