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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgctataaaaacaacaacttaactcaatctttccgaccaatataatctactgaaattaattttaatgtgatggttttactactagACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGGAGCTGAGATTGGTGGAGCTTTTGGAGGCGAGAAAGCGACTGGTGGTGGT

Basic information

species Arabidopsis thaliana
transcript AT1G54100.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G54100.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os09g26880.3 (Oryza sativa), 3'ss of exon 12
gtaagtgctataaaaacaacaacttaactcaatcttt-ccgaccaatataatctactgaaattaattttaatgtgatggttttactact----------agACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGGAGCTGAGATTGGTGGAGCTTTTGGAGGCGAGAAAGCGACTGGTGGTGGT
  |  |    |  | ||     |  |  ||  |   | ||   |   ||||   | |||||| | | |    |||||| | || ||  |          || || |  || ||||||||||||||||| ||||| || || || || ||||| ||||| ||||||||||||||||| || || ||||| ||||||||||| 
acacctttcttttacacgctctcagatttcttttactgccatgccccataagaca-tgaaatgactatggtagtgatgttcttgctcttcttgctgtacagGCCTCATGGTAGTGACTGTGGCATTGTTAATGTAAATATTCCCACAAATGGTGCTGAAATTGGTGGAGCTTTTGGTGGAGAAAAAGCTACTGGTGGTGGA

upper sequence: AT1G54100.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G130440_T02 (Zea mays), 3'ss of exon 12
----gtaagtgctataaaaacaa--caacttaactcaatctttccgaccaatataatctactga--aattaattttaatgtg-atggttttactac-tagACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGGAGCTGAGATTGGTGGAGCTTTTGGAGGCGAGAAAGCGACTGGTGGTGGT
     ||  |  |  |||||     || |||   |       | |||   ||||  | |  |    ||| |   | | |||   |  | ||| ||   || || |  || ||||| ||||| || ||||||||||||||||| || ||||| ||||| ||||||||||| ||||| || || ||||| ||||||||||| 
ttgaatacttattgcaaaaatttctcatcttttgtggggtccttcgagttatattttttgattgccaataagcctcactgtttgttctcttattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAACTGGTGGTGGA

upper sequence: AT1G54100.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM5G820733_T01 (Zea mays), 3'ss of exon 4
----gtaagtgctataaaaa--caacaacttaactcaatctttccgaccaatataatctactga--aattaattttaatgtg-atggttttactac-tagACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGGAGCTGAGATTGGTGGAGCTTTTGGAGGCGAGAAAGCGACTGGTGGTGGT
     ||  |  |  |||||     || |||   |       |  |    ||||  | |  |    ||| | | | | |||   |  | ||| ||   || || |  || ||||| ||||| || ||||||||||||||||| || ||||| ||||| ||||||||||| ||||| || || |||||  |||||||||| 
ttgaatatttattgcaaaaagttctcatcttttgtggggtcctttgggttatattttttgattgccaataagtctcactgtttgttctcttattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA

upper sequence: AT1G54100.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G070514_T02 (Zea mays), 3'ss of exon 5
----gtaagtgctataaaaa--caacaacttaactcaatctttccgaccaatataatct-actgaaattaattttaatgtgatggttttactacta----gACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGGAGCTGAGATTGGTGGAGCTTTTGGAGGCGAGAAAGCGACTGGTGGTGGT
     ||  |  |  |||||     || |||   |       |  |    ||||  | | | ||  | |||   | |  || | ||| |  || ||    | || |  || ||||| ||||| || ||||||||||||||||| || ||||| ||||| ||||||||||| ||||| || || |||||  |||||||||| 
ttgaatatttattgcaaaaagttctcatcttttgtggggtcctttgggttatattttttgattgccaataagcctcac-tgtttgttctgttattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA

upper sequence: AT1G54100.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM5G828253_T01 (Zea mays), 3'ss of exon 1
----gtaagtgctataaaa--acaacaacttaactcaa-tctttccgaccaatataatctactga-aattaattttaatgtg-atggttttactac-tagACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGGAGCTGAGATTGGTGGAGCTTTTGGAGGCGAGAAAGCGACTGGTGGTGGT
     ||  |  |  ||||      || |||   |    || || ||   |   |  |  | ||  ||| |   | | |||   |  | ||| ||   || || |  || ||||| ||||| || ||||||||||||||||| || ||||| ||||| ||||||||||| ||||| || || |||||  |||||||||| 
ttgaatatttattgcaaaatgttctcatcttttgtggggtcctttcggttatattttttgattgccaataagcctcactgtttgttctcttattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA

upper sequence: AT1G54100.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G382159_T01 (Zea mays), 3'ss of exon 3
----gtaagtgctataaaaa--caacaacttaactcaatctttccgaccaatataatct-actga-aattaattttaatgtg-atggttttactac-tagACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGGAGCTGAGATTGGTGGAGCTTTTGGAGGCGAGAAAGCGACTGGTGGTGGT
     ||  |  |  |||||     || |||   |       |  |    ||||  | | | ||  ||| |   | | |||   |  | ||| ||   || || |  || ||||| ||||| || ||||||||||||||||| || ||||| ||||| ||||||||||| ||||| || || |||||  |||||||||| 
ttgaatatttattgcaaaaagttctcatcttttgtggggtcctttgcgttatatttttttattgccaataagcctcactgtttgttctcttattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA

upper sequence: AT1G54100.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA15G19670.1 (Glycine max), 3'ss of exon 12
-------------------------------------------------------------------gtaagtgctataaaaacaacaacttaactcaatctttccgaccaatataatctactgaaattaattttaatgtgat----ggttttactac----tagACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGGAGCTGAGATTGGTGGAGCTTTTGGAGGCGAGAAAGCGACTGGTGGTGGT
                                                                    | ||| ||  |  ||||      |||     |  |   ||   |||   |  |   | | ||  ||| |  || |    ||| | | ||      || ||||  || ||||| ||||| || |||||||  |||||||| || |||||||||||||||||||| || ||||| || || || ||||| |||||||| 
gtaagtacttacaaacttatttttgtcctatcctttcgatctctgctgatgagtttggcctacacacttcagtacttgactaacactcctataagatgtttgtggtgatttata-gttgcataaatagtatattttacttgttcatgggtgtgaatatggtgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAGATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACCGGTGGTGGC

upper sequence: AT1G54100.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA15G19670.4 (Glycine max), 3'ss of exon 12
---------------------------------------------------------------gtaagtgctataaaaacaacaacttaactcaatctttccgaccaatataatctactgaaattaattttaatgtgat----ggttttactac----tagACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGGAGCTGAGATTGGTGGAGCTTTTGGAGGCGAGAAAGCGACTGGTGGTGGT--------
                                                                | ||| ||  |  ||||      |||     |  |   ||   |||   |  |   | | ||  ||| |  || |    ||| | | ||      || ||||  || ||||| ||||| || |||||||  |||||||| || |||||||||||||||||||| || ||||| || || || ||||| ||||||||         
gtacttacaaacttatttttgtcctatcctttcgatctctgctgatgagtttggcctacacacttcagtacttgactaacactcctataagatgtttgtggtgatttata-gttgcataaatagtatattttacttgttcatgggtgtgaatatggtgcaggccacgagGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAGATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACCGGTGGTGGCCGTGAGGC

upper sequence: AT1G54100.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA09G08150.2 (Glycine max), 3'ss of exon 11
-------------------------------------------------------------------gtaagtgctataaaaacaacaacttaactcaatctttccgaccaatataatctactgaaattaattttaatgtgat----ggttttactac------tagACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGGAGCTGAGATTGGTGGAGCTTTTGGAGGCGAGAAAGCGACTGGTGGTGGT
                                                                    | ||| ||  |  |||||     |||     |  |   ||   |||   |  ||  | | ||  ||| |  || |    ||| | | ||        || ||||  || ||||| ||||| || |||||||  |||||||| || ||||||||||| |||||||| || ||||| || || || ||||| |||||||| 
gtaagtactcacaaacttatttttgtcctatcctttggatctctgctaatgagtttggcctacacacttcagtacttgactaacaatcctataagatgtttgtggtgatttata-gttgcacaaatagtatattttacttgttcatgggtgtaaatatggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAAATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACAGGTGGTGGC

upper sequence: AT1G54100.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 12
-------------gtaagtgctataaaa-acaacaacttaactcaatctttccgaccaatataatctactgaaattaattttaatgtgatggttttactactagACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGGAGCTGAGATTGGTGGAGCTTTTGGAGGCGAGAAAGCGACTGGTGGTGGT
              | | ||  || | | | ||    ||   |  ||||     |  ||| |   ||    ||  |  | || || |    || ||| ||| || ||||  |||||||||||||| ||||||||||| || ||||| || ||||||||||||||||||||||||||||| || || || || ||||||||||||
gaagaggcagttgttgaatgtcatgacacataagggattgg-tggatctagtgcattaatgtc-cctgtgaaatattttgttcatatatgagtatta-tac-agGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGGAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGT

upper sequence: AT1G54100.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S237_29V6.1 (Physcomitrella patens), 3'ss of exon 13
----gtaagtgctataaaaacaacaacttaactcaatctttccgaccaatat--aatctactgaaattaattttaa-tgtgatggttttactact---agACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGGAGCTGAGATTGGTGGAGCTTTTGGAGGCGAGAAAGCGACTGGTGGTGGT
    || |         |   | | |||| |  ||     |       || |  ||| |    |  ||| |   ||    |||| || |     |   |||||    || ||||| ||||| ||||| |||||||||||||| || |||||||| |||||||| ||||| || || || ||||| || || || || || 
attagtgacaatgtacgaggaagctacttcatgcacctcatttacttcatttcgaatttttacattttagtgacaagcaagatgtttctctcgtttgcagACCTACAGGCAGTGATTGTGGTATTGTCAATGTGAACATACCAACCAATGGAGCGGAGATTGGGGGAGCATTCGGTGGAGAGAAGGCAACAGGGGGCGGA

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|164124815|gb|EL975319.1|EL975319
EST:     AGCAGCTCGATATTCACTCGGAACCCTGAAAACATCTTCAGGTGGATCGG                         ACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACG
genomic: AGCAGCTCGATATTCACTCGGAACCCTGAAAACATCTTCAGGTGGATCGGgtaagtgcta ... ttactactagACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACG
EST: gi|86080345|gb|DR376102.1|DR376102
EST:     AGCAGCTCGATATTCACTCGGAACCCTGAAAACATCTTCAGGTGGATCGG                         ACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGG
genomic: AGCAGCTCGATATTCACTCGGAACCCTGAAAACATCTTCAGGTGGATCGGgtaagtgcta ... ttactactagACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGG
EST: gi|86080922|gb|DR376679.1|DR376679
EST:     AGCAGCTCGATATTCACTCGGAACCCTGAAAACATCTTCAGGTGGATCGG                         ACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGG
genomic: AGCAGCTCGATATTCACTCGGAACCCTGAAAACATCTTCAGGTGGATCGGgtaagtgcta ... ttactactagACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGG
EST: gi|116414405|gb|EG456997.1|EG456997
EST:     AGCAGCTCGATATTCACTCGGAACCCTGAAAACATTTTCAGGTGGATCGG                         ACCCCTGGGAAGTGACTGTGGCATTGTGAATGTGAACATCCCGACGAATGG
genomic: AGCAGCTCGATATTCACTCGGAACCCTGAAAACATCTTCAGGTGGATCGGgtaagtgcta ... ttactactagACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGG
EST: gi|222357912|gb|GH718553.1|GH718553
EST:     AGCAGCTCGATATTCACTCGGAACCCTGAAAACATCTTCAGGTGGATCGG                         ACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGG
genomic: AGCAGCTCGATATTCACTCGGAACCCTGAAAACATCTTCAGGTGGATCGGgtaagtgcta ... ttactactagACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccgaccaatataatctactgaaattaattttaatgtgatggttttactactagACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGGAGCTGAGATTGGTGGAGCTTTTGGAGGCGAGAAAGCGACTGGTGGTGGT
                             ttttaat  putative branch site (score: 3)
                                           ttttact  putative PPT
        aatataatctactgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgctataaaaacaacaacttaactcaatctttccgaccaatataatctactgaaattaattttaatgtgatggttttactactagACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGGAGCTGAGATTGGTGGAGCTTTTGGAGGCGAGAAAGCGACTGGTGGTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG