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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtactgagctttcttgcttctttgcaagttgtttgctacatatgtgtgcttgtatgtatctccatttgtattgtttgtatataggttcgtgcagggttttctgtttgtatattgttcataaatttcttctggaagcagGTGTGGGATTACCAAACAAAGAGTTGCGTTCAGACTCTCGAAGGTCATACACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTA

Basic information

species Arabidopsis thaliana
transcript AT1G79990.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 7
gtctgtactgagctttcttgcttctttgcaagttgtttgctacatatgtgtgcttgtatgtatctccattt--gtattgtttgtatataggttcgtgcagggttttctgtttgtatattgttcataaatttcttctggaagcagGTGTGGGATTACCAAACAAAGAGTTGCGTTCAGACTCTCGAAGGTCATACACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTA
                                               || |  || | | ||||  | |||  || ||    ||||  | | |  ||    ||  |  | | || |   | ||||            ||| ||||| |||||||||||||| ||||| || |||||||| || ||||| |||||||||||  ||||||| || | ||| ||||| ||||| |||||||| ||||
-----------------------------------------------gttttttttt-tctatccacttttgagtgttccaagtatccacgattctgtgcagtcctaagatggtgt---ggtcatggt---------gaaccagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 7
gtctgtactgagctttcttgcttctttgcaagttgtttgctacatatgtgtgcttgtatgtatctccatttgtattgtt-tgtatataggttcgtgcagggttttctgtttgtatattgttcataaatttcttctggaagcagGTGTGGGATTACCAAACAAAGAGTTGCGTTCAGACTCTCGAAGGTCATACACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTA
                                                                    |||||  | |  || |   |  |     |  |   |  ||  || |   |||    | |||  |  |  || ||||| ||||| |||||||||||||| |||||||| || || ||||| ||| |||| ||||||||||| |||| ||| || ||||||||||||||||| ||||
-------------------------------------------------------------------gtttgtcatatgatgcactgaattgtactcctgtggtcatgcatgcactctgtgatgacattattggtcaaatcagGTTTGGGACTACCAAACAAAGAGCTGCGTTCAAACACTTGAAGGACATGCACATAATGTTTCTGCTGTATGTTTCCACCCAGAGCTACCTATAATAATTA

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 7
gtctgtactgagctttcttgcttctttgcaagttgtttgctacatatgtgtgcttgt-atgtatctccatttgtattgtttgtatataggttcgtgcagggttttctgtttgtatattgttcataaatttcttctggaagcagGTGTGGGATTACCAAACAAAGAGTTGCGTTCAGACTCTCGAAGGTCATACACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTA
                                                   | |||| ||        | ||||| |   |||    | ||  || |           | |||| | || | | |  ||  |  |  || ||||| ||||| ||||| |||||||| || ||||| || || ||||| ||| |||| ||||| || || |||| ||| |||||||||||||||||||||||||
---------------------------------------------------gtttgtcataagcactgaattgtact-cctgtgatcatgtctgtac-----------tctgtacactgatgaca--ttattgatcaaatcagGTTTGGGACTACCAGACAAAGAGCTGTGTTCAAACACTTGAAGGACATGCACATAATGTGTCCGCTGTATGTTTCCATCCAGAGCTACCTATAATTATTA

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 7
gtctgtactgagctttcttgcttctttgcaagttgtttgctacatatgtgtgcttgtatgtatctccatttgtattgtttgtatataggttcgtgcagggttttctgtttgtatattgttcataaatttcttctggaagcagGTGTGGGATTACCAAACAAAGAGTTGCGTTCAGACTCTCGAAGGTCATACACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTA
                                                 || |   | ||||    ||  |||||  ||||  | |  | | || |     | ||   |  ||   ||    |    ||  |    ||  |||| ||||||||||| || ||||| || |||||||| || ||||| |||||||| ||| ||||||| || | ||| ||||| ||||| |||||||| ||||
-------------------------------------------------gtacaattttgtact--cagctgtatgttttgagtgtttgattgttc-----tatccagtcctaaggtg---gtgtgctttatggcaaaatagGTCTGGGATTACCAGACGAAGAGCTGTGTTCAGACACTTGAAGGGCATACACATAATATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTA

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G443953_T01 (Zea mays), 3'ss of exon 8
gtctgtactgagctttcttgcttctttgcaagttgtttgctacatatgtgtgcttgtatgtatctccatttgtattgtttgtatataggttcgtgcagggttttctgtttgtatattgttcataaatttcttctggaagcagGTGTGGGATTACCAAACAAAGAGTTGCGTTCAGACTCTCGAAGGTCATACACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTA
                                                                       ||||    |||  ||  |  | |   | |  || ||    | |||   | ||   ||   |   |||  |||| |||||||| ||||||||||| || ||||| || || ||||| ||| |||| ||||| ||||| |||| ||| ||||| ||||| || ||||| || |
-----------------------------------------------------------------------gtatgacatgttcatttgcacatat-gagcattttggacat-tatgactgattggttaactt--gaattagGTTTGGGATTATCAAACAAAGAGCTGTGTTCAAACACTTGAAGGACATGCACATAATGTCTCTGCTGTATGTTTCCATCCTGAGCTTCCAATAATAATGA

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 6
gtctgtactgagctttcttgcttctttgcaagttgtttgctacatatgtgtgcttgtatgtatctccatttgtattgtttgtatataggttcgtgcagggttttctgtttgtatattgttcataaatttcttctggaagcagGTGTGGGATTACCAAACAAAGAGTTGCGTTCAGACTCTCGAAGGTCATACACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTA
                                        ||||| | ||| ||    ||||| | |   || ||| |||||     | |   |||||             |||  || |  |   |||  |    ||| |||| ||||||||||| || || || || |||||||| || ||||| |||||||| ||  ||||||| || | ||| ||||| ||||| |||||||| ||||
---------------------------------------gtacatttttgtactgaggtgtatgttc---tgaattttttgtt----gctctatgcag-------------tattatgatggtgcgttttatggcaaagtagGTCTGGGATTACCAGACGAAAAGCTGTGTTCAGACACTTGAAGGGCATACACATAACATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTA

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 7
gtctgtactgagctttcttgcttctttgcaagttgtttgctacatatgtgtgcttgtatgtatctccatttgtattgtttgtatataggttcgtgcagggttttctgtttgtatattgttcataaatttcttctggaagcagGTGTGGGATTACCAAACAAAGAGTTGCGTTCAGACTCTCGAAGGTCATACACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTA
                           |   ||| | |  |   | | | | | | |   | |  ||  |  | | ||||     ||  || ||  | || |     ||  |||   |   |||||    ||   ||| ||||| |||||||| ||||| || ||||| || |||||||| |||||||| ||||||||||| ||||| ||||  |||||||| || ||||||||||| ||||
---------------------------gtttgttttctattttctgttttttcctcttcatcttccctctaatttggtttcc---tatatttgtatatggataggaattattatgccg---ataaaaccttt---gaatcagGTATGGGATTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTA

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 7
gtctgtactgagctttcttgcttctttgcaagttgtttgctacatatgtgtgcttgtatgtatctccatttgtattgtttgtatataggttcgtgcagggttttctgtttgtatattgttcataaatttcttctggaagcagGTGTGGGATTACCAAACAAAGAGTTGCGTTCAGACTCTCGAAGGTCATACACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTA
                        ||||     | ||| ||   | | |   |||     |  ||  | ||   |||  | ||| |   |  |   |||  ||  | |         |   |||||    ||   ||| ||||| ||||| || ||||| || ||||| || |||||||| |||||||| ||||||||||| ||||| || |  |||||||| || ||||||||||| ||||
-----------------------gtttgttttctattttctgtttttttcctcttcatcttccctttaatttggttgcctatatgtgtatatggataggaattattat---------gccaataaaaccttt---gaaacagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTTTGCTTTCATCCTGAACTACCTATAATCATTA

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 7
gtctgtactgagctttcttgcttctttgcaagttgtttgctacatatgtgtgcttgtatgtatctccatttgtattgtttgtatataggttcgtgcagggttttctgtttgtatattgttcataaatttcttctggaagcagGTGTGGGATTACCAAACAAAGAGTTGCGTTCAGACTCTCGAAGGTCATACACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTA
                                  ||||  |    || |||   |  || ||||| | | |         | | | |    | || | |           | |||   |  || ||  |      ||| ||||| |||||||| || || || ||||| || ||||| || |||||||| ||||||||||| ||||| ||||  |||||||| || || |||||||| ||||
----------------------------------gttttgttttcatttgttgcttaatctatctgcttgtcgcgcacacgcacacacacacatgtatga------aaaggaataacatggatgaaacttac---gaatcagGTATGGGATTATCAGACCAAAAGTTGTGTCCAGACCCTAGAAGGTCACACACACAATGTATCTGCTGTATGCTTTCATCCTGAACTTCCTATAATCATTA

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 7
gtctgtactgagctttcttgcttctttgcaagttgtttgctacatatgtgtgcttgtatgtatctccatttgtattgtttgtatataggttcgtgcagggttttctgtttgtatattgttcataaatttcttctggaagcagGTGTGGGATTACCAAACAAAGAGTTGCGTTCAGACTCTCGAAGGTCATACACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTA
                   | ||  ||   | ||||| |||  || | | |||||||| | || | ||| |  ||    | ||||||  |  |   |||             |||   |  || ||  |  |   ||| ||||| |||||||| || || || ||||| || ||||| || |||||||| ||||||||||| ||||| ||||  |||||||| || || |||||||| ||||
-------------------gttttgttttcatttgtt-gcttgatctatctgcttgtacgcatttacatatacat-acatatatatatatatgaaaagga------------ataacatggatgaaacttat---gaatcagGTATGGGATTATCAGACCAAAAGTTGTGTCCAGACCCTAGAAGGTCACACACACAATGTATCTGCTGTATGCTTTCATCCTGAACTTCCTATAATCATTA

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 7
gtctgtactgagctttcttgcttctttgcaagttgtttgctacatatgtgtgcttgtatgtatctccatttgtattgtttgtatataggttcgtgcagggttttctgtttgtatattgttcataaatt--tcttctggaagcagGTGTGGGATTACCAAACAAAGAGTTGCGTTCAGACTCTCGAAGGTCATACACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTA
                                               || |||  ||   ||  |   ||     ||| | ||      ||  |||  |||||  |    | | || ||||||  |    || ||   | |||||||||||| || ||||| || ||||| || ||||| || ||||| || |||||||||||||||||||| |  || ||||| || || || ||||| || |
-----------------------------------------------gtctgcc-gttgataattattttcaagctgtgttta---gtatttatgc--ggtttgatagaaggaaat-gttcatggacaaatcctccaaatgcagGTGTGGGACTATCAAACCAAAAGTTGTGTCCAGACACTGGAAGGCCACACACACAATGTTTCTGCAGTCTGCTTCCATCCTGAACTTCCCATAATAATAA

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 7
gtctgtactgagctttcttgcttctttgcaagttgtttgctacatatgtgtgcttgtatgtatctccatttgtattgtttgtatataggttcgtgcagg-gttttctgtttgtatattgttcataaatttcttctgg--aagcagGTGTGGGATTACCAAACAAAGAGTTGCGTTCAGACTCTCGAAGGTCATACACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTA
                                                       || | |||||  ||   |||||  |  |||    | | |  | | |  |||  ||||  || | |   | | |   || |||   | ||||||||||| |||||||| || ||||| |||||||| || ||||| || ||||||||||||||| |||| | ||| ||||||||||| ||||| ||| |||
-------------------------------------------------------gtgtttatctg-atgcttattgactaaata-gcttccatttatgtgcattccatttgattactttctgtgattaaattttggtggaacagGTGTGGGACTACCAAACCAAAAGTTGTGTTCAGACACTAGAAGGCCACACACACAATGTTTCTTCAGTCTGTTTCCATCCAGAGCTTCCTATTATTTTTA

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S243_63V6.1 (Physcomitrella patens), 3'ss of exon 7
gtctgtactgagctttcttgcttctttgcaagttgtttgctacatatgtgtgcttgtatgtatctccatttgtattgtttgtatataggttcgtgcagggttttctgtttgtatattgttcataaatttcttctggaagcagGTGTGGGATTACCAAACAAAGAGTTGCGTTCAGACTCTCGAAGGTCATACACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTA
                                     || || |  |   || ||   || |  ||  || ||         ||  | |||  ||||   ||   || ||   |    ||| |    ||||  | || ||||||||||||||||||||| ||||| || || |||||| | || |||||| | || ||||| |||||||| | ||| ||||| ||||| || || ||| | |
--------------------------------cgacgtggtaaacgt-catgtttaagtgaagatcacttggt--------cattcaagttgttgcata-ttgattgcttagtttcccttcctggcgttctctttgatgcagGTGTGGGATTACCAAACCAAGAGCTGTGTGCAGACTTTAGAGGGTCATTCTCATAATGTGTCTGCAGTGTGTTTCCATCCTGAGCTCCCCATCATTTTAA

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S79_180V6.1 (Physcomitrella patens), 3'ss of exon 7
gtctgtactgagctttcttgcttctttgcaagttgtttgctacatatgtgtgcttgtatgtatctccatttgtattgtttgtatataggttcgtgcagggttttctgtttgtatattgttcataaatttcttctggaagcagGTGTGGGATTACCAAACAAAGAGTTGCGTTCAGACTCTCGAAGGTCATACACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTA
                                       |    | ||   |  |  || | |    | ||||   | ||||   || | |  | |  | |  |   || |||   | |||  |  ||  |  | || ||||||||||||||||||||| ||| |||| || |||||| | || || ||| | |||||||| |||||||  | ||||||||| ||||| ||||| ||  |||
---------------------------------------cggtgtgtggacgagtaaatatttggtaacttgttcaggttgt---taaggtgctacgtgttcatggtttggtaatattttcggatgttattctttgacgcagGTGTGGGATTACCAAACCAAGGGTTGTGTGCAGACTTTAGAGGGCCATTCTCACAATGTATCTGCAGCGTGTTTTCATCCCGAGCTCCCTATCATCCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttcgtgcagggttttctgtttgtatattgttcataaatttcttctggaagcagGTGTGGGATTACCAAACAAAGAGTTGCGTTCAGACTCTCGAAGGTCATACACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTA
                                       tttcttct  CT-rich tract
                    tttgtatattgttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtactgagctttcttgcttctttgcaagttgtttgctacatatgtgtgcttgtatgtatctccatttgtattgtttgtatataggttcgtgcagggttttctgtttgtatattgttcataaatttcttctggaagcagGTGTGGGATTACCAAACAAAGAGTTGCGTTCAGACTCTCGAAGGTCATACACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT