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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgcttaatttgcttatagtttgtatttcgaatgtgctgattatgaaatccctttttgagtaatgtgatggttttgtatgttgttctgcagTATGCATTTAACTTGTTTTCACATAATGCTCCTATTCTTGACAACGGTTACAACGAAGAGGAAATGAAACTTGTGAAGGAGACAAGGAAGATCTGG

Basic information

species Arabidopsis thaliana
transcript AT1G14810.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G14810.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g55280.1 (Oryza sativa), 3'ss of exon 3
gtgagtgcttaatttgcttatagtttgtatttcg-aatgtgctgattatgaaatccctttttgagtaatgtgatggttttgtatgttgttctgcagTATGCATTTAACTTGTTTTCACATAATGCTCCTATTCTTGACAACGGTTACAACGAAGAGGAAATGAAACTTGTGAAGGAGACAAGGAAGATCTGG
                      |||   |||    ||| | |||   |         || ||    | |  | ||  ||||  | |  || |||||||||| |||||  | |||||||||||||| || ||| |||| || || ||||| || ||||| |||||  | ||||||||||| || || ||||||
----------------------gttctaattctataatatcctggacacacgccagattattttcaagtcagctgaatttgcttctccttgtgcagTATGCTTTTAATATATTTTCACATAATGCACCAATTGTTGAAAATGGGTACAATGAGGAGGAGATGAAGATGGTGAAGGAGACCAGAAAAATCTGG

upper sequence: AT1G14810.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G076885_T01 (Zea mays), 3'ss of exon 3
gtgagtgcttaatttgcttatagtttgtatttcgaatgtgctgattatgaaatccctttt----tgagtaat--gtgatggttttgtatgttg-ttctgcagTATGCATTTAACTTGTTTTCACATAATGCTCCTATTCTTGACAACGGTTACAACGAAGAGGAAATGAAACTTGTGAAGGAGACAAGGAAGATCTGG
      | |      ||||| || ||| | |     || || ||| || ||||   |||      ||||  |   || ||  | | | |||   || |||||||||| |||||  | || ||||| ||||| ||  ||||||| || || || ||||| |||||||||||| | ||||||||||| ||||| || |||
------gttgttccagcttacagattgaaatatcc-tgagcagat-atcaaattattttagtcacgagttcttcatgctgaatatctttgtcccttgtgcagTATGCTTTTAATATATTCTCACACAATGCACCAGTTCTTGAGAATGGGTATAACGAGGAGGAAATGAAAATGGTGAAGGAGACCAGGAAAATTTGG

upper sequence: AT1G14810.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0011g05860.t01 (Vitis vinifera), 3'ss of exon 3
--gtgagtgcttaatttgcttat-----agtttgt----atttcgaatgtgctgattatgaaatcccttt--ttgagtaatgtgatggttt--tgtatgttgttc-tgcagTATGCATTTAACTTGTTTTCACATAATGCTCCTATTCTTGACAACGGTTACAACGAAGAGGAAATGAAACTTGTGAAGGAGACAAGGAAGATCTGG
   ||  | || | | | | | |     | ||||     | ||  ||     ||||| || | |   | |  |||  ||   | |    ||  |  || |  ||| |||||||||| |||||  | |||||||| ||||| ||| |||||   || || ||||| ||||||||||||||| | || || ||||||||||| ||||||
gtttgtctactcattatacatgtttaccaatttgacaagaattacaaca-aatgattttgtattttatctagttgcctagaataacctcttaatacatatacttcatgcagTATGCTTTTAATCTCTTTTCACACAATGCACCTGTTCTTCCAAATGGGTACAATGAAGAGGAAATGAAATTAGTAAAAGAGACAAGGAAAATCTGG

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|116453473|gb|EG496065.1|EG496065
EST:     GTTTTAGAGGGTAAACCTCCGACTTGTAACATCTTCGGGCAGCAG                         TATGCATTTAACTTGTTTTCACATAATGCTCCTATTCTTGACAACGGTTAC
genomic: GTTTTAGAGGGTAAACCTCCGACTTGTAACATCTTCGGGCAGCAGgtgagtgctt ... tgttctgcagTATGCATTTAACTTGTTTTCACATAATGCTCCTATTCTTGACAACGGTTAC
EST: gi|125029978|gb|EL102247.1|EL102247
EST:     GTTTTAGAGGGTAAACCTCCGACTTGTAACATCTTCGGGCAGCAG                         TATGCATTTAACTTGTTTTCACATAATGCTCCTATTCTTGACAACGG
genomic: GTTTTAGAGGGTAAACCTCCGACTTGTAACATCTTCGGGCAGCAGgtgagtgctt ... tgttctgcagTATGCATTTAACTTGTTTTCACATAATGCTCCTATTCTTGACAACGG
EST: gi|116396484|gb|EG439076.1|EG439076
EST:     GTTTTAGAGGGTAAACCTCCGACTTGTAACATCTTCGGGCAGCAG                         TATGCATTTAACTTGTTTTCACATAATGCTCCTATTCTTGACAACGGTTAC
genomic: GTTTTAGAGGGTAAACCTCCGACTTGTAACATCTTCGGGCAGCAGgtgagtgctt ... tgttctgcagTATGCATTTAACTTGTTTTCACATAATGCTCCTATTCTTGACAACGGTTAC
EST: gi|124885894|gb|EH964796.1|EH964796
EST:     GTAAACCTCCGACTTGTAACATCTTCGGGCAGCAG                         TATGCATTTAACTTGTTTTCACATAATGCTCCTATTCTTGACAACGGTTAC
genomic: GTAAACCTCCGACTTGTAACATCTTCGGGCAGCAGgtgagtgctt ... tgttctgcagTATGCATTTAACTTGTTTTCACATAATGCTCCTATTCTTGACAACGGTTAC
EST: gi|124934445|gb|EL011515.1|EL011515
EST:     GTAAACCTCCGACTTGTAACATCTTCGGGCAGCAG                         TATGCATTTAACTTGTTTTCACATAATGACTCCTATTCTTGACAACGGTTA
genomic: GTAAACCTCCGACTTGTAACATCTTCGGGCAGCAGgtgagtgctt ... tgttctgcagTATGCATTTAACTTGTTTTCACATAATG-CTCCTATTCTTGACAACGGTTA
EST: gi|124903300|gb|EH977380.1|EH977380
EST:     GTTTTAGAGGGTAAACCTCCGACTTGTAACATCTTCGGGCAGCAG                         TATGCATTTAACTTGTTTTCACATAATGCTCCTATTCTTGACAACGGTTAC
genomic: GTTTTAGAGGGTAAACCTCCGACTTGTAACATCTTCGGGCAGCAGgtgagtgctt ... tgttctgcagTATGCATTTAACTTGTTTTCACATAATGCTCCTATTCTTGACAACGGTTAC
EST: gi|116453474|gb|EG496066.1|EG496066
EST:     GTTTTAGAGGGTAAACCTCCGACTTGTAACATCTTCGGGCAGCAG                         TATGCATTTAACTTGTTTTCACATAATGCTCCTATTCTTGACAACGGTTAC
genomic: GTTTTAGAGGGTAAACCTCCGACTTGTAACATCTTCGGGCAGCAGgtgagtgctt ... tgttctgcagTATGCATTTAACTTGTTTTCACATAATGCTCCTATTCTTGACAACGGTTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgattatgaaatccctttttgagtaatgtgatggttttgtatgttgttctgcagTATGCATTTAACTTGTTTTCACATAATGCTCCTATTCTTGACAACGGTTACAACGAAGAGGAAATGAAACTTGTGAAGGAGACAAGGAAGATCTGG
 tgctgat  putative branch site (score: 3)
                                            ttgttct  putative PPT
     tatgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgcttaatttgcttatagtttgtatttcgaatgtgctgattatgaaatccctttttgagtaatgtgatggttttgtatgttgttctgcagTATGCATTTAACTTGTTTTCACATAATGCTCCTATTCTTGACAACGGTTACAACGAAGAGGAAATGAAACTTGTGAAGGAGACAAGGAAGATCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA