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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctctacctataaagaaccttacttgcctaaagtagctcacatgttcatatagtatcgaattaattgacaacattctctttaccttcagCTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTG

Basic information

species Arabidopsis thaliana
transcript AT1G20260.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 13
gttctctacctataaagaaccttacttgcctaaagtagctcacatgttcatatagtatcgaa-----ttaattgacaacatt--ctctttaccttcagCTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTG
      ||    | |  |  ||||  ||  |    ||  |  |    | |||| |  |  |       |||  |||    ||   | || ||||||||||||| || |||||||| || ||||| ||||| || || ||||||||||| || ||||| ||||| || ||||| |||||||||
-----gtaagattcagaaggcttaagtgtgtttt-taattttctccattatattgctttaaggcctcctaaccgaccctgttgatttttcaccttcagCTATATGCGAATTATGCTATTGGAAAGGATGTCCAGGCAATGAAAGCTGTGGTCGGAGAGGAAGCACTCTCTTCTGAGGATCTG

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 13
---gttctctacctataaagaaccttacttgcctaaagtagctcacatgttcatata---gtatcgaattaattgacaacattctctttacct---tcagCTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTG
    |  |  |   ||  |    || |  ||||||| |    | ||    |||   |    ||  ||| | |     |||||  | ||| |||    ||| | || || |||||||| || ||||| ||||||||||| ||||| ||||| |||||||| |||||| ||||||| || ||||||
tttttgtttcaagcatgcaacttctcaagtgcctaatgcctattacgaaatcaggaatggatagggaacttacacctaacatcatgtttgcctgtcccagTTGTATGCTAATTATGCCATTGGAAAGGATGTTCAAGCAATGAAGGCTGTCGTTGGAGAGGAAGCTTTGTCTTCAGAAGATCTG

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 12
-------------gttctctacctataaagaaccttacttgcctaaagtagctcacatgttcatatagtatcgaattaattgacaacattctctttaccttcagCTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTG
               | | |  | || ||   ||  | ||  || | | ||    | ||     | | | | |  ||||         | | | || |    || | |||||||| ||||| || ||||| ||||| ||||||||||| ||||| || |||||||||||  ||||||| |||||||||
cacatgagagcatcatttgtggccatcaacttccccatttttctgatgaagtctgcttgagtcaagactttgggtttaacatggtgtctacccattgc----agTTGTACGCAAACTATGCGATTGGAAAGGATGTACAAGCCATGAAGGCTGTGGTGGGAGAAGAAGCCTTGTCTTCAGAGGATCTG

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 12
gttctctacctataaag-----aaccttacttgcctaaagtagctcacatgttcat--atagtatcgaatt---aattgacaacattctctttaccttcagCTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTG
 ||   | |   |||       ||  ||   ||   || || | | |     ||    | | |   || ||   | |||||||     |  ||   | ||| | |||||||||||||| ||||| || ||||| ||||||||||| ||||| || ||||| |||||  ||||||| || ||||||
-tttatttcaagtaacttcctcaatttttaatgttcaatgttgataattaactctgtgacaatggggagtttggatttgacaagtcgttgattcattgcagTTGTACGCAAATTATGCTATCGGGAAGGATGTGCAAGCCATGAAGGCTGTGGTGGGAGAGGAAGCCTTGTCTTCAGAAGATCTG

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 12
gttctctacctataaagaaccttacttgcctaaagtagctcacatgttcatatagtatcgaattaattgacaacattctctttaccttcagCTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTG
                                  ||     |  |||   || |  ||        || |||   |   ||     | ||||| || ||||| ||||| || || ||||| |||||||| ||||||||||| || ||||||||||| ||||| || || ||||||
----------------------------------gtgagcgat-tgtgtctacatcattatgccgtttaacactgtctactggttttgcagCTCTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG

upper sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 12
gttctctacctataaagaaccttacttgcctaaagtagctcacatgttcatatagtatcgaattaattgacaacattctctttaccttcagCTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTG
                                  ||     |  |||   || |  ||        || ||||  |   ||     | ||||| || ||||| ||||| || || ||||| |||||||| ||||||||||| || ||||||||||| ||||| || || ||||||
----------------------------------gtgagcgat-tgtgtctacatcattatgccgtttaacaatgtctactggttttgcagCTTTATGCAAACTATGCCATTGGCAAAGACGTTCAAGCGATGAAAGCTGTCGTGGGAGAAGAAGCGCTGTCATCTGAAGATCTG

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|116471554|gb|EG514146.1|EG514146
EST:     CTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAACCAG                         CTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTT
genomic: CTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAACCAGgttctctacc ... ttaccttcagCTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTT
EST: gi|125084301|gb|EL144555.1|EL144555
EST:     CTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAACCAG                         CTATACGCAAATTATGCAATCGGAAAA
genomic: CTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAACCAGgttctctacc ... ttaccttcagCTATACGCAAATTATGCAATCGGAAAA
EST: gi|86084595|gb|DR380354.1|DR380354
EST:     CTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAACCAG                         CTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTT
genomic: CTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAACCAGgttctctacc ... ttaccttcagCTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTT
EST: gi|164089658|gb|ES095046.1|ES095046
EST:     GCAAAGACCATTCTGATGTGTCCAACCAG                         CTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTT
genomic: GCAAAGACCATTCTGATGTGTCCAACCAGgttctctacc ... ttaccttcagCTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTT
EST: gi|116428286|gb|EG470878.1|EG470878
EST:     CTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAACCAG                         CTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTT
genomic: CTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAACCAGgttctctacc ... ttaccttcagCTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTT
EST: gi|116428287|gb|EG470879.1|EG470879
EST:     CTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAACCAG                         CTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTT
genomic: CTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAACCAGgttctctacc ... ttaccttcagCTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTT
EST: gi|125091293|gb|EL149116.1|EL149116
EST:     CTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAACCAG                         CTATACGCAAATTATGCAATCGGAAAAGAT
genomic: CTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAACCAGgttctctacc ... ttaccttcagCTATACGCAAATTATGCAATCGGAAAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctcacatgttcatatagtatcgaattaattgacaacattctctttaccttcagCTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTG
                            aattgac  putative branch site (score: 3)
                                     cattctctttaccttc  putative PPT
                        aattaattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctctacctataaagaaccttacttgcctaaagtagctcacatgttcatatagtatcgaattaattgacaacattctctttaccttcagCTATACGCAAATTATGCAATCGGAAAAGATGTTCAAGCCATGAAAGCTGTTGTTGGAGAAGAAGCTCTGTCTTCCGAGGATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT