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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaggaattctgcagcaaatcgatactttaaactaaaatcattggatggaaaacgaattgatgcaaaactgttgtttgtatgatgcagTTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCTTCCTTTGGCATTTGATTATGCGGGACAGAAACAAGCTGTGAAAGCTGTGTTTTTTGGCAT

Basic information

species Arabidopsis thaliana
transcript AT3G20870.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G20870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g10230.1 (Oryza sativa), 3'ss of exon 10
gtaagtaggaattctgcagcaaatcgatactttaaactaaaatcattggatggaaaacgaattgatgcaaaactgttgtttgtatga-tgcagTTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCTTCCTTTGGCATTTGATTATGCGGGACAGAAACAAGCTGTGAAAGCTGTGTTTTTTGGCAT
                   ||    | || |  |||  ||||    |    | |    | |||  ||   | ||    | ||  |   ||||||||||||  | ||||| ||||| || ||||| |||||| | ||| | |||||||| ||||| || || ||||| ||||| ||||| || ||| |||||||
-----------------gtcagtctgttaataaaaagaaaaactggtatcagtattctgcattt-tgttgacctcccatgtgcctttctgcagTTGGTGGGGTTATGGCCTTCCTCACTTTGCATGAAATGTTACCTCTAGCATTTGACTATGCTGGTCAAAAACAGGCTGTCAAAGCAGTCTTTGTTGGCAT

upper sequence: AT3G20870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G050484_T01 (Zea mays), 3'ss of exon 10
gtaagtaggaattctgcagcaaatcga-tactttaaactaaaatcattggatggaaaacgaattgatgcaaaactgttgtttgtatgatgcagTTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCTTCCTTTGGCATTTGATTATGCGGGACAGAAACAAGCTGTGAAAGCTGTGTTTTTTGGCAT
         | | |   || |||| || || | |    ||   |         ||  ||    || ||    |||  |||   | || |||||| |||||  ||||||||||||| || ||||| |||||||| ||| | |||||||| |||   || ||||| |||||||| |||||||| ||| | |||||
------gtcagtccgttaggaaattgaatagtatttgttatgtttccatacctgagtact--ctgttg----acttctgtgcctttg-tgcagTGGGTGGTGTCATGGCTTTCCTCACTTTGCATGAAATGCTGCCTCTTGCATTTGACTATTGTGGCCAGAAGCAAGCTGTCAAAGCTGTCTTTGTGGGCAT

upper sequence: AT3G20870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G41580.1 (Glycine max), 3'ss of exon 10
gtaagtaggaattctgcagcaaatcgatactttaaactaaaatcattggatggaaaacgaattgatgcaaaactgttgtttgtatgat-----gcagTTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCTTCCTTTGGCATTTGATTATGCGGGACAGAAACAAGCTGTGAAAGCTGTGTTTTTTGGCAT
     | | |||  | |||||  | |||       |||  |||| ||||       | |  || ||||| |  || | | || |||||      ||||||||||| | |||||||| || ||  | || ||||||||||| ||||| |||||||||||||||||||| ||| ||||||| ||||| ||||| || ||
---gtttgcaatgatacagcatctagatgtc----actggaatctttggc--atttatgtttttatgcagatttgatctatg-atgattaattacagTTGGTGGAGTTATGGCTTTTCTGACCCTTCATGAAATGCTTCCATTGGCTTTTGATTATGCGGGACAGAAGCAATCTGTGAAGGCTGTCTTTTTGGGGAT

upper sequence: AT3G20870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G03820.2 (Glycine max), 3'ss of exon 10
gtaagtaggaattctgcagcaaatcgatactttaaactaaaatcattggatggaaaacgaattgatgcaaaactgttgtttgtatgat-----gcagTTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCTTCCTTTGGCATTTGATTATGCGGGACAGAAACAAGCTGTGAAAGCTGTGTTTTTTGGCAT
     | | |||  | |||||  | |||     ||  |  |||  ||||      |    ||| ||||| |  ||   | || |||||      ||||||||||| | |||||||| || ||  | || |||||||| || ||||| |||||||||||||||||||| ||| |||| || ||||| ||||| || ||
---gtttgcaatgatacagcatgtagatgtcacaa--tggaatttttgg-catttattttatt-atgcagatttgacctatg-atgattaattacagTTGGTGGAGTTATGGCTTTTCTGACCCTTCATGAAATGCTGCCATTGGCTTTTGATTATGCGGGACAGAAGCAATCTGTTAAGGCTGTCTTTTTGGGGAT

upper sequence: AT3G20870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 10
--gtaagtaggaattctgcagcaaatcgatactttaaactaaaatc-attggatggaaaacgaattgatgcaaaactgttgtttgtatgatgcagTTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCTTCCTTTGGCATTTGATTATGCGGGACAGAAACAAGCTGTGAAAGCTGTGTTTTTTGGCAT
   |   |  |  || |  ||   ||| |    | |||  || ||   ||   ||  |||     ||||   ||  ||  || |  |   ||||||||||||| | |||||||| || || ||||| |||||||| || ||||||||||| ||||| || | ||| |||||||| || || || || ||||| ||
gtttgcttttggcttttaaagttcatcaagttgtgaaaaaaacatttgttatctgtgaaagttcctgatatgaa-ttggcgtatcca---tgcagTTGGTGGAGTGATGGCTTTTCTTACCTTGCATGAAATGCTGCCATTGGCATTTGACTATGCTGGGCCGAAGCAAGCTGTCAAGGCAGTCTTCTTTGGAAT

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|86083065|gb|DR378824.1|DR378824
EST:     ATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGGGAGCAG                         TTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCTTCCTTTGGCAT
genomic: ATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGGGAGCAGgtaagtagga ... tatgatgcagTTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCTTCCTTTGGCAT
EST: gi|116396456|gb|EG439048.1|EG439048
EST:     ATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGGGAGCAG                         TTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCTTCCTTTGGCAT
genomic: ATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGGGAGCAGgtaagtagga ... tatgatgcagTTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCTTCCTTTGGCAT
EST: gi|116396457|gb|EG439049.1|EG439049
EST:     ATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGGGAGCAG                         TTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCTTCCTTTGGCAT
genomic: ATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGGGAGCAGgtaagtagga ... tatgatgcagTTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCTTCCTTTGGCAT
EST: gi|124714604|gb|EH806006.1|EH806006
EST:     CAGAAATCCTTGAAGGTTTGTTGGGAGCAG                         TTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCT
genomic: CAGAAATCCTTGAAGGTTTGTTGGGAGCAGgtaagtagga ... tatgatgcagTTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCT
EST: gi|116403229|gb|EG445821.1|EG445821
EST:     ATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGGGAGCAG                         TTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCTTCCTTTGGCAT
genomic: ATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGGGAGCAGgtaagtagga ... tatgatgcagTTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCTTCCTTTGGCAT
EST: gi|86082548|gb|DR378307.1|DR378307
EST:     ATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGGGAGCAG                         TTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCTTCCTTTGGCAT
genomic: ATTCCCGAGAAGCTTAAGTCCAGAAATCCTTGAAGGTTTGTTGGGAGCAGgtaagtagga ... tatgatgcagTTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCTTCCTTTGGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaatcattggatggaaaacgaattgatgcaaaactgttgtttgtatgatgcagTTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCTTCCTTTGGCATTTGATTATGCGGGACAGAAACAAGCTGTGAAAGCTGTGTTTTTTGGCAT
                      aattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaggaattctgcagcaaatcgatactttaaactaaaatcattggatggaaaacgaattgatgcaaaactgttgtttgtatgatgcagTTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCTTCCTTTGGCATTTGATTATGCGGGACAGAAACAAGCTGTGAAAGCTGTGTTTTTTGGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG