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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttaaaacctattttaatacttgattaggaaacaaaaccatttcttttttgctatctttaaccaaaatataacagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAATGATTTTCTACAACCTGGTCCTGCTATTGAAGCCATTCAGTACTCAAT

Basic information

species Arabidopsis thaliana
transcript AT4G01480.1
intron # 7
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os05g36260.1 (Oryza sativa), 3'ss of exon 5
---------------------gtatccttaaaacctattttaatacttgattaggaaacaaaaccatttcttttttgctatctttaaccaaaatataacagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAATGATTTTCTACAACCTGGTCCTGCTATTGAAGCCATTCAGTACTCAAT
                      ||   ||   || | ||||| | |||| |   | | |   |   ||||  || |  |||  || | |||||| |  ||||||||||||||||||||||||| ||||| || ||||| ||  | |   ||    | |||  |||||| || |||||||| ||
gtacgcctgcttcctcagctcatacgattgctacatttttta-tgcttggtattgcaccttga---tttcaattgttttattcttgatcaaaatctttcagACAAGAAGAATGAGAACAAGGAGGTTGCTGTCAATGACTTCTTGCCTGCTCCGACAGCTCGTGAAGCAATCCAGTACTCTAT

upper sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 7
gtatccttaaaacctattttaatacttgattagga----------aacaaaac----------catttcttttttgctatctttaaccaaaatataacagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAATGATTTTCTACAACCTGGTCCTGCTATTGAAGCCATTCAGTACTCAAT
||||||| | |  |  |||||    || | | | |          |  | |            |||   | | ||  | || ||||| | |   |   |||||||||||||||||||||||| ||||| ||  |||  ||  | |   |     |||||  ||| |||||||||||||| ||
gtatcctcatagtccgttttatggtttaaattgcatatcccatatagtatagtattggtcatgcatacatctgttattgtccttaacaatatgtttttagACAAGAAGAATGAGAACAAGGAGGTTGCTGTTGATGCATTCTTGCCTGCCAACACTGCTCGTGACGCCATTCAGTACTCCAT

upper sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G015418_T01 (Zea mays), 3'ss of exon 7
------------gtatccttaaaacc------tattttaatacttgattaggaaacaaaaccatttcttttttgctatc--tttaaccaaaatataa----cagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAATGATTTTCTACAACCTGGTCCTGCTATTGAAGCCATTCAGTACTCAAT
               ||   ||| |       | ||||  | |||  |  |     |   | |    |  ||||  |||  ||| ||    || |||    ||||||||||||| ||||||||||| ||||| ||||| |||||  | | |||   | || |  | || ||||||||  |||||||
gtacgcaccatttcgtctccaaatctgtctgattttttttttctttctatgatcgtagcgctacggttgctttgaaatccatttcacatgtatttaatttgcagACAAGAAGAACGAGAACAAGGAGGTTGCTGTGAACGATTTCTTGCCACCAACTACTTCCCTGGAGGCCATTCAACACTCAAT

upper sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G01960.1 (Glycine max), 3'ss of exon 5
-----------------------gtatccttaaaaccta------ttttaa---tacttgattaggaaacaaaaccatttcttttttgctatctttaaccaaaatataacagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAATGATTTTCTACAACCTGGTCCTGCTATTGAAGCCATTCAGTACTCAAT
                        || | || | |||||       |||||   ||||| ||         | |  |    ||  ||||  |  ||||| | | |  | ||||||||||||||||||||||||| || ||||| |||||||||||||   |     ||||| ||||| |||| |||||||||||
gtatccttaaaaatcttattccaataactttgatacctaagttttctttaagattactttatagtattttcataaaaaaaattgattgcatttcttaac-atatttgatcagACAAGAAGAATGAGAACAAGGAGGTAGCAGTTAATGATTTTCTACCTGCATCCACTGCTGTTGAATCCATCCAGTACTCAAT

upper sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 7
---------------------------------------gtatccttaaaacctattttaatacttgattaggaaacaaaaccatttcttttttgctatctttaaccaaaatataacagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAATGATTTTCTACAACCTGGTCCTGCTATTGAAGCCATTCAGTACTCAAT
                                       || || |||| |  || || | || |   ||   ||| ||||  |    ||   |||  |  ||||   | ||  | ||||||||||||||||||||||||| || ||||| |||||||||||||   |     ||||  ||||| |||| |||||||||||
gtatccttaaaaatcttattccaataacttgatacatgagtttctttaagat-tacttca-tagtattttcataaaaaaaataaaaaattgagtgcatttcttaat--atattgatcagACAAGAAGAATGAGAACAAGGAGGTAGCAGTTAATGATTTTCTACCTGCATCCACTGCCGTTGAATCCATCCAGTACTCAAT

upper sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G42280.1 (Glycine max), 3'ss of exon 7
gtatccttaaaacctatttta-atacttgattaggaaacaaaaccatttcttttttgctatctttaaccaaaatataac---agACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAATGATTTTCTACAACCTGGTCCTGCTATTGAAGCCATTCAGTACTCAAT
||||||||        ||||| ||| |  |||          || | ||| ||   ||| | | |   || |||  |     |||||| ||||||||| ||||||| || ||||| |||||||||||||   |  |   |||| |||| ||||| |||||||||||
gtatccttcgtcttagttttatatattaaattt---------actagttcattagcgctgtttcttgacataattcattctaagACAAAAAGAATGAGCACAAGGAGGTAGCAGTTAATGATTTTCTACCTGCAAGCGTTGCTCTTGATGCCATCCAGTACTCAAT

upper sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 6
---------gtatccttaa----aacctattttaatacttgattaggaaacaaaaccatttcttttttgctatctttaaccaaaatataacagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAATGATTTTCTACAACCTGGTCCTGCTATTGAAGCCATTCAGTACTCAAT
           ||| || |    ||||| |  | | | ||  ||| |      ||| ||       ||  | |  || ||  ||| |   |||| || ||||||||||||||||| ||||| |||||||||||  |||   |  || |||||  | ||||  | ||| | || ||
gtatccttttcatctttcagttcaacctttcatgaaaatttgttaaggggatgaacaatagacaaatt--ttttcttgac--aaacaattcagATAAAAAGAATGAGAACAAGGAGGTTGCCGTGAATGATTTCTTACCTTCAAGTTCTGCTCATCAAGCTGTCCAGCATTCCAT

upper sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S315_67V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------------------gtatccttaaaacctattttaatacttgatta-ggaaacaaa-accatttcttttttgctatctttaacc-aaaatataacagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAATGATTTTCTACAACCTGGTCCTGCTATTGAAGCCATTCAGTACTCAAT
                                                ||   | | | |          |  ||| ||  ||  |       | ||| |     ||     |          |  | ||||||||||||||||||||||||||||  | ||| || | || ||    |  |   |||| ||| |||||||     |||| ||
gtaagtgccgagtgaggtgacgcggtgatgtgcataatggtccaagatgtggacgtgagagagggaggtgtctttgcttgtggtgatgtgtgacgtttgtaaccggcagggatgggtttggggtgaatcagACAAGAAGAATGAGAACAAGGAAGTAACGGTGGATAACTTCCTGGGCCACGAAGCTGCGATTCAAGCCATCAGTCACTCCAT

upper sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------------------------------gtatccttaaaacctattttaatacttgatta-ggaaacaaa-accatttcttttttgctatctttaacc-aaaatataacagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAATGATTTTCTACAACCTGGTCCTGCTATTGAAGCCATTCAGTACTCAAT
                                                ||   | | | |   |      |  ||| ||  ||  |       | ||| |     ||     |          |  | ||||||||||||||||||||||||||||  | ||| || | || ||    |  |   |||| ||| |||||||     |||| ||
gtaagtgccgagtgaggtgacgcggtgatgtgcataatggtccaagatgtggacgtgagagagagaggtgtctttgcttgtggtgatgtgtgacgtttgtaaccggcagggatgggtttggggtgaatcagACAAGAAGAATGAGAACAAGGAAGTAACGGTGGATAACTTCCTGGGCCACGAAGCTGCGATTCAAGCCATCAGTCACTCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattaggaaacaaaaccatttcttttttgctatctttaaccaaaatataacagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAATGATTTTCTACAACCTGGTCCTGCTATTGAAGCCATTCAGTACTCAAT
 atctttaac  putative branch site 
                                    tttaaccaaaatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccttaaaacctattttaatacttgattaggaaacaaaaccatttcttttttgctatctttaaccaaaatataacagACAAGAAGAATGAGAACAAGGAAGTTGCAGTGAATGATTTTCTACAACCTGGTCCTGCTATTGAAGCCATTCAGTACTCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC