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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGAGAGCAAGCTAATGAATCTGCTGAATAGCTCTGAGTATGTGCCAAGCTACGAGGACAAAGATGGTGACTGGATGCTCGTTGGCGATGTCCCATGGGAgtgagtcaaatttaatcgtttcatatacttttttttataacttataacttgactcgttaaccacatttcccgaaattggtagagacaaagccaaagatat...

Basic information

species Arabidopsis thaliana
transcript AT3G23050.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G23050.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os12g40890.1 (Oryza sativa), 5'ss of exon 3
ACGAGAGCAAGCTAATGAATCTGCTGAATAGCTCTGAGTATGTGCCAAGCTACGAGGACAAAGATGGTGACTGGATGCTCGTTGGCGATGTCCCATGGGAgtgagtcaaatttaatcgtttcatatacttttttttat---aacttataacttgact--cgttaacca---catttcccgaaat---tggta-gagacaaagccaaagatat--------------------------------------------
||||||||||| |     ||||||| ||  ||||||| |||||||||| |||||||||||| || || |||||||||||||| ||||| ||||||||||||| ||| |  | || |    |  | || | | |  |||   |   | ||| || | |  | | ||  |    | |   |  |||   || || ||| | | ||     || |                                            
ACGAGAGCAAGATTGCTGATCTGCTCAACGGCTCTGAATATGTGCCAACCTACGAGGACAAGGACGGCGACTGGATGCTCGTCGGCGACGTCCCATGGGAgtcagtaatctctacttaaattttctattatctaatatctaagtgtttaattttaataacctgaattaaggtactagtctgaatctctgatatgagtccatgctctgcatctgtgttctgaattctgaccattttgtttggaaatggaaatttcag

upper sequence: AT3G23050.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os03g43400.1 (Oryza sativa), 5'ss of exon 3
-ACGAGAGCAAGCTAATGAATCTGCTGAATAGCTCTGAGTATGTGCCAAGCTACGAGGACAAAGATGGTGACTGGATGCTCGTTGGCGATGTCCCATGGGAgtgagtcaaatttaatcgtttcatatacttttttttataacttataacttgactcgttaaccacatttcccgaaattggtaga--gacaaagccaaagatat--
  |   || |    ||| |  |||    ||  |   ||||| ||||| |  ||||||||||| || || |||||||||||||| ||||| ||||| ||||||| || |         || |    ||| |     || |||    |||     | | | | | | |  |  |  |   | | ||  ||   ||  |  |||    
AGCTGAAGGAGAGCAATAAG-CTGAGAGATGACCTGGAGTACGTGCCGACGTACGAGGACAAGGACGGCGACTGGATGCTCGTCGGCGACGTCCCGTGGGAgtaagcctcgccgtcgcgataagcataatcccagttctaataattaatc---cccatcagcta-agctagcagatcggatggatcgatcgagtaactgatcaac

upper sequence: AT3G23050.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os03g53150.1 (Oryza sativa), 5'ss of exon 3
ACGAGAGCAAGCTAATGAATCTGCTGAATAGCTCTGAGTATGTGCCAAGCTACGAGGACAAAGATGGTGACTGGATGCTCGTTGGCGATGTCCCATGGGAgtgagtcaa-atttaatcgtttcatatacttttttttataacttataacttgactcgttaaccacatttcccgaaattggtagagacaaagccaaagatat---------------------------
    || |||    ||||||  | ||||| |||||||   |||  |||  || || ||||| ||||||||||||||||| ||||| |||||||| ||| |||  || |  | || ||  ||       |||   | | |  |||||       ||| |  |  | | | |      || |      ||    |||   | |                           
---GGAACAAT---ATGAATGAGGTGAATGGCTCTGATGCTGTTACAACTTATGAAGACAAGGATGGTGACTGGATGCTTGTTGGAGATGTCCCGTGGCAgtatgttactacttcattcttgtgcccccttaactgttttccttattttccacctcat-gattagaatgc---ggtttagcgataccacgttcaagtttctcgcattagctgattggttactctgcag

upper sequence: AT3G23050.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G138268_T01 (Zea mays), 5'ss of exon 3
ACGAGAGCAAGCTAATGAATCTGCTGAATAGCTCTGAGTATGTGCCAAGCTACGAGGACAAAGATGGTGACTGGATGCTCGTTGGCGATGTCCCATGGGAgtgagtcaaatttaatcgtttcatatacttttttttataacttataacttgactcgttaaccacatttcccgaaattggtagagacaaagccaaagatat------
|||||||||||||  || ||||||| ||  |||| ||||| ||||| | |||||||||||| || || |||||||||||||| |||||||| || ||||||||||        | |   | |||   ||| ||  |  |   ||   |||      |||    | |   | |||| |  ||   | ||   | |    ||      
ACGAGAGCAAGCTGGTGGATCTGCTCAACGGCTCCGAGTACGTGCCGACCTACGAGGACAAGGACGGGGACTGGATGCTCGTCGGCGATGTGCCGTGGGAgtgagc-------actgcatgcatgcgcttcttcctgcactatactccttattatatta-ttgcctaatcggaaaataata---ataatttccatttcattttcag

upper sequence: AT3G23050.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G159285_T01 (Zea mays), 5'ss of exon 3
ACGAGAGCAAGCTAATGAATCTGCTGAATAGCTCTGAGTATGTGCCAAGCTACGAGGACAAAGATGGTGACTGGATGCTCGTTGGCGATGTCCCATGGGAgtgagtc--aaatttaatcgtttcat-atacttttttttataacttataacttgactcgttaaccacatttcccgaaattggtagagacaaagccaaagatat
| ||| | || ||| |  ||| | | |   |  ||||    ||  | |  ||||| ||||| ||||| |||||||||||||||||||| ||||| |||||||  ||     |||  |  ||  ||| ||      ||| || |   | |  || |  | | | |  | | |        | || ||       ||    |   
ATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATGTGGTCACTACTTACGAAGACAAGGATGGCGACTGGATGCTCGTTGGCGACGTCCCGTGGGAgtatgttctgcattctagtgtgccatcatctaggatttgatcaggcaaatgttcaggcttcagcttcttatatgctgccttgttgattgttgtccctgcag--

upper sequence: AT3G23050.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G077356_T01 (Zea mays), 5'ss of exon 3
ACGAGAGCAAGCTAATGAATCTGCTGAATAGCTCTGAGTATGTG---CCAAGCTACGAGGACAAAGATGGTGACTGGATGCTCGTTGGCGATGTCCCATGGGAgtgagtcaa--atttaatcgtttcatatacttttttttataacttataact--tgactcgttaaccacatttcccgaaattggtagagacaaagccaaagatat-----
   || | |   |  |  ||| |          ||||  |||||    | |  ||||| ||||| ||||||||||||||||| || ||||| ||||| |||||||  ||      ||  | |||  |||     |  |||  ||  |  | ||   ||| | |    |||  | ||  | |  | |    |   |       |         
---AGGGGAGATTGGTTGATCCGGCCGGCGATGCTGATGATGTGGTCACTACTTACGAAGACAAGGATGGTGACTGGATGCTGGTCGGCGACGTCCCGTGGGAgtatgttctccgttctagcgtgccat-cgtctgctttcgtatttactgacccatgattaggactcca-gtgtcttgtatgtcgccttgctgattttctggtccctgcag

upper sequence: AT3G23050.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA20G35270.1 (Glycine max), 5'ss of exon 4
ACGAGAGCAAGCTAATGAATCTGCTGAATAGCTCTGAGTATGTGCCAAGCTACGAGGACAAAGATGGTGACTGGATGCTCGTTGGCGATGTCCCATGGGAgtgagtcaaatttaatcgtttcatatacttttttttataacttataacttgactcgttaaccacatttcccg-aaattggtagag---acaaagccaaagatat
| ||||||||| | ||| |||| || || ||||||||||||||||||||||| || || || |||||||||||||||||||| || |||||||||||||||| |||     || |||     | | || | |      |   ||||   | | |   ||   || |       | ||   || |    |||||  ||   || |
ATGAGAGCAAGTTGATGGATCTTCTTAACAGCTCTGAGTATGTGCCAAGCTATGAAGATAAGGATGGTGACTGGATGCTCGTGGGTGATGTCCCATGGGAgtaagtt---cttcatccaacaaca-acctctgcagccattatatacaataatttcctacatacttgatttatacatccatatattttacaaattcagtaatct

upper sequence: AT3G23050.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G32340.1 (Glycine max), 5'ss of exon 3
ACGAGAGCAAGCTAATGAATCTGCTGAATAGCTCTGAGTATGTGCCAAGCTACGAGGACAAAGATGGTGACTGGATGCTCGTTGGCGATGTCCCATGGGAgtgagtcaaatttaatcgtttcatatacttttttttataacttataacttgactcgttaaccacatttcccg-aaattggtagagacaaagccaaagatat---
| ||||||||| | ||| |||| || || ||||||||||||||||||| ||| || || || |||||||||||||||||||| || |||||||||||||||| |||     || |||     | | || | |     ||   ||||   | | |  |||   | ||       | ||   ||   |   | ||| | || |   
ATGAGAGCAAGTTGATGGATCTTCTTAACAGCTCTGAGTATGTGCCAACCTATGAAGATAAGGATGGTGACTGGATGCTCGTGGGTGATGTCCCATGGGAgtaagtt---cttcatccaacaaca-acctctgcagctattatatacaataatttcttacatatatactttatatatacataactatgtatccatatattttac

upper sequence: AT3G23050.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv05s0020g04690.t01 (Vitis vinifera), 5'ss of exon 3
ACGAGAGCAAGCTAATGAATCTGCTGAATAGCTCTGAGTATGTGCCAAGCTACGAGGACAAAGATGGTGACTGGATGCTCGTTGGCGATGTCCCATGGGAgtgagtcaaatttaatcgtttcatatacttttttttataactta-taacttgactcgttaaccacatttcccgaaattggtaga--gacaaagccaaagatat-----
| ||||||||| | ||| ||||  |||| |||||||| ||||| |||| ||| || || || ||||| |||||||||||||| || ||||| ||||||||||  ||     || ||   |  | | ||  |       || | | |||    | ||   ||| | | |     ||    ||      ||   | | || | ||     
ATGAGAGCAAGTTGATGGATCTTTTGAACAGCTCTGAATATGTTCCAACCTATGAAGATAAGGATGGAGACTGGATGCTCGTGGGTGATGTTCCATGGGAgtatgtt---cttgatttctctagaaaccctaacacgaaaatcaataaaactagtcagaaactaaaat-----aagccagtgagccaactgggtctaatacatggggt

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|124950322|gb|EL025794.1|EL025794
EST:     TACGAGGACAAAGATGGTGACNGGATGCTCGTTGGCGATGTCCCATGGGA                         AATGTTTGTCGAGTCTTGCAAACGTTTGCGCATTATGAAGGGA
genomic: TACGAGGACAAAGATGGTGACTGGATGCTCGTTGGCGATGTCCCATGGGAgtgagtcaaa ... cctatttcagAATGTTTGTCGAGTCTTGCAAACGTTTGCGCATTATGAAGGGA
EST: gi|125204711|gb|EL219665.1|EL219665
EST:     CGATGTCCCATGGGA                         AATGTTTGTCGAGTCTTGCAAACGTTTGCGCATTATGAAGGGATCTGAAGC
genomic: CGATGTCCCATGGGAgtgagtcaaa ... cctatttcagAATGTTTGTCGAGTCTTGCAAACGTTTGCGCATTATGAAGGGATCTGAAGC
EST: gi|47831153|gb|CK120837.1|CK120837
EST:     TACGAGGACAAAGATGGTGACTGGATGCTCGTTGGCGATGTCCCATGGGA                         AATGTTTGTCGAGTCTTGCAAACGTTTGCGCATTATGAAGGGATCTGAAGC
genomic: TACGAGGACAAAGATGGTGACTGGATGCTCGTTGGCGATGTCCCATGGGAgtgagtcaaa ... cctatttcagAATGTTTGTCGAGTCTTGCAAACGTTTGCGCATTATGAAGGGATCTGAAGC
EST: gi|124723798|gb|EH815200.1|EH815200
EST:     ACAAAGATGGTGACTGGATGCTCGTTGGCGATGTCCCATGGGA                         AATGTTTGTCGAGTCTTGCAAAACGTTTGCGCATTATGAAGGGATCTGA
genomic: ACAAAGATGGTGACTGGATGCTCGTTGGCGATGTCCCATGGGAgtgagtcaaa ... cctatttcagAATGTTTGTCGAGTCTTGCAAA-CGTTTGCGCATTATGAAGGGATCTGA
EST: gi|125292945|gb|EL307030.1|EL307030
EST:     TACGAGGACAAAGATGGTGACTGGATGCTCGTTGGCGATGTCCCATGGGA                         AATGTTTGTCGAGT
genomic: TACGAGGACAAAGATGGTGACTGGATGCTCGTTGGCGATGTCCCATGGGAgtgagtcaaa ... cctatttcagAATGTTTGTCGAGT
EST: gi|125322766|gb|EL336851.1|EL336851
EST:     TACGAGGACAAAGATGGTGACTGGATGCTCGTTGGCGATGTCCCATGGGA                         AATGTTTGTCGAGTCTTG
genomic: TACGAGGACAAAGATGGTGACTGGATGCTCGTTGGCGATGTCCCATGGGAgtgagtcaaa ... cctatttcagAATGTTTGTCGAGTCTTG
EST: gi|125079536|gb|EL141506.1|EL141506
EST:     TGCTCGTTGGCGATGTCCCATGGGA                         AATGTTTGTCGAGTCTTGCAAACGTTTGCGCATTATGAAGGGATCTGAAGC
genomic: TGCTCGTTGGCGATGTCCCATGGGAgtgagtcaaa ... cctatttcagAATGTTTGTCGAGTCTTGCAAACGTTTGCGCATTATGAAGGGATCTGAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGAGAGCAAGCTAATGAATCTGCTGAATAGCTCTGAGTATGTGCCAAGCTACGAGGACAAAGATGGTGACTGGATGCTCGTTGGCGATGTCCCATGGGAgtgagtcaaatttaatcgtttcatatacttttttttataacttataacttgactcgttaaccacatttcccgaaattggtagagacaaagccaaagatat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catttccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agacaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaagata