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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttacctcaccatttttttatggctacaaagagatcaactttgatcgttcaaccgaaatgaaaaatagttgagctaacatagtttaacaaaagaacattgctttatatttatataaaaaacaaaagatgcagatgaacagtgcttaatgtggtttccaattttcagGTATAAAGAAGCAGTAGGCGGCTTATGGGTAGTTATGATTCTACTGGCATGCTATTTAGCAACTGAAGTTCTCCGAGTTTCAAGTAGCACATGGTTAAGT

Basic information

species Arabidopsis thaliana
transcript AT1G30410.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G30410.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 22
gtactttacctcaccatttttttatggctacaaagagatcaactttgatcgttcaaccgaaatgaaaaatagttgagctaacatagtttaacaaaagaaca-ttgctttatatttatataaaaaacaaaagatgcagatgaacagtgcttaatgtggtttccaattttcagGTATAAAGAAGCAGTAGGCGGCTTATGGGTAGTTATGATTCTACTGGCATGCTATTTAGCAACTGAAGTTCTCCGAGTTTCAAGTAGCACATGGTTAAGT
                                                                     |   |   ||       ||   |      ||| ||  ||| |  ||  || |||   | | | ||||  |      ||  |  |||| ||    |||| |||||| |||   ||| | || ||  | |||||||||   || ||| |  | ||||||  |  ||| |||||||| ||| |||||||||||||||||||||||
----------------------------------------------------------------ttttttctctttccttttccttttggccttgttgacacttattttgtgcttgaattaaat-tagatgctgcaatttggttatgact--tgtgatt----atttacagGTACAAATCTGCACTGGGAGGACTGTGGGTAGTTTCCATACTATTTTCTTGCTATACATTAACAGAAGTTCTTCGAATTTCAAGTAGCACATGGTTAAGT

upper sequence: AT1G30410.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: Vv10s0003g04470.t01 (Vitis vinifera), 3'ss of exon 21
gtactttacctcaccatttttttatggctacaaagagatcaactttgatcgttcaaccgaaatgaaaaatagttgagctaacatagtttaacaaaagaacattgctttatatttatataaaaaacaaaagatgcagatgaacagtgcttaatgtggtttccaattttcagGTATAAAGAAGCAGTAGGCGGCTTATGGGTAGTTATGATTCTACTGGCATGCTATTTAGCAACTGAAGTTCTCCGAGTTTCAAGTAGCACATGGTTAAGT
                                                ||  |   || |  |||    |  ||    |    |  ||             || ||     ||||| |   | || |   ||   |||| |   | ||   ||   ||||    || |||||||||||| ||| |||| ||| ||||||||||||   | ||  | ||||||||| |    ||||||||||| ||||||| ||||||||| |||||||| 
------------------------------------------------tctcttttccaagttgacttgtcttttttttttttttttt-------------ttcctgagcctttatctggtataccattaatt--gatggattttcct---tgccttttc----ttgcagGTATAAAGATGCATTAGGGGGCCTATGGGTAGTTACACTACTTTTTGCATGCTATGTGTTGACTGAAGTTCTTCGAGTTTTAAGTAGCACCTGGTTAAGC

upper sequence: AT1G30410.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: Vv10s0003g04460.t01 (Vitis vinifera), 3'ss of exon 2
gtactttacctcaccatttttttatggctacaaagagatcaactttgatcgttcaaccgaaatgaaaaatagttgagctaacatagtttaacaaaagaacattgctttat-atttatataaaaaacaaaagat-gcagatgaacag-tgcttaatgtggtttccaattttcagGTATAAAGAAGCAGTAGGCGGCTTATGGGTAGTTATGATTCTACTGGCATGCTATTTAGCAACTGAAGTTCTCCGAGTTTCAAGTAGCACATGGTTAAGT
                                                                       ||    ||    |||| |    | |   | ||  ||| |     |  |||| |  |    || |   |||||||| ||  |  | |   ||||  ||| |||||||||||| ||| |||||||| ||||||||||| || | ||  | ||||||||| |    || |||||||| ||| ||  ||||||||| |||||||| 
-----------------------------------------------------------------------gtct--cttttgtagtctctttagaatgctttcatttgttggacagctaaacatgatcctatagtccatgaacagatgggttttctttgttcctttttgcagGTATAAAGATGCATTAGGCGGCCTATGGGTAGTTGTGGTACTCTTTGCATGCTATGTGTTGACAGAAGTTCTTCGAATTGGAAGTAGCACCTGGTTAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataaaaaacaaaagatgcagatgaacagtgcttaatgtggtttccaattttcagGTATAAAGAAGCAGTAGGCGGCTTATGGGTAGTTATGATTCTACTGGCATGCTATTTAGCAACTGAAGTTCTCCGAGTTTCAAGTAGCACATGGTTAAGT
                              gcttaat  putative branch site (score: 4)
                                         tttcc  putative PPT
     aaaacaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttacctcaccatttttttatggctacaaagagatcaactttgatcgttcaaccgaaatgaaaaatagttgagctaacatagtttaacaaaagaacattgctttatatttatataaaaaacaaaagatgcagatgaacagtgcttaatgtggtttccaattttcagGTATAAAGAAGCAGTAGGCGGCTTATGGGTAGTTATGATTCTACTGGCATGCTATTTAGCAACTGAAGTTCTCCGAGTTTCAAGTAGCACATGGTTAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG