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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatcgtagcttagttgctgagactttaggaagtaaagttttttcctttatttctttctttttcattttctttggcttcctatttttttcctttttgcagATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT

Basic information

species Arabidopsis thaliana
transcript AT1G17370.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17370.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os07g42380.1 (Oryza sativa), 3'ss of exon 1
ttatcgtagctt--agttgctgagactttaggaagtaaagttttttcctttatttct----ttctttttcattttctttggcttcctatttttttcctttttgcagATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
      ||| ||  |  | |   |  | |      ||| |  ||| |  |||||| |    || | |||| | ||  || | ||  |    ||||  |||||||||||||| |||||||  | ||||||||| || ||||| |||||| | ||||| |||||||||||
------tagtttgcatgtaccaggcttctttttgctaaggcgtttcctattatttgtagatttttatttcttctttctttgtttttttacatttttatttttgcagATAGAGCCAATCCTTACTGGAAATCTGCCTCCTGGCTTTGATACGAGTACATGCCGCAGTGT

upper sequence: AT1G17370.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 1
-ttatcgtagcttagttgctgagactttaggaagtaaagttttttcctttatttctttctttttcattttctttggcttcctatttttttcctttttgcagATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
 || ||  |   |   |  ||  |  | |  |   ||  ||||| ||| |   | |  | | ||  |  | | |  | |  |    || | | |||||||||| |||||||| |||||||||||||| || ||||||||||||||||||||||||||||||||
cttctctcattctctgtattggtagat-acaatacaatttttttccctcttgatttgccctctttttcctttctttcctttttcacttcttcattttgcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT

upper sequence: AT1G17370.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 1
--ttatcgtagcttagttgctgagactttaggaagtaaagttttttcctttatttctttctttttcattttctttggcttcctatttttttcctttttgcagATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
  || ||  |   |   |  ||  |  |     |  |   |||||  ||| ||||      ||||   |||||||   ||   | || ||  | |||||||||| ||||||   |||||||||||| | || ||||||||||||||||||||||||||||||||
acttctctcattgtctgtattggtagatacaatacaattttttttctcttgatttgccctctttttcctttctttcctttttcacttctt--cattttgcagATTGAACCATATCCAAGTGGAAATTTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT

upper sequence: AT1G17370.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 1
-ttatcgtagcttagttgctgagac-tttaggaagtaaagttttttcctttatttctttctttttcattttctttggcttcctatttttttcctttttgcagATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
 ||   || | |   |   | ||    ||      | |  || |||   || ||| | | | ||| |||||||||   ||  ||  |||||   ||||||||||||| ||||| |||||||||||||| || |||||||||||| ||||||| |||||||||||
cttgatgtgggtagatgatttaggggcttgtctttttatattatttttgttctttttctttcttttattttcttttcttttttacattttt--attttgcagATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGT

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|116477129|gb|EG519721.1|EG519721
EST:     TTATGCAGCAACAGTCTCTCTACCATCCTGGTCTCCTTGCCCCGCCACAG                         ATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACT
genomic: TTATGCAGCAACAGTCTCTCTACCATCCTGGTCTCCTTGCCCCGCCACAGgtttgctcta ... ctttttgcagATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACT
EST: gi|116486725|gb|EG529317.1|EG529317
EST:     GCCCCGCCACAG                         ATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACT
genomic: GCCCCGCCACAGgtttgctcta ... ctttttgcagATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACT
EST: gi|124706133|gb|EH797535.1|EH797535
EST:     CAACAGTCTCTCTACCATCCTGGTCTCCTTGCCCCGCCACAG                         ATAGAACCAATCCCAAGTGGAAATCTCCCCC-TGGTTTTGATCCAAGTACT
genomic: CAACAGTCTCTCTACCATCCTGGTCTCCTTGCCCCGCCACAGgtttgctcta ... ctttttgcagATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACT
EST: gi|116386137|gb|EG428729.1|EG428729
EST:     TTATGCAGCAACAGTCTCTCTACCATCCTGGTCTCCTTGCCCCGCCACAG                         ATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACT
genomic: TTATGCAGCAACAGTCTCTCTACCATCCTGGTCTCCTTGCCCCGCCACAGgtttgctcta ... ctttttgcagATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACT
EST: gi|124828874|gb|EH913710.1|EH913710
EST:     TCTCCTTGCCCCGCCACAG                         ATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACT
genomic: TCTCCTTGCCCCGCCACAGgtttgctcta ... ctttttgcagATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACT
EST: gi|125221163|gb|EL235248.1|EL235248
EST:     CTACCATCCTGGTCTCCTTGCCCCGCCACAG                         ATAGAACCAATCCCAAGTGGAAATCTCCCCC-TGGTTTTGATCCAAGTACT
genomic: CTACCATCCTGGTCTCCTTGCCCCGCCACAGgtttgctcta ... ctttttgcagATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACT
EST: gi|116386087|gb|EG428679.1|EG428679
EST:     TTATGCAGCAACAGTCTCTCTACCATCCTGGTCTCCTTGCCCCGCCACAG                         ATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACT
genomic: TTATGCAGCAACAGTCTCTCTACCATCCTGGTCTCCTTGCCCCGCCACAGgtttgctcta ... ctttttgcagATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttatttctttctttttcattttctttggcttcctatttttttcctttttgcagATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
       tctttctttttcattt  CT-rich tract
                                   tatttttttccttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatcgtagcttagttgctgagactttaggaagtaaagttttttcctttatttctttctttttcattttctttggcttcctatttttttcctttttgcagATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - aagtaaa