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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttctttctctgaacttgtatacaattagttagaatattggtttttgtagtccggtgagttcttttcagttctcacactctgcttcttatactctcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAA

Basic information

species Arabidopsis thaliana
transcript AT4G23850.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
gtatttctttctctgaacttgtatacaattagttagaata--ttggtttttgtagtccggtgagttcttttc--agttctcacactctgcttcttatactctcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAA
   |||   | ||  ||       ||   |    |||||   |||   |||         ||| | ||| |   |     | |||| || |   | |||| | ||| ||  |||||||||||||  | ||||||||||||||||| |||||  | |||||||| ||||| || ||||| |||||||| ||||| || ||||||||
---ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccctgattgaatgcttcttgtaaccggctcactttgatatct-tactgt-agGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA

upper sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
gtatttctttctctgaacttgtatacaattagttagaatattg-gtttttgtagtc-cggtgagttcttttcagttctcacactctgcttcttatactctcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAA
 || |   || |   ||  |||       |      | || |  | |    ||||  |   |||   |||  |  |   |   |||| |   |   ||  |||| ||  |||||||||||||||| |||||||| ||||| || || ||  | || ||||||||||| || || ||||||||||| ||||| || || || ||
-tactctcttttactaaactgtgcctggatgacagtactaatatgatcagctagttgcaaagagaggtttgaaaattgaaacatctgttctctg--cttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA

upper sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G152127_T01 (Zea mays), 3'ss of exon 15
gtatttctttctctgaacttgtatacaattagttagaatattggtttttgtagtccggtgagttcttttcagttctcacactctgcttcttatactc---tcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAA
     ||||       |     ||  || | |  |  | |   |  |||| | |      |  |||      |  ||||   |   |  | ||| |     |||| ||  |||||||||||||  | || |||||||||||||| |||||| | |||||||| ||||| || |||||||| |||||||| |||||||| |||||
----gtcttgaaagagatcctgatttaacttgccatcagaaatgcctttgaaattttcccaagtctaacgtttgttcactgccaaatattaatatttactgcagGAGACATTGGTGAGTGGCAGTCTGACGGAAGCATGAAGATCATTGACCGCAAGAAGAACATCTTCAAGCTCTCACAGGGAGAGTACGTTGCGGTTGAGAA

upper sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA01G43470.2 (Glycine max), 3'ss of exon 15
gtatttctttctctgaacttgtatacaatta--gttagaatattggtttttgtagtccggtgagttcttttcagttctcacactc-tgcttcttatactct-cagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAA
    || ||||  | |  || |  | ||||   |||   ||  |  | || |  ||  |||  | ||       | ||   | ||     |  |||| ||  |||| ||| |||| |||||||||||  ||||||||||||| || |||||  ||||||||||||| ||||| || ||||||||||| |||||||| || || ||
---gttatttcatttatgttttccaaaattgaggtttatattcttatattagctgttgggttgggtcacaattttccttttattcacaaatgatatattcaacagGGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA

upper sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 15
gtatttctttctctgaacttgtatacaatta--gttagaatattggtttttgtagtccggtgagttcttttcagttctcacactctgcttcttatactct-cagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAA
    || ||||  | |  || |  | | ||   |||   ||  |  | || |  ||  ||| |    ||| |  ||     ||      |  |||| ||  |||| ||| |||| |||||||||||  | ||||||||||| || |||||  ||||||||||||| ||||| || ||||||||||| |||||||| || || ||
---gttatttcatttatgttttccaaatttgaggtttatattcttatattagctgttgggtcacagttttcctttttattaac---aaatgatatattcaacagGGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA

upper sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA05G36910.1 (Glycine max), 3'ss of exon 15
gtatttctttctctgaacttgtatacaattagttagaatattggtttttgtagtccggtgagttcttttcagttctcacactctgcttcttatactctcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAA
   ||  ||| ||  |  || | |    ||   ||  ||||   | |  || |   |     |  | ||   |||    |   | ||  ||| ||    ||| ||| |||| ||||||| |||  |||||| |||||| || |||||  ||||||||||||| ||||| || ||||||||||| |||||||| || || ||
--gttcatttttc--agtttatgt----ttgaataagatatgcttctacgtggattgcatgatcatattttattcatgaatggt-ctatttaaac----agGGGATATTGGAGAGTGGCTACCCAATGGAACCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTTGAAAA

upper sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 15
gtatttctttctctgaacttgtatacaattagttagaatattggtttttgtagtccggtgagt--tcttttcagttctcacactc-tgcttcttatactctcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAA
   |||  |  | |   | | | | |  | | |||   | |  | |  | || |  |  || |  | | || |     |   ||  ||  |  | |  || |||| |||||||||||||||||||| ||||| |||||||| || || ||| | |||||||| || || || || ||||||||||| || ||||| || |||||
--gtttgctcatattggcatttcttct-tgaattaagttttgaggtcctctattttgtggattcgtttctttaacaaccttgctgatgacttatcttttcacagGGGATGTTGGTGAGTGGCAACCTGATGGGAGCATGAAAATTATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAA

upper sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: PP1S113_124V6.1 (Physcomitrella patens), 3'ss of exon 15
----------gtatttctttctctgaac-ttgtatacaattagttagaatattggtttttgtagtccggtgagttcttttcagttctcacactctgcttcttatactctcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAA
             ||| | ||| |||   ||  |   ||  || ||||         |  ||||    |||       |  ||| || |   | ||    |  ||||  ||||||||||||| || ||||||   |||||   ||||||||| || ||||||||||| || || |||||| | ||||||||||| || ||||| || |||||
ccccctctagaagtttttctctttgagtatttcaggtaacaagctaga---------tccgtagcgtagtgctgatgatgtagtgctgat--tttgaccatagtactg-cagGTGATGTTGGAGAATGGCAAGAGGATGGTGCCATGAAGATTATCGACAGGAAGAAAAACATTTTTAAATTGTCACAAGGAGAATACGTTGCAGTCGAGAA

upper sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: PP1S108_163V6.1 (Physcomitrella patens), 3'ss of exon 15
gtatttctttctctgaacttgtatacaattagttagaatattggtttttgtagtcc----ggtgagttcttttcagttctcacactctgcttcttatactctcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAA
          |  |  || || | | ||  |   ||  |||         | || |    || |||  ||  |   |||| |  || |  |  |       ||||||||| |||| ||||||||  ||||||| ||||||||||| |||||| | ||||||||||| || || || || || ||||| ||| |||| || || ||
-----gtcaccaatatacgtggaaaaaacgatgcagtttatgtaaacgaatggtgctggaggagagcgctgatgtattctgattcttttataatgcatgaatcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA

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|124899903|gb|EH974521.1|EH974521
EST:     AGGTTCTCATTGATGGATGGCTGCACACAG                         GTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGA
genomic: AGGTTCTCATTGATGGATGGCTGCACACAGgtatttcttt ... atactctcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGA
EST: gi|124752008|gb|EH842138.1|EH842138
EST:     TTGATGGATGGCTGCACACAG                         GTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGA
genomic: TTGATGGATGGCTGCACACAGgtatttcttt ... atactctcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGA
EST: gi|124861166|gb|EH945603.1|EH945603
EST:     GATGGATGGCTGCACACAG                         GTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGA
genomic: GATGGATGGCTGCACACAGgtatttcttt ... atactctcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGA
EST: gi|124781152|gb|EH871095.1|EH871095
EST:     TCACGAAAGAGGTTCTCATTGATGGATGGCTGCACACAG                         GTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGG
genomic: TCACGAAAGAGGTTCTCATTGATGGATGGCTGCACACAGgtatttcttt ... atactctcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGG
EST: gi|125034208|gb|EL106477.1|EL106477
EST:     ACGTGAAGATCTCACGAAAGAGGTTCTCATTGATGGATGGCTGCACACAG                         GTGATGTTGGTGAGTGGCAACCAG
genomic: ACGTGAAGATCTCACGAAAGAGGTTCTCATTGATGGATGGCTGCACACAGgtatttcttt ... atactctcagGTGATGTTGGTGAGTGGCAACCAG
EST: gi|124753481|gb|EH843611.1|EH843611
EST:     ATCTCACGAAAGAGGTTCTCATTGATGGATGGCTGCACACAG                         GTGATGTTGGTGAGTAGGCAACCAGATGGAAGCATGAAGATAATT
genomic: ATCTCACGAAAGAGGTTCTCATTGATGGATGGCTGCACACAGgtatttcttt ... atactctcagGTGATGTTGGTGAGT-GGCAACCAGATGGAAGCATGAAGATAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtagtccggtgagttcttttcagttctcacactctgcttcttatactctcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAA
                          ttctcac  putative branch site (score: 2)
                                       cttcttatactctc  putative PPT
                                        ttcttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttctttctctgaacttgtatacaattagttagaatattggtttttgtagtccggtgagttcttttcagttctcacactctgcttcttatactctcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA